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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor</title><author><name sortKey="Dagdas, Yasin F" sort="Dagdas, Yasin F" uniqKey="Dagdas Y" first="Yasin F" last="Dagdas">Yasin F. Dagdas</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Belhaj, Khaoula" sort="Belhaj, Khaoula" uniqKey="Belhaj K" first="Khaoula" last="Belhaj">Khaoula Belhaj</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Maqbool, Abbas" sort="Maqbool, Abbas" uniqKey="Maqbool A" first="Abbas" last="Maqbool">Abbas Maqbool</name><affiliation><nlm:aff id="aff2"><institution content-type="dept">Department of Biological Chemistry</institution>,<institution>John Innes Centre</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Chaparro Garcia, Angela" sort="Chaparro Garcia, Angela" uniqKey="Chaparro Garcia A" first="Angela" last="Chaparro-Garcia">Angela Chaparro-Garcia</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Pandey, Pooja" sort="Pandey, Pooja" uniqKey="Pandey P" first="Pooja" last="Pandey">Pooja Pandey</name><affiliation><nlm:aff id="aff3"><institution content-type="dept">Department of Life Sciences</institution>,<institution>Imperial College London</institution>,<addr-line>London</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Petre, Benjamin" sort="Petre, Benjamin" uniqKey="Petre B" first="Benjamin" last="Petre">Benjamin Petre</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Tabassum, Nadra" sort="Tabassum, Nadra" uniqKey="Tabassum N" first="Nadra" last="Tabassum">Nadra Tabassum</name><affiliation><nlm:aff id="aff3"><institution content-type="dept">Department of Life Sciences</institution>,<institution>Imperial College London</institution>,<addr-line>London</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Cruz Mireles, Neftaly" sort="Cruz Mireles, Neftaly" uniqKey="Cruz Mireles N" first="Neftaly" last="Cruz-Mireles">Neftaly Cruz-Mireles</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Hughes, Richard K" sort="Hughes, Richard K" uniqKey="Hughes R" first="Richard K" last="Hughes">Richard K. Hughes</name><affiliation><nlm:aff id="aff2"><institution content-type="dept">Department of Biological Chemistry</institution>,<institution>John Innes Centre</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Sklenar, Jan" sort="Sklenar, Jan" uniqKey="Sklenar J" first="Jan" last="Sklenar">Jan Sklenar</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Win, Joe" sort="Win, Joe" uniqKey="Win J" first="Joe" last="Win">Joe Win</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Menke, Frank" sort="Menke, Frank" uniqKey="Menke F" first="Frank" last="Menke">Frank Menke</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Findlay, Kim" sort="Findlay, Kim" uniqKey="Findlay K" first="Kim" last="Findlay">Kim Findlay</name><affiliation><nlm:aff id="aff4"><institution content-type="dept">Department of Cell and Developmental Biology</institution>,<institution>John Innes Centre</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Banfield, Mark J" sort="Banfield, Mark J" uniqKey="Banfield M" first="Mark J" last="Banfield">Mark J. Banfield</name><affiliation><nlm:aff id="aff2"><institution content-type="dept">Department of Biological Chemistry</institution>,<institution>John Innes Centre</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Kamoun, Sophien" sort="Kamoun, Sophien" uniqKey="Kamoun S" first="Sophien" last="Kamoun">Sophien Kamoun</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Bozkurt, Tolga O" sort="Bozkurt, Tolga O" uniqKey="Bozkurt T" first="Tolga O" last="Bozkurt">Tolga O. Bozkurt</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff3"><institution content-type="dept">Department of Life Sciences</institution>,<institution>Imperial College London</institution>,<addr-line>London</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26765567</idno><idno type="pmc">4775223</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775223</idno><idno type="RBID">PMC:4775223</idno><idno type="doi">10.7554/eLife.10856</idno><date when="????">????</date><idno type="wicri:Area/Pmc/Corpus">000B50</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B50</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor</title><author><name sortKey="Dagdas, Yasin F" sort="Dagdas, Yasin F" uniqKey="Dagdas Y" first="Yasin F" last="Dagdas">Yasin F. Dagdas</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Belhaj, Khaoula" sort="Belhaj, Khaoula" uniqKey="Belhaj K" first="Khaoula" last="Belhaj">Khaoula Belhaj</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Maqbool, Abbas" sort="Maqbool, Abbas" uniqKey="Maqbool A" first="Abbas" last="Maqbool">Abbas Maqbool</name><affiliation><nlm:aff id="aff2"><institution content-type="dept">Department of Biological Chemistry</institution>,<institution>John Innes Centre</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Chaparro Garcia, Angela" sort="Chaparro Garcia, Angela" uniqKey="Chaparro Garcia A" first="Angela" last="Chaparro-Garcia">Angela Chaparro-Garcia</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Pandey, Pooja" sort="Pandey, Pooja" uniqKey="Pandey P" first="Pooja" last="Pandey">Pooja Pandey</name><affiliation><nlm:aff id="aff3"><institution content-type="dept">Department of Life Sciences</institution>,<institution>Imperial College London</institution>,<addr-line>London</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Petre, Benjamin" sort="Petre, Benjamin" uniqKey="Petre B" first="Benjamin" last="Petre">Benjamin Petre</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Tabassum, Nadra" sort="Tabassum, Nadra" uniqKey="Tabassum N" first="Nadra" last="Tabassum">Nadra Tabassum</name><affiliation><nlm:aff id="aff3"><institution content-type="dept">Department of Life Sciences</institution>,<institution>Imperial College London</institution>,<addr-line>London</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Cruz Mireles, Neftaly" sort="Cruz Mireles, Neftaly" uniqKey="Cruz Mireles N" first="Neftaly" last="Cruz-Mireles">Neftaly Cruz-Mireles</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Hughes, Richard K" sort="Hughes, Richard K" uniqKey="Hughes R" first="Richard K" last="Hughes">Richard K. Hughes</name><affiliation><nlm:aff id="aff2"><institution content-type="dept">Department of Biological Chemistry</institution>,<institution>John Innes Centre</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Sklenar, Jan" sort="Sklenar, Jan" uniqKey="Sklenar J" first="Jan" last="Sklenar">Jan Sklenar</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Win, Joe" sort="Win, Joe" uniqKey="Win J" first="Joe" last="Win">Joe Win</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Menke, Frank" sort="Menke, Frank" uniqKey="Menke F" first="Frank" last="Menke">Frank Menke</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Findlay, Kim" sort="Findlay, Kim" uniqKey="Findlay K" first="Kim" last="Findlay">Kim Findlay</name><affiliation><nlm:aff id="aff4"><institution content-type="dept">Department of Cell and Developmental Biology</institution>,<institution>John Innes Centre</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Banfield, Mark J" sort="Banfield, Mark J" uniqKey="Banfield M" first="Mark J" last="Banfield">Mark J. Banfield</name><affiliation><nlm:aff id="aff2"><institution content-type="dept">Department of Biological Chemistry</institution>,<institution>John Innes Centre</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Kamoun, Sophien" sort="Kamoun, Sophien" uniqKey="Kamoun S" first="Sophien" last="Kamoun">Sophien Kamoun</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author><author><name sortKey="Bozkurt, Tolga O" sort="Bozkurt, Tolga O" uniqKey="Bozkurt T" first="Tolga O" last="Bozkurt">Tolga O. Bozkurt</name><affiliation><nlm:aff id="aff1"><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff3"><institution content-type="dept">Department of Life Sciences</institution>,<institution>Imperial College London</institution>,<addr-line>London</addr-line>,<country>United Kingdom</country></nlm:aff></affiliation></author></analytic><series><title level="j">eLife</title><idno type="eISSN">2050-084X</idno><imprint><date when="????">????</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Plants use autophagy to safeguard against infectious diseases. However, how plant pathogens interfere with autophagy-related processes is unknown. Here, we show that PexRD54, an effector from the Irish potato famine pathogen <italic>Phytophthora infestans</italic>, binds host autophagy protein ATG8CL to stimulate autophagosome formation. PexRD54 depletes the autophagy cargo receptor Joka2 out of ATG8CL complexes and interferes with Joka2's positive effect on pathogen defense. Thus, a plant pathogen effector has evolved to antagonize a host autophagy cargo receptor to counteract host defenses.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.001">http://dx.doi.org/10.7554/eLife.10856.001</ext-link></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bassham, Dc" uniqKey="Bassham D">DC Bassham</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baxt, La" uniqKey="Baxt L">LA Baxt</name></author><author><name 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rid="aff2">2</xref><xref ref-type="fn" rid="con9"></xref><xref ref-type="fn" rid="conf1"></xref></contrib><contrib id="author-41049" contrib-type="author"><name><surname>Sklenar</surname><given-names>Jan</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="other" rid="par-2"></xref><xref ref-type="fn" rid="con10"></xref><xref ref-type="fn" rid="conf1"></xref></contrib><contrib id="author-41050" contrib-type="author"><name><surname>Win</surname><given-names>Joe</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="other" rid="par-1"></xref><xref ref-type="other" rid="par-2"></xref><xref ref-type="fn" rid="con11"></xref><xref ref-type="fn" rid="conf1"></xref></contrib><contrib id="author-41051" contrib-type="author"><name><surname>Menke</surname><given-names>Frank</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="other" rid="par-2"></xref><xref ref-type="fn" rid="con12"></xref><xref ref-type="fn" rid="conf1"></xref></contrib><contrib id="author-41052" contrib-type="author"><name><surname>Findlay</surname><given-names>Kim</given-names></name><xref ref-type="aff" rid="aff4">4</xref><xref ref-type="fn" rid="con13"></xref><xref ref-type="fn" rid="conf1"></xref></contrib><contrib id="author-3524" contrib-type="author"><name><surname>Banfield</surname><given-names>Mark J</given-names></name><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0001-8921-3835</contrib-id><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="fn" rid="con14"></xref><xref ref-type="fn" rid="conf1"></xref></contrib><contrib id="author-12701" contrib-type="author"><name><surname>Kamoun</surname><given-names>Sophien</given-names></name><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0002-0290-0315</contrib-id><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="other" rid="par-1"></xref><xref ref-type="other" rid="par-2"></xref><xref ref-type="fn" rid="con15"></xref><xref ref-type="fn" rid="conf1"></xref></contrib><contrib id="author-12952" contrib-type="author"><name><surname>Bozkurt</surname><given-names>Tolga O</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="corresp" rid="cor2">*</xref><xref ref-type="other" rid="par-3"></xref><xref ref-type="fn" rid="con16"></xref><xref ref-type="fn" rid="conf1"></xref></contrib><aff id="aff1"><label>1</label><institution>The Sainsbury Laboratory</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></aff><aff id="aff2"><label>2</label><institution content-type="dept">Department of Biological Chemistry</institution>,<institution>John Innes Centre</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></aff><aff id="aff3"><label>3</label><institution content-type="dept">Department of Life Sciences</institution>,<institution>Imperial College London</institution>,<addr-line>London</addr-line>,<country>United Kingdom</country></aff><aff id="aff4"><label>4</label><institution content-type="dept">Department of Cell and Developmental Biology</institution>,<institution>John Innes Centre</institution>,<addr-line>Norwich</addr-line>,<country>United Kingdom</country></aff></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Greenberg</surname><given-names>Jean T</given-names></name><role>Reviewing editor</role><aff id="aff5"><institution>University of Chicago</institution>,<country>United States</country></aff></contrib></contrib-group><author-notes><corresp id="cor1"><email>sophien.kamoun@tsl.ac.uk</email> (SK);</corresp><corresp id="cor2"><email>o.bozkurt@imperial.ac.uk</email> (TOB)</corresp><fn fn-type="con" id="equal-contrib"><label>†</label><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date date-type="pub" publication-format="electronic"><day>14</day><month>1</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>5</volume><elocation-id>e10856</elocation-id><history><date date-type="received"><day>15</day><month>8</month><year>2015</year></date><date date-type="accepted"><day>13</day><month>1</month><year>2016</year></date></history><permissions><copyright-statement>© 2016, Dagdas et al</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Dagdas et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="elife-10856.pdf"></self-uri><abstract><p>Plants use autophagy to safeguard against infectious diseases. However, how plant pathogens interfere with autophagy-related processes is unknown. Here, we show that PexRD54, an effector from the Irish potato famine pathogen <italic>Phytophthora infestans</italic>, binds host autophagy protein ATG8CL to stimulate autophagosome formation. PexRD54 depletes the autophagy cargo receptor Joka2 out of ATG8CL complexes and interferes with Joka2's positive effect on pathogen defense. Thus, a plant pathogen effector has evolved to antagonize a host autophagy cargo receptor to counteract host defenses.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.001">http://dx.doi.org/10.7554/eLife.10856.001</ext-link></p></abstract><abstract abstract-type="executive-summary"><title>eLife digest</title><p>Plants and other living organisms can survive stress and starvation by digesting and recycling parts of their own cells. This process is known as autophagy and it involves engulfing cellular material inside spherical structures called autophagosomes, before delivering it to sites in the cell where digestive enzymes can break the material down. A form of autophagy, known as selective autophagy, can specifically degrade toxic substances such as disease-causing microbes. Selective autophagy works through proteins called autophagy cargo receptors that define which molecules are targeted for degradation. However, it was not clear whether autophagy protects plants from infections, or how much disease-causing microbes interfere with this process for their own benefit.</p><p>The microbe that causes late blight of potatoes (called <italic>Phytophthora infestans</italic>) is infamous for triggering widespread famines in Ireland in the 19<sup>th</sup> century. This disease-causing microbe continues to pose a serious threat to food security today, and parasitizes plant tissues by releasing proteins called effectors that enter the plant’s cells to subvert the plant’s physiology and counteract its defenses.</p><p>Dagdas, Belhaj et al. now report that an effector from <italic>P. infestans,</italic> called PexRD54, can bind to autophagy-related protein from potato, called ATG8CL, and stimulate the formation of autophagosomes. Further experiments revealed that the PexRD54 effector could outcompete a plant autophagy cargo receptor that would otherwise bind to ATG8CL. This plant cargo receptor contributes to the plant’s defences, and by preventing it from interacting with ATG8CL, PexRD54 makes the plant more susceptible to infection by <italic>P. infestans</italic>.</p><p>These findings show that the PexRD54 effector has evolved to interact with an autophagy-related protein to counteract the plant’s defences. Dagdas, Belhaj et al. suggest that PexRD54 might do this by activating autophagy to selectively eliminate some of the molecules that the plant use to defend itself. Furthermore, <italic>P. infestans</italic> might also benefit from the nutrients that are released when cellular material is broken down via autophagy. Future work could test these two hypotheses and explore whether other effectors from disease-causing microbes work in a similar way.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.002">http://dx.doi.org/10.7554/eLife.10856.002</ext-link></p></abstract><kwd-group kwd-group-type="author-keywords"><title>Author Keywords</title><kwd>Nicotiana benthamiana</kwd><kwd>Phytophthora infestans</kwd><kwd>autophagy</kwd><kwd>effectors</kwd><kwd>Irish potato famine</kwd><kwd>late blight disease</kwd></kwd-group><kwd-group kwd-group-type="research-organism"><title>Research Organism</title><kwd>Other</kwd></kwd-group><funding-group><award-group id="par-1"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100000781</institution-id><institution>European Research Council</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Maqbool</surname><given-names>Abbas</given-names></name><name><surname>Petre</surname><given-names>Benjamin</given-names></name><name><surname>Win</surname><given-names>Joe</given-names></name><name><surname>Kamoun</surname><given-names>Sophien</given-names></name></principal-award-recipient></award-group><award-group id="par-2"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100000324</institution-id><institution>Gatsby Charitable Foundation</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Dagdas</surname><given-names>Yasin F</given-names></name><name><surname>Belhaj</surname><given-names>Khaoula</given-names></name><name><surname>Cruz-Mireles</surname><given-names>Neftaly</given-names></name><name><surname>Sklenar</surname><given-names>Jan</given-names></name><name><surname>Win</surname><given-names>Joe</given-names></name><name><surname>Menke</surname><given-names>Frank</given-names></name><name><surname>Kamoun</surname><given-names>Sophien</given-names></name></principal-award-recipient></award-group><award-group id="par-3"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100000268</institution-id><institution>Biotechnology and Biological Sciences Research Council</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Pandey</surname><given-names>Pooja</given-names></name><name><surname>Tabassum</surname><given-names>Nadra</given-names></name><name><surname>Bozkurt</surname><given-names>Tolga O</given-names></name></principal-award-recipient></award-group><funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement></funding-group><custom-meta-group><custom-meta><meta-name>elife-xml-version</meta-name><meta-value>2.5</meta-value></custom-meta><custom-meta specific-use="meta-only"><meta-name>Author impact statement</meta-name><meta-value>A plant pathogen effector evolved a short linear motif to subvert autophagic defenses by antagonising a host cargo receptor.</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec sec-type="intro" id="s1"><title>Introduction</title><p>Autophagy is conserved catabolic pathway that sequesters unwanted cytosolic components into newly formed double membrane vesicles, autophagosomes, to direct them to the cell’s lytic compartment (<xref rid="bib17" ref-type="bibr">He and Klionsky, 2009</xref>). The process plays a vital role in survival of the organism by improving cellular adaptation to environmental and stress conditions (<xref rid="bib40" ref-type="bibr">Shintani and Klionsky, 2004</xref>). Autophagy provides building blocks and energy for elementary cellular processes by degrading dysfunctional or unnecessary cellular components during nutrient deprivation (<xref rid="bib40" ref-type="bibr">Shintani and Klionsky, 2004</xref>). However, even though autophagy was initially thought to be a bulk degradation process activated during starvation, recent studies showed that it can act selectively, capturing specific substrates through specialized cargo receptors to respond to a variety of environmental and stress conditions (<xref rid="bib42" ref-type="bibr">Stolz et al., 2014</xref>).</p><p>Autophagy is executed through coordinated action of more than 30 core proteins known as the ATG (autophagy-related) proteins (<xref rid="bib24" ref-type="bibr">Lamb et al., 2013</xref>). Selective autophagy is regulated through specific interactions of autophagy cargo receptors and ATG8 proteins (<xref rid="bib42" ref-type="bibr">Stolz et al., 2014</xref>). Autophagy cargo receptors carry a short sequence motif called ATG8-interaction motif (AIM) that binds lipidated ATG8 proteins anchored on autophagosomal membranes. Cargo receptors mediate recognition of a diverse set of cargo (<xref rid="bib42" ref-type="bibr">Stolz et al., 2014</xref>). For instance, mammalian autophagy cargo receptors NDP52 and optineurin can recognize intracellular pathogenic bacteria and mediate their autophagic removal by sorting the captured bacteria inside the ATG8-coated autophagosomes (<xref rid="bib6" ref-type="bibr">Boyle and Randow, 2013</xref>). Nevertheless, the precise molecular mechanisms of selective autophagy and the components that regulate it remain unknown (<xref rid="bib18" ref-type="bibr">Huang and Brumell, 2014</xref>; <xref rid="bib32" ref-type="bibr">Mostowy, 2013</xref>; <xref rid="bib37" ref-type="bibr">Randow, 2011</xref>).</p><p>In plants, autophagy plays important roles in stress tolerance, senescence, development, and defense against invading pathogens (<xref rid="bib34" ref-type="bibr">Patel and Dinesh-Kumar, 2008</xref>; <xref rid="bib26" ref-type="bibr">Lenz et al., 2011</xref>; <xref rid="bib45" ref-type="bibr">Vanhee and Batoko, 2011</xref>; <xref rid="bib27" ref-type="bibr">Li and Vierstra, 2012</xref>; <xref rid="bib30" ref-type="bibr">Lv et al., 2014</xref>; <xref rid="bib44" ref-type="bibr">Teh and Hofius, 2014</xref>). Specifically, autophagy is implicated in the accumulation of defense hormones and the hypersensitive response, a form of plant cell death that prevents spread of microbial infection (<xref rid="bib48" ref-type="bibr">Yoshimoto et al., 2009</xref>). However, the molecular mechanisms that mediate defense-related autophagy and the selective nature of this process are poorly understood. Furthermore, how adapted plant pathogens manipulate defense-related autophagy and/or subvert autophagy for nutrient uptake is unknown.</p><p>In this study, we investigated how a pathogen interferes with and coopts a plant autophagy pathway. The potato blight pathogen, <italic>Phytophthora infestans</italic>, is a serious threat to food security, causing crop losses that, if alleviated, could feed hundreds of millions of people (<xref rid="bib14" ref-type="bibr">Fisher et al., 2012</xref>). This pathogen delivers RXLR-type effector proteins inside plant cells to enable parasitism (<xref rid="bib31" ref-type="bibr">Morgan and Kamoun, 2007</xref>). RXLR effectors form a diverse family of modular proteins that alter a variety of host processes and therefore serve as useful probes to dissect key pathways for pathogen invasion (<xref rid="bib31" ref-type="bibr">Morgan and Kamoun, 2007</xref>; <xref rid="bib8" ref-type="bibr">Bozkurt et al., 2012</xref>). Here, we show that the RXLR effector PexRD54 has evolved to bind host autophagy protein ATG8CL to stimulate autophagosome formation. In addition, PexRD54 depletes the autophagy cargo receptor Joka2 out of ATG8CL complexes to counteract host defenses against <italic>P. infestans</italic>.</p></sec><sec id="s2"><title>Results and discussion</title><p>As part of an <italic>in planta</italic>screen for host interactors of RXLR effectors, we discovered that the <italic>P. infestans</italic> effector PexRD54 associates with ATG8CL, a member of the ATG8 family (Materials and methods, <xref ref-type="supplementary-material" rid="SD1-data">Supplementary files 1</xref>,<xref ref-type="supplementary-material" rid="SD2-data">2</xref>). The association between PexRD54 and ATG8CL was retained under stringent binding conditions in contrast to other candidate interactors (<xref ref-type="supplementary-material" rid="SD1-data">Supplementary file 1</xref>). We validated the association with reverse coimmunoprecipitation after co-expressing the potato ATG8CL protein with the C-terminal effector domain of PexRD54 <italic>in planta</italic> (<xref ref-type="fig" rid="fig1">Figure 1A,B</xref>). In addition, PexRD54 expressed and purified from <italic>Escherichia coli</italic> directly bound ATG8CL in vitro with high affinity and in a one to one ratio (<italic>K</italic><sub>D</sub> = 383 nM based on isothermal titration calorimetry) (<xref ref-type="fig" rid="fig1">Figure 1C</xref>). PexRD54 has two predicted ATG8 Interacting Motifs (AIMs) that match the consensus amino acid sequence W/F/Y-x-x-L/I/V (AIM1 and AIM2, <xref ref-type="fig" rid="fig1">Figure 1A</xref>). <italic>In planta</italic> coimmunoprecipitations of single and double AIM mutants of PexRD54 revealed that AIM2, which spans the last four amino acids of the protein (positions 378–381), is required for association with ATG8CL (<xref ref-type="fig" rid="fig1">Figure 1D</xref>). PexRD54<sup>AIM2</sup> mutant also failed to bind ATG8CL in vitro (<xref ref-type="fig" rid="fig1">Figure 1E</xref>). In addition, ATG8CL bound with high affinity to a synthetic peptide (KPLDFDWEIV) that matches the last 10 C-terminal amino acids of PexRD54 (<italic>K</italic><sub>D</sub> = 220 nM) (<xref ref-type="fig" rid="fig1s1">Figure 1—figure supplement 1</xref>). We conclude that the C-terminal AIM of PexRD54 is necessary and sufficient to bind ATG8CL.<fig id="fig1" position="float" orientation="portrait"><object-id pub-id-type="doi">10.7554/eLife.10856.003</object-id><label>Figure 1.</label><caption><title>PexRD54 binds to ATG8CL via a C-terminal ATG8 interacting motif (AIM).</title><p>(<bold>A</bold>) Domain organization of PexRD54. PexRD54 is a canonical RXLR effector with five WY folds (<xref rid="bib47" ref-type="bibr">Win et al., 2012</xref>). The amino acid sequences of candidate AIMs are highlighted in yellow color and indicated in brackets. (<bold>B</bold>) Validation of PexRD54-ATG8CL association <italic>in planta</italic>. RFP:PexRD54 or RFP:EV (Empty vector) were transiently co-expressed with GFP:ATG8CL or GFP:EV in <italic>N. benthamiana</italic> leaves. Immunoprecipitates (IPs) obtained with anti-GFP antiserum and total protein extracts were immunoblotted with appropriate antisera. Stars indicate the expected band sizes. (<bold>C</bold>) PexRD54 binds ATG8CL in vitro. The binding affinity of PexRD54 to ATG8CL was determined using isothermal titration calorimetry (ITC). Upper panel shows heat differences upon injection of ATG8CL into buffer or PexRD54 and the bottom panel show integrated heats of injection (■) and the best fit (solid line) to a single site binding model using MicroCal Origin. <italic>K</italic><sub>D</sub>=383 nM, N=0.998, ΔH= −8.966 kJ.mol<sup>-1</sup> and ΔS = 0.092 J.mol<sup>-1</sup>.K<sup>-1</sup>. The values of <italic>K</italic><sub>D</sub>, N, ΔH and ΔS are representative of two independent ITC experiments. (<bold>D</bold>) ATG8 Interacting Motif 2 (AIM2) mediates ATG8CL binding <italic>in planta</italic>. RFP:PexRD54, RFP:PexRD54<sup>AIM1</sup>, RFP:PexRD54<sup>AIM2</sup> or RFP:PexRD54<sup>AIM1&AIM2</sup> were transiently co-expressed with GFP:ATG8CL or GFP:EV in <italic>N. benthamiana</italic> leaves. IPs obtained with anti-GFP antiserum and total protein extracts were immunoblotted with appropriate antisera. Stars indicate the expected band sizes. (<bold>E</bold>) AIM2 mediates ATG8CL binding in vitro. The binding affinity of PexRD54<sup>AIM2</sup> to ATG8CL was determined using ITC. Upper panel shows heat differences upon injection of PexRD54<sup>AIM2</sup> and the bottom panel show integrated heats of injection (■). No binding was detected between PexRD54<sup>AIM2</sup> and ATG8CL.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.003">http://dx.doi.org/10.7554/eLife.10856.003</ext-link></p></caption><graphic xlink:href="elife-10856-fig1"></graphic><p content-type="supplemental-figure"><fig id="fig1s1" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.004</object-id><label>Figure 1—figure supplement 1.</label><caption><title>A synthetic peptide composed of the last ten amino acids of PexRD54 is sufficient for binding to ATG8CL.</title><p>(<bold>A</bold>) A synthetic peptide (KPLDFDWEIV) containing the AIM of PexRD54 binds ATG8CL as documented by ITC. (<bold>B</bold>) A mutant AIM peptide (KPLDFDAEIA) was used as negative control and did not bind ATG8CL. Heat differences upon injection of peptides and integrated heats of injection are shown for both peptides. The values of <italic>K</italic><sub>D</sub>, ΔH and ΔS are representative of two independent experiments.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.004">http://dx.doi.org/10.7554/eLife.10856.004</ext-link></p></caption><graphic xlink:href="elife-10856-fig1-figsupp1"></graphic></fig></p></fig></p><p>ATG8 occurs as a family of nine proteins in potato (<xref ref-type="fig" rid="fig2s1">Figure 2—figure supplements 1</xref>–<xref ref-type="fig" rid="fig2s2">2</xref>). PexRD54 bound ATG8CL with ~10 times higher affinity than another ATG8 family member, ATG8IL, in both <italic>in planta</italic> and in vitro assays (<xref ref-type="fig" rid="fig2">Figure 2</xref>). These findings prompted us to use ATG8IL as a negative control in the subsequent experiments.<fig id="fig2" position="float" orientation="portrait"><object-id pub-id-type="doi">10.7554/eLife.10856.005</object-id><label>Figure 2.</label><caption><title>PexRD54 has higher binding affinity to ATG8CL than ATG8IL.</title><p>(<bold>A</bold>) RFP:PexRD54, RFP:AVRblb2 or RFP:EV were transiently co-expressed with GFP:ATG8CL, GFP:ATG8IL or GFP:EV in <italic>N. benthamiana</italic> leaves and proteins were extracted two days after infiltration and used in immunoprecipitation experiments (IPs). IPs obtained with anti-GFP or anti-RFP antisera and total protein extracts were immunoblotted with appropriate antisera. RFP:AVRblb2 (<xref rid="bib9" ref-type="bibr">Bozkurt et al., 2011</xref>), an RFP fusion to a different <italic>P. infestans</italic> RXLR effector, did not associate with ATG8CL or ATG8IL. Both the GFP and RFP IPs indicate higher binding affinity of PexRD54 to ATG8CL than ATG8IL. Stars indicate the expected band sizes. (<bold>B</bold>) PexRD54 has lower binding affinity to ATG8IL in vitro. The binding affinity of PexRD54 to ATG8IL was determined using isothermal titration calorimetry (ITC). Upper panel shows heat generated upon injection of ATG8IL into buffer or PexRD54 and lower panel shows integrated heats of injection (■) and the best fit (solid line) to a single site binding model using MicroCal Origin. The values of <italic>K</italic><sub>D</sub> = 4100 nM, N = 0.938, ΔH = −11.305 kJ.mol<sup>-1 </sup>and ΔS= 0.064 J.mol<sup>-1</sup>K<sup>-1 </sup>are representative values of two independent ITC experiments. The data show that PexRD54 binds ATG8CL with ~10 times higher affinity than ATGIL.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.005">http://dx.doi.org/10.7554/eLife.10856.005</ext-link></p></caption><graphic xlink:href="elife-10856-fig2"></graphic><p content-type="supplemental-figure"><fig id="fig2s1" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.006</object-id><label>Figure 2—figure supplement 1.</label><caption><title>Amino acid sequence alignment of ATG8 proteins from <italic>Arabidopsis thaliana</italic> (At), <italic>Solanum tuberosum</italic> (St), <italic>Solanum lycopersicum</italic> (Sl) and <italic>Nicotiana benthamiana</italic> (Nb).</title><p>Sequences were aligned using ClustalW and visualized using Boxshade v3.21. Identical amino acids are highlighted in black and amino acids with similar biochemical properties are shown in grey. Red arrowhead points to ATG8CL and blue arrowhead points to ATG8IL.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.006">http://dx.doi.org/10.7554/eLife.10856.006</ext-link></p></caption><graphic xlink:href="elife-10856-fig2-figsupp1"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig2s2" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.007</object-id><label>Figure 2—figure supplement 2.</label><caption><title>Phylogenetic analysis of ATG8 proteins.</title><p>A neighbor-joining tree was generated with ATG8 sequences obtained from genomes of <italic>A. thaliana, S. tuberosum, S. lycopersium,</italic> and <italic>N. benthamiana</italic>, using MEGA5 with a 1000 bootstrap value. ATG8CL and ATG8IL are highlighted in pink and the ATG8CL variant that was identified in <italic>N. benthamiana</italic> is highlighted in green.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.007">http://dx.doi.org/10.7554/eLife.10856.007</ext-link></p></caption><graphic xlink:href="elife-10856-fig2-figsupp2"></graphic></fig></p></fig></p><p>We then investigated the subcellular localization of PexRD54 within plant cells. N-terminal fusions of PexRD54 to the green fluorescent protein (GFP) or red fluorescent protein (RFP) labelled the nucleo-cytoplasm and mobile punctate structures (<xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1</xref> and <xref ref-type="other" rid="media1">Video 1</xref>). Immunogold labelling in transmission electron micrographs of cells expressing GFP:PexRD54 revealed a strong signal in electron dense structures that are not peroxisomes (<xref ref-type="fig" rid="fig3s2">Figure 3—figure supplements 2</xref>–<xref ref-type="fig" rid="fig3s3">3</xref>, <xref rid="bib13" ref-type="bibr">Dagdas et al., 2016</xref>). To determine whether these structures are ATG8CL autophagosomes, we transiently co-expressed RFP:PexRD54 with GFP:ATG8CL in plant cells and observed an overlap between the two fluorescent signals in sharp contrast to RFP:PexRD54<sup>AIM2</sup> and RFP:EV negative controls (<xref ref-type="fig" rid="fig3">Figure 3</xref> and <xref ref-type="other" rid="media2">Video 2</xref>). This indicates that PexRD54 localizes to ATG8CL-marked autophagosomes and its C-terminal AIM is necessary for autophagosome localization. In contrast, RFP:PexRD54 signal overlapped with GFP:ATG8IL-labelled autophagosomes in only 15–20% of observations consistent with its weaker binding affinity to ATG8IL (<xref ref-type="fig" rid="fig3s4">Figure 3—figure supplement 4</xref>).<fig id="media1" position="anchor"><label>Video 1.</label><caption><title>PexRD54 localizes to mobile endomembrane compartments. </title><p>GFP:PexRD54 was transiently expressed in <italic>N. benthamiana</italic> leaves and examined by confocal laser scanning microscopy, 3 days post infiltration. (Related to <xref ref-type="fig" rid="fig3">Figure 3</xref>)</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.008">http://dx.doi.org/10.7554/eLife.10856.008</ext-link></p></caption><media xlink:href="elife-10856-media1.mp4" mimetype="video" mime-subtype="mp4"><object-id pub-id-type="doi">10.7554/eLife.10856.008</object-id></media></fig><fig id="fig3" position="float" orientation="portrait"><object-id pub-id-type="doi">10.7554/eLife.10856.009</object-id><label>Figure 3.</label><caption><title>PexRD54 localizes to ATG8CL labelled autophagosomes.</title><p>Transient co-expression of GFP:ATG8CL with (<bold>A</bold>) RFP:PexRD54, (<bold>B</bold>) RFP:PexRD54<sup>AIM2</sup> and (<bold>C</bold>) RFP control (RFP:EV) in <italic>N. benthamiana</italic> leaves. Confocal micrographs show single optical sections of RFP:PexRD54, RFP:PexRD54<sup>AIM2</sup> and RFP:EV in red, GFP:ATG8CL in green and the overlay indicating colocalization in yellow. White arrowheads point to punctate structures and yellow arrowheads point to puncta where GFP and RFP signals overlap. Far right panels highlight the dotted square region focusing on GFP:ATG8CL labelled puncta in overlaid GFP/RFP channels. Scale bar = 10 μm; scale bar in inset = 1 μm. (<bold>D</bold>) The intensity plots represent relative GFP and RFP fluorescence signals along the dotted line connecting points a-b, c-d and e-f that span GFP:ATG8CL marked puncta at far right panels. GFP:ATG8CL fluorescence intensity peak overlapped with fluorescence intensity peak of RFP:PexRD54 (left panel) but not with RFP:PexRD54<sup>AIM2</sup> (mid panel) or RFP:EV (right panel) validating the localization of RFP:PexRD54 at GFP:ATG8CL labelled autophagosomes. (<bold>E</bold>) Bar charts showing colocalization of GFP:ATG8CL puncta with RFP:PexRD54, RFP:PexRD54<sup>AIM2</sup> or RFP:EV punctate structures. Data are representative of 500 individual images from two biological replicates. Each replicate consists of five independent Z stacks with 50 images each, acquired from five independent leaf areas. (***p<0.001). Error bars represent ± SD.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.009">http://dx.doi.org/10.7554/eLife.10856.009</ext-link></p></caption><graphic xlink:href="elife-10856-fig3"></graphic><p content-type="supplemental-figure"><fig id="fig3s1" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.010</object-id><label>Figure 3—figure supplement 1.</label><caption><title>PexRD54 localizes to vesicle like structures.</title><p>GFP:PexRD54 or RFP:PexRD54 were transiently expressed in <italic>N. benthamiana</italic> and examined by confocal laser scanning microscopy 3 days post infiltration. Confocal micrographs show single optical sections of GFP:PexRD54 (left panel) and RFP:PexRD54 (right panel). With both tags, PexRD54 localized to vesicular structures pointed with arrowheads. Scale bar=10 μm.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.010">http://dx.doi.org/10.7554/eLife.10856.010</ext-link></p></caption><graphic xlink:href="elife-10856-fig3-figsupp1"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig3s2" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.011</object-id><label>Figure 3—figure supplement 2.</label><caption><title>PexRD54 localizes to high electron dense structures.</title><p>(<bold>A</bold>) Transmission electron microscopy (TEM) imaging of PexRD54. <italic>N. benthamiana</italic> cells transiently expressing GFP:PexRD54 or GFP:EV were collected 3 days post infiltration and probed with anti-GFP antibodies conjugated to gold particles. GFP:PexRD54 labelling were mainly at high electron dense structures, whereas GFP:EV showed cytosolic distribution. Scale bar=200 nm (<bold>B</bold>) Bar charts showing electron dense labelling in GFP:EV and GFP:PexRD54 expressing samples (*p<0.05).</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.011">http://dx.doi.org/10.7554/eLife.10856.011</ext-link></p></caption><graphic xlink:href="elife-10856-fig3-figsupp2"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig3s3" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.012</object-id><label>Figure 3—figure supplement 3.</label><caption><title>PexRD54 labelled high electron dense structures that are not peroxisomes.</title><p>Serial sections of <italic>N. benthamiana</italic> leaves transiently expressing GFP:PexRD54 were collected 3 days post infiltration and probed with anti-GFP and anti-catalase antibodies conjugated to gold particles. High electron dense structures labelled with GFP antibody were different than the regions labelled with catalase antibody, confirming that PexRD54 labelled structures are not peroxisomes. Stars indicate regions that are labelled by gold particles in the other image. Scale bar=500 nm</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.012">http://dx.doi.org/10.7554/eLife.10856.012</ext-link></p></caption><graphic xlink:href="elife-10856-fig3-figsupp3"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig3s4" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.013</object-id><label>Figure 3—figure supplement 4.</label><caption><title>PexRD54 labelled puncta rarely include GFP:ATGIL signal.</title><p>GFP:ATG8IL was transiently co-expressed with RFP:PexRD54 or RFP:EV in <italic>N. benthamiana</italic> leaves and examined by confocal laser scanning microscopy 3 days post infiltration. Maximum intensity projection of confocal micrographs shows that RFP:PexRD54 only partially colocalizes with GFP:ATG8IL. White arrowheads point to vesicles labelled with only GFP:ATG8IL or RFP:PexRD54, whereas the red-filled arrowheads point to puncta where colocalization occurs. Regions where GFP or RFP labelled puncta do not overlap are indicated with dotted squares. Scale bar=50 μm (<bold>B</bold>) Bar charts showing the number of RFP-labelled puncta that colocalized with GFP:ATG8IL puncta. The data are representative of 500 individual images from two biological replicates. Each replicate consists of five independent Z stack images with 50 images each, acquired from five independent leaf areas. (ns=statistically not significant). Error bars represent ± SD.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.013">http://dx.doi.org/10.7554/eLife.10856.013</ext-link></p></caption><graphic xlink:href="elife-10856-fig3-figsupp4"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig3s5" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.014</object-id><label>Figure 3—figure supplement 5.</label><caption><title>Inhibition of autophagy hinders PexRD54 vesicular distribution.</title><p><italic>N. benthamiana</italic> leaves transiently expressing GFP:ATG8CL/RFP:PexRD54, GFP:PexRD54/RFP:ATG8CL or trans-golgi network marker YFP:VTI12 were infiltrated with autophagy inhibitor 3-methyl adenine (3-MA) at a concentration of 5 mM or water and imaged 6 hr post infiltration. 3-MA prevented formation of punctate structures of PexRD54 and ATG8CL but not of VTI12. Scale bar= 50 μm (<bold>B</bold>) Bar charts showing the number of punctate structures in 3-MA or water-treated samples. The data are representative of 500 individual images from two biological replicates. Each replicate consists of five independent Z stacks with 50 images each, acquired from five independent leaf areas. (***p<0.001, ns=statistically not significant). Error bars represent ± SD.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.014">http://dx.doi.org/10.7554/eLife.10856.014</ext-link></p></caption><graphic xlink:href="elife-10856-fig3-figsupp5"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig3s6" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.015</object-id><label>Figure 3—figure supplement 6.</label><caption><title>Conservation of terminal glycine residue in ATG8 proteins from various species.</title><p>Amino acid sequence alignment of ATG8 variants from different species that belong to different kingdoms shows conservation of terminal glycine residue (highlighted with an orange arrow). Residues that are responsible for interaction with core ATG8 interacting motif (AIM) residues are highlighted in purple (W pocket) and green (L pocket). Red and blue arrowheads point to ATG8CL and ATG8IL variants, respectively. Abbreviations for species: <italic>Hs: Homo sapiens; Tb: Trypanosoma brucei; Sc:Saccharomyces cerevisiae; Ce: Caenorhabditis elegans; At: Arabidopsis thaliana; Sl: Solanum lycopersium, Nb: Nicotiana benthamiana.</italic></p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.015">http://dx.doi.org/10.7554/eLife.10856.015</ext-link></p></caption><graphic xlink:href="elife-10856-fig3-figsupp6"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig3s7" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.016</object-id><label>Figure 3—figure supplement 7.</label><caption><title>ATG8CL terminal glycine deletion mutant prevents formation of PexRD54 labelled puncta in a dominant negative manner.</title><p>(<bold>A</bold>) A glycine to alanine mutation in the conserved terminal glycine residue of GFP:ATG8CL does not prevent binding to RFP:PexRD54. GFP:ATG8CL or GFP:ATG8CLΔ were transiently co-expressed with RFP:PexRD54 or RFP:PexRD54<sup>AIM2</sup> in <italic>N. benthamiana</italic> leaves and total proteins were extracted two days after infiltration and used in immunoprecipitation experiments (IPs). IPs obtained with anti-GFP and total protein extracts were immunoblotted with appropriate antisera. Stars indicate the expected band sizes. (<bold>B</bold>) GFP:ATG8CL or GFP:ATG8CLΔ were transiently co-expressed with RFP:EV or RFP:PexRD54 in <italic>N. benthamiana</italic> leaves and examined by confocal laser scanning microscopy 3 days post infiltration. GFP:ATG8CL showed distinct punctate structures, whereas GFP:ATG8CLΔ was mainly cytosolic with few visible puncta. When RFP:PexRD54 was co-expressed with GFP:ATG8CLΔ, the punctate localization was lost consistent with the recruitment of PexRD54 to ATG8CL labelled autophagosomes. (<bold>C</bold>) Co-expression of GFP:ATG8ILΔ and RFP:PexRD54, did not alter punctate localization of RFP:PexRD54. Arrowheads point to puncta labelled with GFP or RFP fusion constructs. Regions where GFP or RFP labelled puncta do not colocalize are indicated with dotted squares. Scale bar=50 μm (<bold>D</bold>) Bar charts confirming punctate distribution of PexRD54 depends on localization at ATG8CL labelled autophagosomes. The data are representative of 500 individual images from two biological replicates. Each replicate consists of five independent Z stacks with 50 images each, acquired from five independent leaf areas. (***p<0.001, ns=statistically not significant). Error bars represent ± SD.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.016">http://dx.doi.org/10.7554/eLife.10856.016</ext-link></p></caption><graphic xlink:href="elife-10856-fig3-figsupp7"></graphic></fig></p></fig><fig id="media2" position="anchor"><label>Video 2.</label><caption><title>PexRD54 and ATG8CL colocalize at mobile endomembrane compartments. </title><p>RFP:PexRD54 was transiently co-expressed with GFP:ATG8CL in <italic>N. benthamiana</italic> leaves and examined by confocal laser scanning microscopy, 3 days post infiltration. (Related to <xref ref-type="fig" rid="fig3">Figure 3</xref>)</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.017">http://dx.doi.org/10.7554/eLife.10856.017</ext-link></p></caption><media xlink:href="elife-10856-media2.mp4" mimetype="video" mime-subtype="mp4"><object-id pub-id-type="doi">10.7554/eLife.10856.017</object-id></media></fig></p><p>To further confirm that PexRD54-labelled endomembrane compartments are indeed autophagosomes, we investigated the effect of the autophagy inhibitor 3-methyl adenine (3-MA) (<xref rid="bib16" ref-type="bibr">Hanamata et al., 2013</xref>) on PexRD54 localization. Compared to water, 3-MA treatment reduced the number of PexRD54 and ATG8CL puncta but did not reduce the number of puncta of the trans-Golgi network (TGN) marker VTI12 (<xref rid="bib15" ref-type="bibr">Geldner et al., 2009</xref>) (<xref ref-type="fig" rid="fig3s5">Figure 3—figure supplement 5</xref>).</p><p>Phospholipid modification of a conserved glycine residue at the C-terminus of ATG8 proteins is required for autophagosome formation, and deletion of this terminal glycine yields a dominant negative ATG8 (<xref rid="bib16" ref-type="bibr">Hanamata et al., 2013</xref>). We deployed a terminal glycine deletion mutant of ATG8CL (ATG8CLΔ) to determine its effect on subcellular distribution of PexRD54 (<xref ref-type="fig" rid="fig3s6">Figure 3—figure supplement 6</xref>). As expected, deletion of the terminal glycine did not affect binding of ATG8CL to PexRD54 (<xref ref-type="fig" rid="fig3s7">Figure 3—figure supplement 7A</xref>). However, GFP:ATG8CLΔ led to the depletion of RFP:PexRD54 labelled puncta presumably because the dominant negative effect of ATG8CLΔ prevented accumulation of RFP:PexRD54 in ATG8CL-labelled autophagosomes (<xref ref-type="fig" rid="fig3s7">Figure 3—figure supplement 7B–D</xref>). In contrast, GFP:ATG8ILΔ, a terminal glycine deletion mutant of ATG8IL, had no effect on the punctate localization of RFP:PexRD54 (<xref ref-type="fig" rid="fig3s7">Figure 3—figure supplement 7C–D</xref>). These experiments independently support the finding that PexRD54 accumulates in ATG8CL autophagosomes.</p><p>Increase in ATG8 labelled puncta is widely used as a functional readout of autophagic activity (<xref rid="bib16" ref-type="bibr">Hanamata et al., 2013</xref>; <xref rid="bib2" ref-type="bibr">Bassham, 2015</xref>). In samples expressing PexRD54, we noticed a ~fivefold increase in the number of ATG8CL marked autophagosomes compared to control samples expressing PexRD54<sup>AIM2</sup> or empty vector control (<xref ref-type="fig" rid="fig4">Figure 4</xref>, <xref ref-type="other" rid="media3">Video 3</xref>). In contrast, PexRD54 did not alter the number of ATG8IL autophagosomes consistent with the weak binding noted between these two proteins (<xref ref-type="fig" rid="fig4">Figure 4A</xref>). This indicates that PexRD54 stimulates the formation of ATG8CL autophagosomes.<fig id="fig4" orientation="portrait" position="float"><object-id pub-id-type="doi">10.7554/eLife.10856.018</object-id><label>Figure 4.</label><caption><title>PexRD54 increases the number of ATG8CL autophagosomes.</title><p>(<bold>A</bold>) Co-expression of RFP:PexRD54, but not RFP:PexRD54<sup>AIM2</sup> or RFP:EV significantly enhanced the number of GFP:ATG8CL-labelled autophagosomes in <italic>N. benthamiana</italic>. Bar charts display the number of GFP:ATG8CL or GFP:ATG8IL-labelled autophagosomes in the presence of RFP:PexRD54, RFP:PexRD54<sup>AIM2</sup> or RFP:EV. GFP:ATG8CL autophagosomes were significantly enhanced by the expression of RFP:PexRD54 (***p<0.001). GFP:ATG8IL autophagosomes were not significantly enhanced by expression of RFP:PexRD54 (ns=statistically not significant). The data are representative of 500 individual images from two biological replicates. Each replicate consists of five independent Z stacks with 50 images each, acquired from five independent leaf areas. (<bold>B</bold>) GFP:ATG8CL was transiently co-expressed with RFP:PexRD54, RFP:PexRD54<sup>AIM2</sup> or RFP:EV in <italic>N. benthamiana</italic> leaves and examined by confocal laser scanning microscopy 3 days post infiltration. Maximum projections of images show that RFP:PexRD54 increases the number of GFP:ATG8CL- labelled autophagosomes. RFP:PexRD54<sup>AIM2</sup> and RFP:EV were used as controls. Arrowheads point to punctate structures. Regions where GFP or RFP-labelled puncta do not overlap are indicated with dotted squares. Scale bar=50 μm. Zoomed single plane images shown in the second panel indicate that larger puncta co-labelled by RFP:PexRD54 and GFP:ATG8CL are ring-shaped autophagosome clusters. Scale bar=10 μm.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.018">http://dx.doi.org/10.7554/eLife.10856.018</ext-link></p></caption><graphic xlink:href="elife-10856-fig4"></graphic></fig><fig id="media3" position="anchor"><label>Video 3.</label><caption><title>RFP:PexRD54 and GFP:ATG8CL colocalize at mobile ring shaped clusters. </title><p>RFP:PexRD54 was transiently co-expressed with GFP:ATG8CL in <italic>N. benthamiana</italic> leaves and examined by confocal laser scanning microscopy, 3 days post infiltration. (Related to <xref ref-type="fig" rid="fig4">Figure 4</xref>)</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.019">http://dx.doi.org/10.7554/eLife.10856.019</ext-link></p></caption><media xlink:href="elife-10856-media3.mp4" mimetype="video" mime-subtype="mp4"><object-id pub-id-type="doi">10.7554/eLife.10856.019</object-id></media></fig></p><p>Next, we set out to determine the effect of PexRD54 on autophagic flux. Treatment of RFP:ATG8CL expressing leaves with the specific vacuolar ATPase inhibitor concanamycin-A (<xref rid="bib2" ref-type="bibr">Bassham, 2015</xref>) increased the number of ATG8CL-labelled puncta both in the presence of PexRD54 or controls (PexRD54<sup>AIM2</sup> or vector control) indicating that PexRD54 does not block autophagic flux (<xref ref-type="fig" rid="fig5">Figure 5A–B</xref>). We also confirmed these observations using western blot analyses. PexRD54, but neither PexRD54<sup>AIM2</sup> or vector control, increased the levels of GFP:ATG8CL protein 3 days after co-expression <italic>in planta</italic> (<xref ref-type="fig" rid="fig5">Figure 5C</xref>). Treatment of three-day samples with E64d, an inhibitor of vacuolar cysteine proteases (<xref rid="bib2" ref-type="bibr">Bassham, 2015</xref>), further increased protein levels of GFP:ATG8CL. This further confirms that PexRD54 stimulates autophagy rather than blocking autophagic flux (<xref ref-type="fig" rid="fig5">Figure 5C</xref>). PexRD54 did not alter the accumulation of GFP:ATG8IL or control GFP protein, confirming that PexRD54 increases ATG8CL protein accumulation specifically (<xref ref-type="fig" rid="fig5">Figure 5C</xref>). Consistent with these observations, we noted an increase in GFP:ATG8CL levels, but not in control GFP, during <italic>P. infestans</italic> infection relative to the mock infection (<xref ref-type="fig" rid="fig5s1">Figure 5—figure supplement 1</xref>).<fig id="fig5" position="float" orientation="portrait"><object-id pub-id-type="doi">10.7554/eLife.10856.020</object-id><label>Figure 5.</label><caption><title>PexRD54 does not block autophagic flux.</title><p>(<bold>A–B</bold>) ConcanamycinA treatment increases the number of autophagosomes in PexRD54 expressing samples.RFP:ATG8CL was transienly coexpressed with PexRD54, PexRD54<sup>AIM2</sup> and empty vector controls in <italic>N. benthamiana</italic>. Two days after infiltration, leaves were treated with concanamycinA (conA) or infiltration buffer and number of autophagosomes was counted 24 hr after treatment. ConA treatment significantly increased the number of autophagosomes in PexRD54 expressing cells (p<0.05), confirming PexRD54 does not block autophagic flux. Scale bar=10 μm. (<bold>C</bold>) E64D treatment increases ATG8CL protein levels in PexRD54 expressing samples. GFP:ATG8CL, GFP:ATG8IL and GFP:EV were transiently coexpressed with RFP:GUS, RFP:PexRD54 or RFP:PexRD54<sup>AIM2</sup> in <italic>N. benthamiana</italic> leaves and protein levels in total extracts were determined two and 3 days post infiltration (dpi). RFP:PexRD54 increased protein levels of GFP:ATG8CL but not GFP:ATG8IL consistent with stronger binding affinity of PexRD54 to ATG8CL. RFP:PexRD54 did not increase protein levels of GFP:EV, suggesting that protein level increase depends on ATG8CL binding and that PexRD54 does not increase protein levels in general. The samples were also treated with E64d to measure autophagic flux. In RFP:PexRD54 coexpressed 3 dpi samples, E64d treatment increased ATG8CL protein levels even more suggesting PexRD54 does not block autophagic flux. Hence, protein level increase is a result of stimulation of autophagy. The blots were stained with Ponceau stain (PS) to show equal loading.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.020">http://dx.doi.org/10.7554/eLife.10856.020</ext-link></p></caption><graphic xlink:href="elife-10856-fig5"></graphic><p content-type="supplemental-figure"><fig id="fig5s1" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.021</object-id><label>Figure 5—figure supplement 1.</label><caption><title>GFP:ATG8CL protein levels increase <italic>in N. benthamiana</italic> during <italic>P. infestans</italic> infection.</title><p><italic>N. benthamiana</italic> leaves transiently expressing GFP:ATG8CL or GFP:EV were sprayed with <italic>P. infestans</italic> zoospore solution or water control (mock treatment). Protein levels of GFP:ATG8CL or GFP were determined 2 and 3 days after infection. The samples were run on the same gel and blots were developed with the same conditions. Gels were stained with coomassie brilliant blue (CBB) to show equal loading. Stars indicate expected band sizes.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.021">http://dx.doi.org/10.7554/eLife.10856.021</ext-link></p></caption><graphic xlink:href="elife-10856-fig5-figsupp1"></graphic></fig></p></fig></p><p>The presence of a functional AIM in PexRD54 prompted us to hypothesize that this effector perturbs the autophagy cargo receptors of its host plants. Recently, Joka2 was reported as a selective autophagy cargo receptor of Solanaceous plants that also binds ATG8 via an AIM (<xref rid="bib43" ref-type="bibr">Svenning et al., 2011</xref>; <xref rid="bib49" ref-type="bibr">Zientara-Rytter et al., 2011</xref>) (<xref ref-type="fig" rid="fig6">Figure 6A</xref>). Indeed, <italic>in planta</italic> coimmunoprecipitation assays confirmed that potato Joka2, but not the AIM mutant, Joka2<sup>AIM</sup>, associated with ATG8CL (<xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref>). Joka2 association with ATG8CL was somewhat specific given that this cargo receptor failed to coimmunoprecipitate with ATG8IL (<xref ref-type="fig" rid="fig6s2">Figure 6—figure supplement 2</xref>). Joka2, but not Joka2<sup>AIM</sup>, also markedly increased the number of GFP:ATG8CL autophagosomes (<xref ref-type="fig" rid="fig6s3">Figure 6—figure supplement 3</xref>, <xref ref-type="other" rid="media4">Video 4</xref>), and enhanced ATG8CL protein levels (<xref ref-type="fig" rid="fig6s4">Figure 6—figure supplement 4</xref>). This indicates that Joka2 also activates ATG8CL-mediated selective autophagy.<fig id="fig6" position="float" orientation="portrait"><object-id pub-id-type="doi">10.7554/eLife.10856.022</object-id><label>Figure 6.</label><caption><title>PexRD54 is a competitive antagonist of the plant selective autophagy cargo receptor Joka2.</title><p>(<bold>A</bold>) Domain organization of Joka2. (<bold>B</bold>) PexRD54 reduces binding of Joka2 to ATG8CL in a dose-dependent manner. GFP:ATG8CL (OD=0.2) and Joka2:RFP (OD=0.2) were transiently co-expressed with varying Agrobacterium concentrations (from OD=0 to OD=0.4) carrying HA:PexRD54 construct in <italic>N. benthamiana</italic> (OD=optical density of Agrobacterium cells). Joka2:RFP is depleted in GFP:ATG8CL pulldowns as the expression of HA:PexRD54 increased. Immunoprecipitates (IPs) obtained with anti-GFP antiserum and total protein extracts were immunoblotted with appropriate antisera. Stars indicate expected band sizes. (<bold>C</bold>) Schematic illustrations of PexRD54 variants (PexRD54<sup>J2AIM1</sup> and PexRD54<sup>J2AIM2</sup>) with Joka2 AIM peptides. (<bold>D</bold>) Replacement of PexRD54 AIM with Joka2 AIM fragments decreases ATG8CL binding affinity. Immunoblots showing binding affinity of PexRD54, PexRD54<sup>AIM2</sup>, PexRD54<sup>J2AIM1</sup> or PexRD54<sup>J2AIM2 </sup>to GFP:ATG8CL. IPs obtained with anti-GFP antiserum and total protein extracts were immunoblotted with appropriate antisera. Stars indicate expected band sizes.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.022">http://dx.doi.org/10.7554/eLife.10856.022</ext-link></p></caption><graphic xlink:href="elife-10856-fig6"></graphic><p content-type="supplemental-figure"><fig id="fig6s1" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.023</object-id><label>Figure 6—figure supplement 1.</label><caption><title>Joka2 has a functional ATG8 interacting motif (AIM).</title><p>Mutation of the predicted AIM in Joka2 (819-WDPI-822) to ADPA resulted in loss of ATG8CL binding. GFP:EV and GFP:ATG8CL were co-expressed with Joka2:RFP and Joka2<sup>AIM</sup>:RFP in <italic>N. benthamiana</italic> and proteins were extracted two days after infiltration and used in immunoprecipitation experiments (IPs). IPs were obtained with anti-GFP antiserum and total protein extracts were immunoblotted with appropriate antisera. Stars indicate expected band sizes.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.023">http://dx.doi.org/10.7554/eLife.10856.023</ext-link></p></caption><graphic xlink:href="elife-10856-fig6-figsupp1"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig6s2" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.024</object-id><label>Figure 6—figure supplement 2.</label><caption><title>Joka2 has higher binding affinity to ATG8CL than ATG8IL.</title><p>Joka2:RFP was transiently co-expressed with GFP:ATG8CL, GFP:ATG8IL or GFP:EV in <italic>N. benthamiana</italic> and proteins were extracted two days after infiltration and used in immunoprecipitation experiments (IPs). IPs obtained with anti-GFP and total protein extracts were immunoblotted with appropriate antisera. IP experiments confirmed higher binding affinity of Joka2 to ATG8CL than ATG8IL. Stars indicate expected band sizes.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.024">http://dx.doi.org/10.7554/eLife.10856.024</ext-link></p></caption><graphic xlink:href="elife-10856-fig6-figsupp2"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig6s3" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.025</object-id><label>Figure 6—figure supplement 3.</label><caption><title>Joka2 increases the number of ATG8CL labelled autophagasomes.</title><p>(<bold>A</bold>) Joka2:RFP partially colocalizes with GFP:ATG8CL. Joka2:RFP and GFP:ATG8CL were transiently co-expressed in <italic>N. benthamiana</italic> leaves and examined by confocal laser scanning microscopy 3 days post infiltration. Maximum projections of stacks of images indicate that Joka2:RFP colocalizes with GFP:ATG8CL-labelled autophagosomes. Scale bar= 50 μm (<bold>B</bold>) Zoomed single plane images of the puncta co-labelled by Joka2:RFP and GFP:ATG8CL. Scale bar= 10 μm (<bold>C</bold>) Joka2<sup>AIM</sup>:RFP and GFP:ATG8CL were transiently co-expressed in <italic>N. benthamiana</italic> leaves and examined by confocal laser scanning microscopy 3 days post infiltration. Arrowheads point to puncta co-labelled by Joka2<sup>AIM</sup>:RFP and GFP:ATG8CL. Scale bar= 50 μm (<bold>D</bold>) EV:RFP and GFP:ATG8CL were transiently co-expressed in <italic>N. benthamiana</italic> leaves and examined by confocal laser scanning microscopy 3 days post infiltration. Arrowheads point to puncta labelled by GFP:ATG8CL. Dotted squares highlight the absence of control RFP signal at the GFP:ATG8CL puncta. Scale bar= 50 μm (<bold>E</bold>) Bar charts showing colocalization of GFP:ATG8CL with Joka2:RFP, Joka2<sup>AIM</sup>:RFP or EV:RFP. Joka2<sup>AIM</sup>:RFP or EV:RFP display significantly low co-localization with GFP:ATG8CL-labelled puncta in contrast to Joka2:RFP. The data are representative of 500 individual images from two biological replicates. Each replicate consists of five independent Z stacks with 50 images each, acquired from five independent leaf areas. (*p<0.05). Error bars represent ± SD.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.025">http://dx.doi.org/10.7554/eLife.10856.025</ext-link></p></caption><graphic xlink:href="elife-10856-fig6-figsupp3"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig6s4" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.026</object-id><label>Figure 6—figure supplement 4.</label><caption><title>Joka2 increases ATG8CL protein levels.</title><p>GFP:ATG8CL was transiently co-expressed with RFP:GUS, Joka2:RFP or Joka2<sup>AIM</sup>:RFP in <italic>N. benthamiana</italic> leaves and protein levels in total extracts were determined 2 and 3 days after infiltration, using appropriate antisera. At 3 dpi GFP:ATG8CL protein levels were higher in Joka2:RFP expressing samples compared to Joka2<sup>AIM</sup>:RFP or RFP:GUS expressing samples. Blots were stained with Ponceau stain (PS) to show equal loading.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.026">http://dx.doi.org/10.7554/eLife.10856.026</ext-link></p></caption><graphic xlink:href="elife-10856-fig6-figsupp4"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig6s5" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.027</object-id><label>Figure 6—figure supplement 5.</label><caption><title>PexRD54 outcompetes Joka2 for ATG8CL binding.</title><p>Joka2:RFP and GFP:ATG8CL were transiently co-expressed with HA:EV, HA:PexRD54 and HA:PexRD54<sup>AIM2</sup> in <italic>N. benthamiana</italic> leaves and proteins were extracted two days after infiltration and used in immunoprecipitation experiments (IPs). IPs obtained with anti-GFP and total protein extracts were immunoblotted with appropriate antisera. In the presence of HA:PexRD54, Joka2:RFP was depleted from GFP:ATG8CL complexes.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.027">http://dx.doi.org/10.7554/eLife.10856.027</ext-link></p></caption><graphic xlink:href="elife-10856-fig6-figsupp5"></graphic></fig></p><p content-type="supplemental-figure"><fig id="fig6s6" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.028</object-id><label>Figure 6—figure supplement 6.</label><caption><title>PexRD54 AIM has a higher affinity to ATG8CL than Joka2 AIM.</title><p>GFP:ATG8CL and Joka2:RFP were transiently co-expressed with HA:PexRD54, HA:PexRD54<sup>AIM2</sup>, HA:PexRD54<sup>J2AIM1</sup>, HA:PexRD54 <sup>J2AIM2</sup> in <italic>N. benthamiana</italic> and proteins were extracted two days after infiltration and used in immunoprecipitation experiments (IPs). IPs obtained with anti-GFP and total protein extracts were immunoblotted with appropriate antisera. Joka2:RFP levels in GFP:ATG8CL complexes were higher in the presence of HA:PexRD54<sup>AIM2</sup>, HA:PexRD54<sup>J2AIM1</sup> and HA:PexRD54<sup>J2AIM2</sup> compared to HA:PexRD54 expressing samples suggesting PexRD54 variants carrying Joka2 AIM peptides (HA:PexRD54<sup>J2AIM1</sup>, HA:PexRD54<sup>J2AIM2</sup>) were less effective in depleting Joka2:RFP from GFP:ATG8CL complexes.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.028">http://dx.doi.org/10.7554/eLife.10856.028</ext-link></p></caption><graphic xlink:href="elife-10856-fig6-figsupp6"></graphic></fig></p></fig><fig id="media4" position="anchor"><label>Video 4.</label><caption><title>RFP:ATG8CL and Joka2:GFP colocalize at mobile endomembrane compartments.</title><p>RFP:ATG8CL was transiently coexpressed with Joka2:GFP in <italic>N. benthamiana</italic> leaves and examined by confocal laser scanning microscopy, 3 days post infiltration. (Related to <xref ref-type="fig" rid="fig6">Figure 6</xref>)</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.029">http://dx.doi.org/10.7554/eLife.10856.029</ext-link></p></caption><media xlink:href="elife-10856-media4.mp4" mimetype="video" mime-subtype="mp4"><object-id pub-id-type="doi">10.7554/eLife.10856.029</object-id></media></fig></p><p>Given that both PexRD54 and Joka2 bind ATG8CL via their respective AIMs, we hypothesized that PexRD54 interferes with the Joka2-ATG8CL complex. We tested our hypothesis by performing coimmunoprecipitation experiments between Joka2:RFP and GFP:ATG8CL in the presence or absence of PexRD54. Remarkably, ATG8CL complexes were depleted in Joka2 in the presence of PexRD54 relative to the PexRD54<sup>AIM2</sup> and vector control (<xref ref-type="fig" rid="fig6s5">Figure 6—figure supplement 5</xref>). Consistently, Joka2 binding to ATG8CL decreased with increasing PexRD54 concentrations (<xref ref-type="fig" rid="fig6">Figure 6B</xref>). The distinct AIMs of PexRD54 and Joka2 presumably determine the effect observed in these competition experiments. To further test this, we replaced the functional PexRD54 AIM with two sequences that cover the Joka2 AIM:GVAEWDPI (PexRD54<sup>J2AIM1</sup>) and GVAEWDPILEELKEMG (PexRD54<sup>J2AIM2</sup>) (<xref ref-type="fig" rid="fig6">Figure 6C</xref>). Both PexRD54<sup>J2AIM1</sup> and PexRD54<sup>J2AIM2</sup> associated with ATG8CL to a lesser extent than wild-type PexRD54 (<xref ref-type="fig" rid="fig6">Figure 6D</xref>), and were less effective than PexRD54 in depleting Joka2 out of ATG8CL complexes (<xref ref-type="fig" rid="fig6s6">Figure 6—figure supplement 6</xref>). These findings reveal that PexRD54 antagonizes Joka2 for ATG8CL binding.</p><p>Finally, we investigated the degree to which activation of Joka2-ATG8CL-mediated autophagy contributes to pathogen defense. Overexpression of Joka2, but not Joka2<sup>AIM</sup>, significantly restricted the size of the disease lesions caused by <italic>P. infestans</italic> (<xref ref-type="fig" rid="fig7">Figure 7A–B</xref>). Conversely, virus-induced gene silencing of Joka2 resulted in increased disease lesions (<xref ref-type="fig" rid="fig7s1">Figure 7—figure supplement 1</xref>). This indicates that Joka2-mediated selective autophagy contributes to defense against this pathogen. Remarkably, PexRD54 counteracted the enhanced resistance conferred by Joka2 whereas PexRD54<sup>AIM2</sup> failed to reverse this effect (<xref ref-type="fig" rid="fig7">Figure 7C–D</xref>). We conclude that PexRD54 counteracts the positive role of Joka2-mediated selective autophagy in pathogen defense.<fig id="fig7" position="float" orientation="portrait"><object-id pub-id-type="doi">10.7554/eLife.10856.030</object-id><label>Figure 7.</label><caption><title>PexRD54 counteracts the enhanced resistance conferred by Joka2.</title><p>(<bold>A</bold>) Overexpression of Joka2:RFP limits <italic>P. infestans</italic> colonization. Halves of <italic>N. benthamiana</italic> leaves expressing RFP:EV, Joka2:RFP and Joka2<sup>AIM</sup>:RFP were infected with <italic>P. infestans</italic> and pathogen growth was determined by lesion sizes measured 6 days post-inoculation. (<bold>B</bold>) Categorical scatter plots show lesion diameters of 11 infections sites from three independent biological replicates pointed out by three different colors. Similar p values (p<0.001) were obtained in three independent biological repeats. (<bold>C</bold>) PexRD54 counteracts the effect of Joka2 on <italic>P. infestans</italic> colonization. Joka2:RFP was co-expressed with HA:EV, HA:PexRD54 or HA:PexRD54<sup>AIM2</sup> in <italic>N. benthamiana</italic> leaves which are then inoculated with <italic>P. infestans</italic>. Joka2:RFP failed to limit pathogen growth in the presence of PexRD54, whereas it could still restrict pathogen growth in the presence of PexRD54<sup>AIM2</sup> or vector control (EV). (<bold>D</bold>) Categorical scatter plots show lesion diameters of 11 infections sites from three independent biological replicates pointed out by three different colors. Similar p values (p<0.001) were obtained in three independent biological repeats.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.030">http://dx.doi.org/10.7554/eLife.10856.030</ext-link></p></caption><graphic xlink:href="elife-10856-fig7"></graphic><p content-type="supplemental-figure"><fig id="fig7s1" specific-use="child-fig" orientation="portrait" position="anchor"><object-id pub-id-type="doi">10.7554/eLife.10856.031</object-id><label>Figure 7—figure supplement 1.</label><caption><title>Silencing of Joka2 enhances susceptibility to <italic>P. infestans</italic>.</title><p>(<bold>A</bold>) Cartoon showing Joka2 sites targeted for VIGs. (<bold>B</bold>) TRV:Joka2-1, TRV:Joka2-2 and TRV:GFP control plants were inoculated with <italic>P. infestans 88,069</italic> and pathogen growth was determined by lesion areas measured 5 days post-inoculation. (<bold>C</bold>) Categorical scatter plots show lesion areas of 10 infections sites from four independent biological replicates pointed out by four different colors. Similar p values (p<0.001) were obtained in four independent biological repeats. (<bold>D</bold>) RT-PCR confirmed Joka2 silencing. cDNA generated from silenced and control plants were used for the RT-PCR experiments. Transcript abundance was normalized using <italic>NbEF1α</italic>.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.031">http://dx.doi.org/10.7554/eLife.10856.031</ext-link></p></caption><graphic xlink:href="elife-10856-fig7-figsupp1"></graphic></fig></p></fig></p><p>As demonstrated in mammalian systems, eukaryotic cells employ autophagy to defend against invading pathogens (<xref rid="bib6" ref-type="bibr">Boyle and Randow, 2013</xref>; <xref rid="bib36" ref-type="bibr">Randow and Youle, 2014</xref>). In turn, pathogens can deploy effectors to avoid autophagy and enable parasitic infection (<xref rid="bib3" ref-type="bibr">Baxt et al., 2013</xref>). For instance, to counteract antimicrobial autophagy, intracellular bacterial pathogen <italic>Legionella pneumophila</italic> secretes a type IV effector protein RavZ that impedes autophagy by uncoupling ATG8-lipid linkage (<xref rid="bib12" ref-type="bibr">Choy et al., 2012</xref>). In this study, we show that a plant pathogen effector has evolved an ATG8 interacting motif to bind with high affinity to the autophagy protein ATG8CL and stimulate the formation of ATG8CL-marked autophagosomes. Unlike the Legionella effector RavZ, PexRD54 activates selective autophagy possibly to eliminate defense-related compounds or to reattribute cellular resources by promoting nutrient recycling. Our results show that, in addition to disrupting, pathogens can also activate autophagy for their own benefit (<xref ref-type="fig" rid="fig8">Figure 8</xref>).<fig id="fig8" orientation="portrait" position="float"><object-id pub-id-type="doi">10.7554/eLife.10856.032</object-id><label>Figure 8.</label><caption><title>PexRD54 outcompetes the autophagy cargo receptor Joka2 and enhances virulence.</title><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.032">http://dx.doi.org/10.7554/eLife.10856.032</ext-link></p></caption><graphic xlink:href="elife-10856-fig8"></graphic></fig></p><p>Additionally, we show that the effector competes with the host cargo receptor Joka2 and depletes it out of ATG8CL autophagosomes to promote disease susceptibility. Thus <italic>P. infestans</italic> coopts the host cell’s endomembrane compartment to promote its own growth at the cost of the cell’s physiology (<xref rid="bib7" ref-type="bibr">Bozkurt et al., 2015</xref>). Joka2 could contribute to immunity by inducing autophagic removal of plant or pathogen molecules that negatively affect host defenses. It will be interesting in the future to determine the identity of potential defense-related cargo carried by Joka2 (<xref ref-type="fig" rid="fig8">Figure 8</xref>).</p><p>The physiological roles of selective autophagy and the molecular mechanisms involved remain to be determined both in plants and animals. Characterization of additional host cargo receptors and interactome analysis of particular ATG8 proteins should improve our understanding of how selective autophagy operates in response to a variety of stress conditions including immunity. In the potato genome, we identified nine ATG8 genes. Both Joka2 and the effector showed higher affinity to ATG8CL compared to ATG8IL (<xref ref-type="fig" rid="fig2">Figure 2</xref> and <xref ref-type="fig" rid="fig6s2">Figure 6—figure supplement 2</xref>). This indicates that variation between plant ATG8 proteins may contribute to the selective nature of autophagy.</p><p>This work further highlights the intricate changes in endomembrane compartment formation that take place during plant-microbe interactions (<xref rid="bib7" ref-type="bibr">Bozkurt et al., 2015</xref>; <xref rid="bib28" ref-type="bibr">Lipka and Panstruga, 2005</xref>; <xref rid="bib23" ref-type="bibr">Kwon et al., 2008</xref>; <xref rid="bib19" ref-type="bibr">Ivanov et al., 2010</xref>; <xref rid="bib46" ref-type="bibr">Wang et al., 2010</xref>). Future studies will need to consider pathogen-directed modulation of the spatio-temporal dynamics of autophagy and subcellular trafficking during host infection. It will be interesting to determine whether other plant pathogens also secrete effectors that evolved an ATG8 interacting motif or target autophagy in other ways. These effectors would serve as valuable tools to dissect the mechanisms of defense-related selective autophagy.</p></sec><sec id="s3"><title>Materials and methods</title><sec id="s3-1"><title>Identification of candidate ATG8 interacting motifs in PexRD54</title><p><underline>A</underline>TG8 <underline>i</underline>nteracting <underline>m</underline>otif (AIM), also known as <underline>L</underline>C3 <underline>i</underline>nteracting <underline>r</underline>egion (LIR), mediates interaction of cargo receptors or adaptors with ATG8 proteins anchored in autophagosome membranes (<xref rid="bib5" ref-type="bibr">Birgisdottir et al., 2013</xref>). It follows the W/F/Y-xx-L/I/V amino acid consensus. Initially, we identified two AIM candidates in PexRD54, AIM1 and AIM2 based on the manual search of the consensus sequence mentioned earlier. Then, we confirmed these AIM candidates using the recently published iLIR software (<xref rid="bib20" ref-type="bibr">Kalvari et al., 2014</xref>). This software assigned AIM1 with an iLIR score of 12 (1.1e<sup>-1</sup>) and AIM2 with an iLIR score of 23 (3.2e<sup>-3</sup>).</p></sec><sec id="s3-2"><title>Sequence analyses and identification of ATG8CL</title><p>To determine the ATG8 variant(s) specifically targeted by PexRD54 among various host ATG8 family members, we performed a BLASTP search (<xref rid="bib1" ref-type="bibr">Altschul et al., 1990</xref>) against solanaceous plant proteomes including <italic>Solanum tuberosum</italic> (potato), <italic>Solanum lycopersicum</italic> (tomato) and <italic>Nicotiana benthamiana</italic> using <italic>Arabidopsis thaliana</italic> ATG8C as the query protein sequence. We found nine ATG8 members in <italic>S. tuberosum</italic>, seven in <italic>S. lycopersicum</italic>, and eight in <italic>N. benthamiana</italic>. To verify the gene calls and open reading frame predictions of the putative orthologs in these three species, we performed a sequence alignment of the family members in each species using the Clustal X program (v2) (<xref rid="bib25" ref-type="bibr">Larkin et al., 2007</xref>) and compared it to the published <italic>A. thaliana</italic> ATG8 sequences. We found evidence of misannotation for two <italic>S. lycopersicum</italic> sequences (Solyc10g006270 and Solyc08g078820) and three others in <italic>N. benthamiana</italic> (NbS00015425g0005, NbS00003316g0005 and NbS00003005g0010). The two <italic>S. lycopersium</italic> sequences and the NbS00003005g0010 sequence from <italic>N. benthamiana</italic> carried extra nucleotides before the likely start codon, which were corrected accordingly. A TBLASTN search against the <italic>N. benthamiana</italic> scaffolds followed by a BLASTP search of the different exons allowed curation of the two other sequences. Clustal X program was used for multiple sequence alignment of ATG8 variants. Boxshade server (<ext-link ext-link-type="uri" xlink:href="http://embnet.vital-it.ch/software/BOX_form.html">http://embnet.vital-it.ch/software/BOX_form.html</ext-link>) was used to visualize the sequence alignment.</p></sec><sec id="s3-3"><title>Phylogenetic analyses</title><p>The phylogenetic tree of ATG8 homologs in plants was constructed with the neighbor-joining method using ATG8-like curated proteins from <italic>S. tuberosum, S. lycopersium, N. benthamina</italic>, and <italic>A. thaliana</italic>. The phylogenetic tree was constructed using MEGA5 (<xref rid="bib22" ref-type="bibr">Kumar et al., 2001</xref>) with bootstrap values based on 1000 iterations. ATG8CL variants in <italic>N. benthamiana</italic> and potato have identical amino acid sequences.</p></sec><sec id="s3-4"><title>Cloning procedures and plasmid constructs</title><p>All primers used in this study are listed in <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>. PexRD54 and Joka2 were amplified using polymerase chain reaction (PCR) from genomic DNA of <italic>Phytophthora infestans</italic> isolate T30-4 and <italic>Solanum tuberosum</italic> cv. Désirée cDNA, respectively. To amplify both amplicons, we used Phusion proof reading polymerase (New England Biolabs, UK) and primer pairs listed in <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>. All amplicons were subsequently cloned into the pENTR/D-Topo Gateway entry vector (Invitrogen, UK). The ATG8CL, ATG8CLΔ, ATG8IL, and ATG8ILΔ entry clones were custom synthesized into pUC57-Amp<sup>R</sup> using the sequences matching <italic>S. tuberosum ATG8CL</italic> or <italic>ATG8IL</italic> genes flanked by attL1 and attL2 gateway sites (Genewiz, UK). The destination constructs GFP:PexRD54, RFP:PexRD54, Joka2:RFP, Joka2:GFP, RFP:ATG8CL, GFP:ATG8CL, GFP:ATG8CLΔ, GFP:ATG8ILΔ, HA:PexRD54 were generated by Gateway LR recombination reaction (Invitrogen) of the corresponding entry clone and Gateway destination vectors pH7WGR2 (N-terminal RFP fusion), pK7WGF2 (N-terminal GFP fusion), pB7FWR2 (C-terminal GFP fusion), pB7RWG2 (C-terminal RFP fusion) and pK7WGF2 (N-terminal HA fusion, generated in house by replacement of GFP with an HA tag), respectively (<xref rid="bib21" ref-type="bibr">Karimi et al., 2002</xref>). The GFP:PexRD54<sup>AIM2</sup>, RFP:PexRD54<sup>AIM1</sup>, RFP:PexRD54<sup>AIM2</sup>, RFP:PexRD54<sup>AIM1+2</sup> RFP:PexRD54<sup>KPLDFDWEIV</sup>, RFP:PexRD54<sup>J2AIM1</sup>, RFP:PexRD54<sup>J2AIM2</sup>, HA:PexRD54<sup>AIM2</sup>, HA:PexRD54<sup>AIM2</sup>, HA:PexRD54<sup>J2AIM1</sup>, HA:PexRD54<sup>J2AIM2</sup>, Joka2<sup>AIM</sup>:RFP constructs were generated as follows:PexRD54 and Joka2 mutant constructs (PexRD54<sup>AIM1</sup>, PexRD54<sup>AIM2</sup>, PexRD54<sup>AIM1+2</sup>, PexRD54<sup>KPLDFDWEIV</sup>, RFP:PexRD54<sup>J2AIM1</sup>, RFP:PexRD54<sup>J2AIM2</sup>, and Joka2<sup>AIM</sup>:RFP) were cloned into the pENTR/D-Topo Gateway entry vector (Invitrogen) by PCR amplification with the primers carrying desired mutations (<xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>) using PexRD54 and Joka2 entry clones as templates followed by TOPO cloning procedure (Invitrogen). Templates were then eliminated by one-hour <italic>Dpn</italic>-I (New England Biolabs) restriction digestion at 37°C. Next, the entry clones of PexRD54 and Joka2 mutants were recombined into destination vectors pH7WGR2 or pB7RWG2 by Gateway LR reaction (Invitrogen). pTRBO FLAG:PexRD54 construct used for coimmunoprecipitations was custom synthesized (Genscript, , New Jersey, USA).</p></sec><sec id="s3-5"><title>Generation of ATG8 interacting motif (AIM) mutants</title><p>To generate <underline>A</underline>TG8 <underline>i</underline>nteracting <underline>m</underline>otif (AIM) mutants in PexRD54 and Joka2, the conserved tryptophan and leucine residues of the canonical AIMs were both mutated to Alanine as previously done (<xref rid="bib49" ref-type="bibr">Zientara-Rytter et al., 2011</xref>). In PexRD54<sup>AIM1</sup>, PexRD54<sup>AIM2</sup> and Joka2<sup>AIM</sup>, the AIM motifs e.g. 'WLRL', 'WEIV' and 'WDPI' were mutated to 'ALRA', 'AEIA' and 'ADPA', respectively.</p></sec><sec id="s3-6"><title>Biological material</title><p><italic>Nicotiana benthamiana</italic> plants were grown and maintained throughout the experiments in a greenhouse at 22<bold>–</bold>25°C with high light intensity. <italic>Phytophthora infestans</italic> cultures were grown in plates with rye sucrose agar (RSA) media for 12–14 days as described elsewhere (<xref rid="bib41" ref-type="bibr">Song et al., 2009</xref>). Sporangia were harvested from plates using cold water and zoospores were collected 1–3 hr after incubation at 4°C. Infection assays were performed by droplet inoculations of zoospore solutions of <italic>P. infestans</italic> on 3–4-week-old detached <italic>N. benthamiana</italic> leaves as described previously (<xref rid="bib41" ref-type="bibr">Song et al., 2009</xref>; <xref rid="bib38" ref-type="bibr">Saunders et al., 2012</xref>). For all infection assays, <italic>P. infestans</italic> isolate 88,069 was used.</p></sec><sec id="s3-7"><title>Transient gene-expression assays <italic>in N. benthamiana</italic></title><p>Transient gene-expression <italic>in planta</italic> was performed by delivering T-DNA constructs with <italic>Agrobacterium tumefaciens</italic> GV3101 strain into 3–4-week-old <italic>N. benthamiana</italic> plants as described previously (<xref rid="bib9" ref-type="bibr">Bozkurt et al., 2011</xref>). For transient co-expression assays, <italic>A. tumefaciens</italic> strains carrying the plant expression constructs were mixed in a 1:1 ratio in agroinfiltration medium [10 mM MgCl<sub>2</sub>, 5 mM 2-(N-morpholine)-ethanesulfonic acid (MES), pH 5.6] to a final OD<sub>600</sub> of 0.2, unless otherwise stated.</p></sec><sec id="s3-8"><title>Coimmunoprecipitation (Co-IP) experiments and liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis</title><p>Proteins were transiently expressed by <italic>A. tumefaciens</italic>-mediated transient expression (agroinfiltration) in <italic>N. benthamiana</italic> leaves and harvested 2 or 3 days post infiltration. Co-IP experiments and preparation of peptides for liquid chromatography–tandem mass spectrometry (LC-MS/MS) was performed as described previously (<xref rid="bib9" ref-type="bibr">Bozkurt et al., 2011</xref>). Except the stringent PexRD54 immunoprecipitation assay (Stringent IP), all IPs were done using 150 mM NaCl buffer and 0.15% detergent concentration. For the stringent IP, the concentrations of salt and the detergent were increased to 250 mM and to 0.5%, respectively. LC-MS/MS analysis was performed with a LTQ Orbitrap mass spectrometer (Thermo Fisher Scientific, UK) and a nanoflow-HPLC system (nanoACQUITY; Waters Corp., UK) as described previously (<xref rid="bib35" ref-type="bibr">Petre et al., 2015</xref>). LC-MS/MS data processing and protein identification were done as described previously (<xref rid="bib35" ref-type="bibr">Petre et al., 2015</xref>).</p><p><italic>In planta</italic> association of PexRD54 and Joka2 with either ATG8CL, ATG8CLΔ or ATG8IL constructs was tested by co-IP assays as follows: constructs were transiently co-expressed in <italic>N. benthamiana</italic> leaves by agroinfiltration followed by protein extraction 2–3 days post infiltrations. Protein extraction, purification and western blot analysis steps were performed as described previously (<xref rid="bib38" ref-type="bibr">Saunders et al., 2012</xref>; <xref rid="bib9" ref-type="bibr">Bozkurt et al., 2011</xref>; <xref rid="bib33" ref-type="bibr">Oh et al., 2009</xref>). Monoclonal FLAG M2 antibody (Sigma-Aldrich, UK), polyclonal GFP/RFP antibodies (Invitrogen, UK), and polyclonal HA (Sigma-Aldrich, UK) antibody were used as primary antibodies, and anti-mouse antibody (Sigma-Aldrich, UK) and anti-rat (Sigma-Aldrich, UK) antibodies were used as secondary antibodies.</p></sec><sec id="s3-9"><title>Determination of ATG8CL protein levels</title><p>To test if PexRD54 increased protein levels of ATG8CL, GFP:ATG8CL was co-expressed with RFP:GUS, RFP:PexRD54 and RFP:PexRD54<sup>AIM2</sup> in <italic>N. benthamiana</italic> leaves. Leaf samples were collected 2 and 3 days after infiltration. Total proteins were extracted as described previously (<xref rid="bib38" ref-type="bibr">Saunders et al., 2012</xref>; <xref rid="bib33" ref-type="bibr">Oh et al., 2009</xref>) and immunoblots were performed using the appropriate antisera. The same experimental setup was also used to test whether Joka2 increases protein levels of ATG8CL. Joka2:RFP, Joka2<sup>AIM</sup>:RFP and RFP:GUS constructs were co-expressed with GFP:ATG8CL construct in <italic>N. benthamina</italic> leaves and total proteins were extracted 2 and 3 days after infiltration. Immunoblots were developed using appropriate antisera. To assay ATG8CL protein levels during infection with <italic>P. infestans, N. benthamiana</italic> leaves were first infiltrated with GFP:ATG8CL construct and infected one day later with droplets from a zoospore solution of <italic>P. infestans</italic> as described earlier (<xref rid="bib41" ref-type="bibr">Song et al., 2009</xref>). Water droplets were used as mock treatment. Protein extracts were prepared 2 and 3 days after infection and protein levels of GFP:ATG8CL were detected by immunoblots using a polyclonal GFP-HRP antibody (Santa Cruz, Texas, USA).</p></sec><sec id="s3-10"><title>PexRD54/Joka2 <italic>in planta</italic> competition assays for ATG8CL binding</title><p>Joka2:RFP was transiently co-expressed with GFP:ATG8CL in the presence of HA:PexRD54, HA:PexRD54<sup>AIM</sup>, or HA:EV constructs in <italic>N. benthamiana</italic> leaves. Total proteins extracts prepared 2 days after infiltration were then used in anti-GFP Co-IPs. Purified protein complexes were separated by SDS/PAGE and immunoblotted to detect RFP, GFP and HA signals. Similar competition experiment was conveyed with increased HA:PexRD54 <italic>A. tumefaciens</italic> concentrations (OD<sub>600</sub>=0, 0.05, 0.1, 0.2 or 0.4) while Joka2:RFP and GFP:ATG8CL <italic>A. tumefaciens</italic> concentrations were kept fixed at OD<sub>600</sub>= 0.2. Protein extracts prepared two days after infiltration were used in GFP-IPs as described above. Joka2-ATG8CL binding assays were carried out by co-expressing Joka2:RFP and GFP:ATG8CL in the presence of HA:PexRD54, HA:PexRD54<sup>AIM2</sup>, HA:PexRD54<sup>J2AIM1</sup> (PexRD54 AIM (LDFDWEIV) replaced by Joka2 AIM (GVAEWDPI)), HA:PexRD54<sup>J2AIM2</sup> (PexRD54 AIM replaced by Joka2 AIM plus 8 additional amino acids at the C-terminus (GVAEWDPILEELKEMG)) or HA:EV. GFP-IPs were performed as described above.</p></sec><sec id="s3-11"><title>Infection assays</title><p>Infection assays assessing the effect of Joka2 overexpression on <italic>P. infestans</italic> colonization were performed as follow: Joka2:RFP, Joka2<sup>AIM</sup>:RFP or RFP EV were transiently overexpressed side by side on either halves of independent <italic>N. benthamiana</italic> leaves. Twenty-four hours after expression, the infiltrated leaves were detached and inoculated with <italic>P. infestans</italic> 88,069 on two or three spots on each half leaf. <italic>P. infestans</italic> growth was monitored by UV photography 6 days after infection. Colonization was quantified by measuring the diameter of the lesion on each inoculated spot and values from three independent biological replicates were used to generate the scatter plots.</p><p>To demonstrate whether PexRD54 could alleviate the effect of Joka2 on pathogen growth, Joka2:RFP was co-expressed with HA:PexRD54, HA:PexRD54<sup>AIM2</sup> or HA:EV in <italic>N. benthamiana</italic> leaves, which were infected and monitored as described above. For all infection assays, experiments were repeated three times with minimum 10 infection spots. Lesion diameters were measured 6 days after infection.</p></sec><sec id="s3-12"><title>Joka2 silencing assays</title><p>Virus induced gene silencing of Joka2 was performed in <italic>N. benthamiana</italic> as described previously (<xref rid="bib29" ref-type="bibr">Liu et al., 2002</xref>). Two different TRV2/pYL279 constructs were designed to target both 5’-and 3’ ends of Joka2. TRV:Joka2-1 and TRV2:Joka2-2 targeted the region between 340 and 639 and between 1942 and 2241, respectively. The primers were used for generating TRV2:Joka2-1 and TRV2:Joka2-2 are listed in <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>. TRV2:GFP was used as a negative control as described previously (<xref rid="bib11" ref-type="bibr">Chaparro-Garcia et al., 2015</xref>).</p><p>Suspensions of <italic>Agrobacterium tumefaciens</italic> strain <italic>GV3101</italic> harboring TRV1/pYL155 and TRV2:Joka2-1 or TRV2:Joka2-2 were mixed in a 2:1 ratio in infiltration buffer (10 mM MES (2-[N-morpholino]ethanesulfonic acid), 10 mM magnesium chloride (MgCl<sub>2</sub>), pH 5.6) to a final OD600 of 0.3. As a control, we used TRV2:GFP. Two-week-old <italic>N. benthamiana</italic> plants were infiltrated with <italic>A. tumefaciens</italic> for VIGS assays and upper leaves were used 2–3 weeks later for <italic>P. infestans</italic> infections. UV photographs were taken 5 days post infection. Each experiment was repeated at least three times with minimum 10 infection spots and disease lesion areas were measured using ImageJ. Each lesion size value was normalized following the formula 'Nr = Or * Ar /A', where N is the normalized lesion size value, O is the original lesion size value, r is the biological repeat, Xr is the average of all O values of the biological repeat r, and A is the average of all O values. Silencing levels were confirmed using RT-PCR. Total RNA was extracted using RNAeasy Plant Mini Kit (Qiagen, UK) and treated with Ambion TURBO DNA-<italic>free</italic> according to manufacturer’s protocol. 1.0 μg of DNase treated RNA was used for cDNA synthesis using SuperScript III Reverse Transcriptase (Invitrogen). RT-PCR was performed with the following program: 1 cycle with 3 min at 95°C, followed by 35 cycles with 95°C at 30 s, 56°C at 30 s and 72°C at 30 s. Primers pairs used for cDNA amplification were Joka2-TRV1-F and Joka2-TRV1-R, and Joka2-TRV2-R and Joka2-TRV2-F (described in <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>). <italic>NbEF1α</italic> was used to normalize transcript abundance (<xref rid="bib39" ref-type="bibr">Segonzac et al., 2011</xref>).</p></sec><sec id="s3-13"><title>Live-cell imaging by confocal laser scanning microscopy</title><p>All microscopy analyses were performed on live leaf tissue 3 days post agroinfiltration. <italic>N. benthamiana</italic> leaf patches were cut and mounted in water and analyzed on a Leica TCS SP5 confocal microscope (Leica Microsystems, Germany) using 63x water immersion objective. The GFP and RFP probes were excited using 488 and 561 nm laser diodes and their fluorescent emissions were collected at 495–550 nm and 570–620 nm, respectively. To avoid bleed-through from different fluorophores, co-localization images were taken using sequential scanning between lines and acquired using multi-channels.</p></sec><sec id="s3-14"><title>Image processing and data analysis</title><p>Confocal microscopy images were processed with the Leica LAS AF software, ImageJ (2.0) and Adobe PHOTOSHOP CS5 (12.0) programs. Images for quantification of autophagosome numbers were obtained from 50 Z stacks consisting of 1 μm depth field multi-layered images with similar settings for all samples. To detect and quantify punctate structures in one channel (green channel or red channel or overlay channel (green channel images superimposed with red channel ones)), the Z stacks were separated into individual images with the ImageJ (2.0) program and analyzed. The counting procedure was based on a naked-eye detection of punctate structures to avoid cytoplasm noise and dual counting of autophagosomes within the same stack. Histograms were generated with mean of punctate numbers generated from stacks obtained in two independent biological experiments. Statistical differences were assessed by means of a two-tailed t-test assuming unequal variance as implemented in StatPlus LE package (AnalystSoft, Washington, USA). Measurements were significant when p<0.05 and highly significant when p<0.001.</p></sec><sec id="s3-15"><title>Electron microscopy and immunogold labelling</title><p>Leaf samples were embedded in LR White as described (<xref rid="bib29" ref-type="bibr">Liu et al., 2002</xref>) except sections were picked up on gold grids before immunogold labeling. All labeling procedures were carried out at room temperature. Grids were floated, section-side down, on drops of 50 mM glycine/PBS (150 mM NaCl, 10 mM phosphate, pH 7.4) for 15 min then on Aurion blocking buffer (5% BSA/0.1% cold water fish gelatin/5–10% normal goat serum/15 mM NaN<sub>3</sub>/PBS, pH7.4) (Aurion, the Netherlands) for 30 min then briefly equilibrated in incubation buffer (0.1% (v/v) BSA-C (actetylated BSA; Aurion) /PBS, pH 7.3) before a 90 min’ incubation with the primary antibody. Serial sections on separate grids were labelled with either a rabbit polyclonal anti-GFP Abcam ab6556 (Abcam, UK) at 1/250, or a rabbit polyclonal anti-catalase AS09 501 (Newmarket Scientific, UK) at 1/1000. Grids were washed 6x5 min in drops of incubation buffer then placed on the drops of goat anti-rabbit secondary antibody conjugated to 10 nm gold (BioCell, Agar Scientific Ltd., Essex, UK), diluted to 1/50 in incubation buffer, for 90 min. After 6x5 min washes in incubation buffer and 2x5 min washes in PBS, the grids were briefly washed in water and contrast stained with 2% (w/v) uranyl acetate. Grids were viewed in a FEI Tecnai 20 transmission electron microscope (FEI, the Netherlands) at 200 kV and digital TIFF images were taken using an AMT XR60B digital camera (Deben, UK) to record TIFF files. Bar charts were generated by counting the clustered (>4 gold particles close to each other) gold particles on each image.</p></sec><sec id="s3-16"><title>Chemical treatments</title><p>3-Methyl adenine (3-MA), a phosphatidylinositol 3-kinase (PI3K) inhibitor is widely used to inhibit autophagosome formation (<xref rid="bib16" ref-type="bibr">Hanamata et al., 2013</xref>). <italic>N. benthamiana</italic> leaves transiently expressing GFP:ATG8CL-RFP:PexRD54, GFP:PexRD54-RFP:ATG8CL or YFP:VTI12 were infiltrated with 5 mM 3-MA. Both GFP:PexRD54 and RFP:ATG8CL constructs were expressed side by side to monitor the effect of 3-MA treatment on stimulation of autophagosome formation by PexRD54. Punctate structures were visualized using confocal microscopy 6–10 hr after 3-MA treatment. Bar charts were generated with the number of punctate structures obtained from maximum projections of Z-stack images of two independent biological experiments.</p><p>The cysteine protease inhibitor E64d is widely used for measuring autophagic flux (<xref rid="bib2" ref-type="bibr">Bassham, 2015</xref>). To determine whether PexRD54 blocked autophagic flux, at 2 dpi we infiltrated leaves with 100 μM E64D and kept them overnight in the dark. At 3 dpi, we collected E64d treated and untreated samples and analyzed total protein levels using appropriate antisera. Concanamycin A (2 μM in agro infiltration medium) was infiltrated into leaves of <italic>N. benthamiana</italic> transiently expressing ATG8CL and PexRD54, PexRD54<sup>AIM2</sup> or empty vector control constructs. The leaves were than incubated in dark at 20°C for 24 hr. ATG8CL-labelled puncta were visualized using confocal microscopy 24 hr after concanamycin A treatment.</p></sec><sec id="s3-17"><title>Cloning, expression and purification of PexRD54 and PexRD54<sup>AIM2</sup> variants for in vitro studies</title><p>DNA encoding PexRD54 residues Val92 to Val381 (lacking secretion and translocation signals) was amplified from RFP:PexRD54 (using primers shown in <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>) and cloned into the vector pOPINS3C, resulting in an N-terminal 6xHis-SUMO tag with PexRD54, linked by a 3C cleavage site (<xref rid="bib4" ref-type="bibr">Berrow et al., 2007</xref>). Recombinant protein was produced using <italic>E. coli</italic> BL21-Arabinose Inducible (AI) cells. Cell cultures were grown in Power Broth at 37°C to an <italic>A</italic><sub>650</sub> 0.4–0.6 followed by induction with 0.2% (w/v) L-arabinose and overnight incubation at 18°C. Pelleted cells were resuspended in buffer A (50 mM Tris-HCl pH 8, 500 mM NaCl, 50 mM glycine, 5% (v/v) glycerol and 20 mM imidazole supplemented with EDTA free protease inhibitor tablets (one tablet per 40 ml buffer)) and lysed by sonication. The clarified cell lysate was applied to a Ni<sup>2+</sup>-NTA column connected to an AKTA Xpress system. 6xHis-SUMO-PexRD54 was step-eluted with elution buffer (buffer A containing 500 mM imidazole) and directly injected onto a Superdex 75 26/600 gel filtration column pre-equilibrated in buffer C (20 mM HEPES pH 7.5, 150 mM NaCl). The fractions containing 6xHis-SUMO-PexRD54 were pooled and concentrated to 2–3 mg/mL. The 6xHis-SUMO tag was cleaved by addition of 3C protease (10 µg/mg fusion protein) and incubated at 4°C overnight. Cleaved PexRD54 was further purified using Ni<sup>2+</sup>-NTA column (collecting eluate) followed by gel filtration. The purified protein was concentrated as appropriate, and the final concentration was judged by absorbance at 280 nm (using a calculated molar extinction coefficient of PexRD54, 57,040 M<sup>-1</sup>cm<sup>-1</sup>).</p><p>The PexRD54<sup>AIM2</sup> variant was amplified from RFP:RD54<sup>AIM2</sup> (using primers shown in <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>) and cloned into the vector pOPINS3C as above. Recombinant protein was expressed and purified as for wild-type PexRD54; with protein concentration measured using a calculated molar extinction coefficient of 51,350 M<sup>-1</sup>cm<sup>-1</sup>.</p></sec><sec id="s3-18"><title>Cloning, expression and purification of ATG8CL and ATG8IL</title><p>DNA encoding Met1 to Ser119 of ATG8CL and Gly2 to Ser119 of ATG8IL were amplified from GFP:ATG8CL and GFP:ATG8IL (using primers shown in <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>) and cloned into the vector pOPINF, generating a cleavable N-terminal 6xHis-tag with ATG8CL and ATG8IL. Recombinant proteins were produced using <italic>E. coli</italic> strain BL21 (DE3) grown in lysogeny broth at 37°C to an <italic>A</italic><sub>600</sub> of 0.4–0.6 followed by induction with 1 mM IPTG and overnight incubation at 18°C. Pelleted cells were resuspended in buffer A and pure, concentrated protein prepared as described for PexRD54 above (concentration determined using a calculated molar extinction coefficient of 7680 M<sup>-1</sup>cm<sup>-1</sup> and 9080 M<sup>-1</sup>cm<sup>-1</sup> for ATG8CL and ATG8IL, respectively).</p></sec><sec id="s3-19"><title>Isothermal titration calorimetry (ITC)</title><p>Calorimetry experiments were carried out at 15°C in 20 mM HEPES pH 7.5, 500 mM NaCl, using an iTC200 instrument (MicroCal Inc.). For protein:protein interactions, the calorimetric cell was filled with 100 μM PexRD54 and titrated with 1.1 mM ATG8CL or ATG8IL from the syringe. A single injection of 0.5 μl of ATG8CL or ATG8IL was followed by 19 injections of 2 μl each. Injections were made at 150 s intervals with a stirring speed of 750 rpm. For the heats of dilution control experiments, equivalent volumes of ATG8CL or ATG8IL were injected into buffer using the parameters above. For protein:peptide interactions, the calorimetric cell was filled with 90 μM ATG8CL or ATG8IL and titrated with 1 mM peptide from the syringe. The titrations were performed at 25°C, but otherwise as above. The raw titration data were integrated and fitted to a one-site binding model using the MicroCal Origin software.</p></sec><sec id="s3-20"><title>Accession numbers</title><p>PexRD54 (PITG_09316); <italic>St</italic>ATG8CL (PGSC0003DMP400038670), <italic>St</italic>ATG8IL (PGSC0003DMP400009229), <italic>Sl</italic>ATG8CL (Solyc10g006270 and Solyc07g064680), <italic>Sl</italic>ATG8IL (Solyc01g068060), <italic>Nb</italic>ATG8CL (Nb_S00003316g0005, KR021366), <italic>Nb</italic>ATG8IL (Nb_S00005942g0011, KR021365), and Joka2 (XM_006344410).</p></sec></sec></body><back><sec sec-type="funding-information"><title>Funding Information</title><p>This paper was supported by the following grants:</p><list list-type="bullet"><list-item><p><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100000781</institution-id><institution>European Research Council</institution></institution-wrap></funding-source> to Abbas Maqbool, Benjamin Petre, Joe Win, Sophien Kamoun.</p></list-item><list-item><p><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100000324</institution-id><institution>Gatsby Charitable Foundation</institution></institution-wrap></funding-source> to Yasin F Dagdas, Khaoula Belhaj, Neftaly Cruz-Mireles, Jan Sklenar, Joe Win, Frank Menke, Sophien Kamoun.</p></list-item><list-item><p><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100000268</institution-id><institution>Biotechnology and Biological Sciences Research Council</institution></institution-wrap></funding-source> to Pooja Pandey, Nadra Tabassum, Tolga O Bozkurt.</p></list-item></list></sec><ack id="ack"><title>Acknowledgements</title><p>We thank Elaine Barclay, Liliana M. Cano, Frédéric Fragnière, Marina Franceschetti, Artemis Giannakopoulou, Ricardo Oliva, Egem Ozbudak, Stephen Whisson for technical support and/or providing materials. We are grateful to Zlay Taftacs and all members of the Kamoun Lab for helpful suggestions. This project was funded by the Gatsby Charitable Foundation, European Research Council (ERC), Biotechnology Biological Sciences Research Council (BBSRC) and the John Innes Foundation.</p></ack><sec id="s4" sec-type="additional-information"><title>Additional information</title><fn-group content-type="competing-interest"><title><bold>Competing interests</bold></title><fn fn-type="COI-statement" id="conf1"><p>The authors declare that no competing interests exist.</p></fn></fn-group><fn-group content-type="author-contribution"><title><bold>Author contributions</bold></title><fn fn-type="con" id="con1"><p>YFD, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con2"><p>KB, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con3"><p>AM, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con4"><p>AC-G, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con5"><p>PP, Conception and design, Acquisition of data, Analysis and interpretation of data.</p></fn><fn fn-type="con" id="con6"><p>BP, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con7"><p>NT, Conception and design, Acquisition of data, Analysis and interpretation of data.</p></fn><fn fn-type="con" id="con8"><p>NC-M, Conception and design, Acquisition of data, Analysis and interpretation of data.</p></fn><fn fn-type="con" id="con9"><p>RKH, Conception and design, Acquisition of data, Analysis and interpretation of data.</p></fn><fn fn-type="con" id="con10"><p>JS, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con11"><p>JW, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con12"><p>FM, Conception and design, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con13"><p>KF, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con14"><p>MJB, Conception and design, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con15"><p>SK, Conception and design, Analysis and interpretation of data, Drafting or revising the article.</p></fn><fn fn-type="con" id="con16"><p>TOB, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.</p></fn></fn-group></sec><sec id="s5" sec-type="supplementary-material"><title>Additional files</title><supplementary-material content-type="local-data" id="SD1-data"><object-id pub-id-type="doi">10.7554/eLife.10856.033</object-id><label>Supplementary file 1.</label><caption><title>Plant proteins that associate with PexRD54 as identified by mass spectrometry after immunoprecipitation (IP).</title><p>FLAG:PexRD54 was transiently expressed in <italic>N. benthamiana</italic> leaves and proteins were extracted two days after infiltration and used in IP experiments. Unique spectral counts are given for each control and PexRD54 sample. Proteins related to vesicle trafficking and autophagy are highlighted in yellow. ATG8CL is highlighted in blue and found in several replicates including the stringent IP experiment.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.033">http://dx.doi.org/10.7554/eLife.10856.033</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-10856-supp1.xlsx" orientation="portrait" id="d35e2674" position="anchor"></media></supplementary-material><supplementary-material content-type="local-data" id="SD2-data"><object-id pub-id-type="doi">10.7554/eLife.10856.034</object-id><label>Supplementary file 2.</label><caption><title>Unique peptides obtained from liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of PexRD54 immunoprecipitation experiments suggest specific association with ATG8CL.</title><p>Although ATG8 protein family is highly conserved, and there are eight ATG8 variants in <italic>N. benthamiana,</italic> unique peptides obtained from LC-MS/MS analysis enabled specific identification of ATG8CL variant (Nb_S00003316g0005) from <italic>N. benthamiana</italic>. ATG8CL variant of <italic>N. benthamiana</italic> has identical amino acid sequence with the potato ATG8CL variant that is used for other experiments.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.034">http://dx.doi.org/10.7554/eLife.10856.034</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-10856-supp2.xlsx" orientation="portrait" id="d35e2700" position="anchor"></media></supplementary-material><supplementary-material content-type="local-data" id="SD3-data"><object-id pub-id-type="doi">10.7554/eLife.10856.035</object-id><label>Supplementary file 3.</label><caption><title>Primers used in this study.</title><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.10856.035">http://dx.doi.org/10.7554/eLife.10856.035</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-10856-supp3.xlsx" orientation="portrait" id="d35e2715" position="anchor"></media></supplementary-material><sec id="s6" sec-type="datasets"><title>Major datasets</title><p>The following datasets were generated:</p><p><related-object content-type="generated-dataset" id="data-ro1" source-id="http://www.ncbi.nlm.nih.gov/nuccore/XM_002903553.1" source-id-type="uri"><collab>Nusbaum C</collab><x xml:space="preserve">,</x><collab>Haas B</collab><x xml:space="preserve">,</x><collab>Kamoun S</collab><x xml:space="preserve">,</x><collab>Fry W</collab><x xml:space="preserve">,</x><collab>Judelson H</collab><x xml:space="preserve">,</x><collab>Ristaino J</collab><x xml:space="preserve">,</x><collab>Govers F</collab><x xml:space="preserve">,</x><collab>Whis- son S</collab><x xml:space="preserve">,</x><collab>Birch P</collab><x xml:space="preserve">,</x><collab>Birren B</collab><x xml:space="preserve">,</x><collab>Lander E</collab><x xml:space="preserve">,</x><collab>Gala- gan J</collab><x xml:space="preserve">,</x><collab>Zody M</collab><x xml:space="preserve">,</x><collab>De- von K</collab><x xml:space="preserve">,</x><collab>O’Neil K</collab><x xml:space="preserve">,</x><collab>Zembek L</collab><x xml:space="preserve">,</x><collab>Ander- son S</collab><x xml:space="preserve">,</x><collab>Jaffe D</collab><x xml:space="preserve">,</x><collab>But- ler J</collab><x xml:space="preserve">,</x><collab>Alvarez P</collab><x xml:space="preserve">,</x><collab>Gnerre S</collab><x xml:space="preserve">,</x><collab>Grabherr M</collab><x xml:space="preserve">,</x><collab>Mauceli E</collab><x xml:space="preserve">,</x><collab>Brockman W</collab><x xml:space="preserve">,</x><collab>Young S</collab><x xml:space="preserve">,</x><collab>LaButti K</collab><x xml:space="preserve">,</x><collab>Sykes S</collab><x xml:space="preserve">,</x><collab>DeCaprio D</collab><x xml:space="preserve">,</x><collab>Craw- ford M</collab><x xml:space="preserve">,</x><collab>Koehrsen M</collab><x xml:space="preserve">,</x><collab>Engels R</collab><x 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A lightly edited version of the letter sent to the authors after peer review is shown, indicating the most substantive concerns; minor comments are not usually included.</p></boxed-text><p>Thank you for submitting your work entitled "An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor" for consideration by <italic>eLife</italic>. Your article has been reviewed by three peer reviewers, and the evaluation has been overseen by Jean Greenberg (Reviewing Editor) and Detlef Weigel (Senior Editor).</p><p>The reviewers have discussed the reviews with one another and the Reviewing Editor has drafted this decision to help you focus on the additional work we consider essential for a favorable decision on this submission.</p><p>Summary:</p><p>This manuscript presents exciting data suggesting that the <italic>P. infestans</italic> effector PexRD54 targets the autophagy system and may affect autophagy through a competition mechanism. We appreciate the rigor of the work presented and its clarity of exposition. However, we think there are important issues that require additional work, which is explained below.</p><p>Essential revisions:</p><p>1) The quality of the TEM experiment:</p><p>The TEM data in the manuscript show somewhat different localization compared to the confocal images. For example, the confocal image shows GFP-tagged PexRD54 mainly localized in some foci and the cytosol (<xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1</xref>), but the TEM image (<xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2</xref>, please correct the figure legend, which explains A and B but not panel C) does not show any particles in the cytosol. Moreover the vesicles in which particles accumulate do not have the appearance of autophagosomes (they seem more like an aggresome due to overexpression) and this cannot explain the ring-like structure of PexRD54 (<xref ref-type="fig" rid="fig4">Figure 4</xref>). There should be a good control photo showing an autophagosome, probably marked with ATG8CL. We suggest observing the sample expressing both constructs of PexRD54 and ATG8CL for TEM to see both at the autophagosome. Since the autophagosomes induced by PexRD54 have altered morphology (compare <xref ref-type="fig" rid="fig4">Figure 4</xref> to <xref ref-type="fig" rid="fig6s3">Figure 6—figure supplement 3</xref>), please address the morphology difference in the manuscript. Differences in morphology could also affect quantification. Are the differences the same when overlap is quantified in a 50x50 micron area compared to all puncta found in the area? The TEM data is very important and should be in the main figure. Instead, <xref ref-type="fig" rid="fig2">Figure 2</xref> can be in the supplement.</p><p>2) Biological relevance:</p><p>A weakness of the work is a lack of information about the relevance of autophagy for this pathosystem and the relevance of PexRD54 for virulence. We think these issues can be addressed by: (<xref rid="bib1" ref-type="bibr">1</xref>) silencing PexRD54 to address its role in virulence and its effect on autophagy during infection; and/or (<xref rid="bib2" ref-type="bibr">2</xref>) performing an experiment to test the importance of autophagy for this pathosystem.</p><p>Additional critique:</p><p>You should address the following comments:</p><p>3) <xref ref-type="fig" rid="fig3s4">Figure 3—figure supplement 4</xref> shows expression of GFP-ATG8CL, with only about 50 puncta/10,000 µm^2, while <xref ref-type="fig" rid="fig4">Figure 4A</xref> counts about 10 puncta/10,000 µm^2 (with EV control). Please explain the discrepancy. It is important to address this as you claim that PexRD54 enhances autophagy activity based on the ATG8CL counts (about 40 puncta/10,000 µm^2 in <xref ref-type="fig" rid="fig4">Figure 4</xref>).</p><p>4) Can you assay for autophagy flux biochemically to bolster your conclusion thatPexRD54 is affecting autophagy flux?</p><p>5) <xref ref-type="fig" rid="fig2">Figure 2</xref> – it seems that AVRBlb2 interacts weakly with ATG8IL. Does it have an AIM domain or is ATG8IL a bit sticky? Can you please quantify binding in the protein blot?</p><p>6) All experiments are performed using transient overexpression in <italic>Nicotiana</italic>. Please comment on the caveats with this approach and consider doing some validation using native promoters to validate findings in a more biologically relevant context.</p><p>7) Since PexRD54 can stimulate the formation of ATG8CL-marked autophagosomes, you suggest that PexRD54 can activate autophagy for the pathogen's own benefit (Pro-death?). You conclude at the same time that PexRD54 counteracts the positive role of Joka2-mediated selective autophagy in pathogen defense (Pro-survival?). Is it either or both? Please clarify.</p><p>[Editors' note: further revisions were requested prior to acceptance, as described below.]</p><p>Thank you for resubmitting your work entitled "An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor" for further consideration at <italic>eLife</italic>. Your revised article has been favorably evaluated by Detlef Weigel (Senior editor), a Reviewing editor, and four reviewers. The manuscript has been improved, but there are some minor remaining issues that need to be addressed before acceptance, as outlined below:</p><p>The work is substantially improved. An EM expert has suggested a number of improvements that we would like you to implement (none of which require additional experimentation):</p><p>1) About <xref ref-type="fig" rid="fig3s3">Figure 3—figure supplement 3</xref>:</p><p>The upper and lower photos seem to have different magnification. Please add size bars in the upper images.</p><p>Legends: "Vesicles labelled with GFP antibody were different than the vesicles labelled with catalase antibody, confirming that PexRD54 labelled vesicles are not peroxisomes." Please do not use the term "vesicles" here, since it is not sure that they are not vesicles. Instead, the description can be considered as: high electron dense regions (structures)</p><p>Also the statement: "Stars indicate vesicular structures that are labelled by gold particles in the other image" is improper. The stars in two images obviously indicate different structures- the upper image indicates electron-dense structure and the lower image indicates peroxisomes (organelle). It is better to use different labels.</p><p>For anti-GFP, the upper image indicates that gold particles were labeled in the electron-dense portion, which was neither associated with vesicle-like structures nor peroxisomes.</p><p>2) About <xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2</xref>:</p><p>Based on the total set of supplemental EM images which authors provided, <xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2A</xref> seems not to be a typical image. Since most of images do not have vesicle like structures, the photo of number 11 seems to represent the total set of images.</p><p>3) Methods – Electron Microscopy and Immunogold labelling:</p><p>Since authors used high pressure freezing to get immunogold labelling, the authors need to describe the process in the Methods. I think authors may have cited the wrong reference (Liu, Schiff and Dinesh-Kumar et al., 2002), please check it.</p><p>In your revision, please include your archive of EM images as supplemental material so that readers can see the whole range of data.</p><p>Major reviewer comments were:</p><p>Reviewer #1:</p><p>I think the authors improved the manuscript. The effector biology has a limited way of doing experiments but this manuscript dealt with it with a lot of controls, thus convincing.</p><p>Reviewer #2:</p><p>The revised manuscript of Dagdas and colleagues report the novel finding that an oomycete effector (PexRD54) binds to a plant host autophagy protein (ATG8CL) to trigger autophagosome production. As a result plant defense are circumvented. The original manuscript was extensively reviewed and in general, this exciting paper was well received. However, there were two major points of concern:</p><p>1) TEM-image quality</p><p>2) Biological Relevance</p><p>My main concern was point #2; biological relevance. In my view, while this is an excellent study with numerous nuggets that will be of interest to the <italic>eLife</italic> community. This work would be significantly compromised without some discussion, experimentation to indicate that autophagy is relevant to this pathosystem.</p><p>Briefly, to demonstrate the importance of autophagy in this system the cargo receptor Joka2 was silenced and oomycete colonization, measured using two distinct constructs; thus strengthening the argument outlined in <xref ref-type="fig" rid="fig7">Figure 7</xref> and <xref ref-type="fig" rid="fig7s1">Figure 7—figure supplement 1</xref>; conclusions indicating the importance of selective autophagy in this pathosystem.</p><p>The authors also discuss the very real technical difficulties in this system and the relatively high levels of variation that complicate interpretation of these studies/this system has a high degree of difficulty in and of itself.</p><p>In summary, by performing silencing experiments and demonstrating, the importance of autophagy regulation in this system, it is my view that the authors have adequately met the reviewers’ concerns regarding biological relevance.</p><p>Reviewer #3:</p><p>In this revision, the authors have addressed some of the previous concerns about the manuscript. My primary concern previously was about biological relevance due to experiments using overexpression in <italic>Nicotiana</italic>. To address biological relevance, Joka2 was silenced using VIGS in <italic>Nicotiana</italic> and demonstrated enhanced susceptibility to <italic>P. infestans</italic>. These results are consistent with the observation that overexpression of Joka2 enhances resistance. The authors provide a detailed rebuttal to why they have not performed silencing in <italic>P. infestans</italic>. While I would like to see the field move away from primarily relying on overexpression to deduce phenotypes, this manuscript does present significant insight into the role of effector-modification of autophagy and is worthy of publication.</p><p>Reviewer #4:</p><p>In this revised version, in response to the reviewers’ suggestions, the authors have done TEM on serial sections and confirmed that anti-catalase conjugated gold particles did not co-localize with GFP coated gold particles, indicating that cells expressing GFP:PexRD54 revealed a strong signal in certain portions that are not peroxisomes.</p><p>The movies are a good evidence to confirm that the mobile structures are vesicles.</p></body></sub-article><sub-article id="SA2" article-type="reply"><front-stub><article-id pub-id-type="doi">10.7554/eLife.10856.057</article-id><title-group><article-title>Author response</article-title></title-group></front-stub><body><p>Essential revisions:</p><p>1) The quality of the TEM experiment:</p><p>The TEM data in the manuscript show somewhat different localization compared to the confocal images. For example, the confocal image shows GFP-tagged PexRD54 mainly localized in some foci and the cytosol (<xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1</xref>), but the TEM image (<xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2</xref>, please correct the figure legend, which explains A and B but not panel C) does not show any particles in the cytosol. Moreover the vesicles in which particles accumulate do not have the appearance of autophagosomes (they seem more like an aggresome due to overexpression) and this cannot explain the ring-like structure of PexRD54 (<xref ref-type="fig" rid="fig4">Figure 4</xref>). There should be a good control photo showing an autophagosome, probably marked with ATG8CL. We suggest observing the sample expressing both constructs of PexRD54 and ATG8CL for TEM to see both at the autophagosome. Since the autophagosomes induced by PexRD54 have altered morphology (compare <xref ref-type="fig" rid="fig4">Figure 4</xref> to <xref ref-type="fig" rid="fig6s3">Figure 6—figure supplement 3</xref>), please address the morphology difference in the manuscript. Differences in morphology could also affect quantification. Are the differences the same when overlap is quantified in a 50x50 micron area compared to all puncta found in the area? The TEM data is very important and should be in the main figure. Instead, <xref ref-type="fig" rid="fig2">Figure 2</xref> can be in the supplement.</p><p>We agree that the provided image is not conclusive on its own regarding the autophagosome localization of the effector. Because of that we were very careful not to use the term autophagosome to define the observed localization pattern. This is what we said in the manuscript: “Immunogold labeling in transmission electron micrographs of cells expressing GFP:PexRD54 revealed a strong signal in vesicular compartments”. Our most conclusive experiments with regards to autophagosome localization of PexRD54 are (i) autophagy inhibitor 3-methyl adenine, (ii) confocal live cell imaging, (iii) ATG8 terminal glycine dominant negative mutant. We are also confident that PexRD54 labeled endomembrane compartments are not aggresomes, because unlike the protein aggregates they are mobile (<xref ref-type="other" rid="media1">Video 1</xref>). We have changed the electron micrograph image that we used in the figure. We believe the current image delivers our message clearly. Additionally we are providing a selection of images as a supplementary data set. These images were used to create the bar chart in <xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2</xref> B and they clearly demonstrate accumulation of PexRD54 at vesicles.</p><p>As the reviewers suggested we have done TEM on serial sections of GFP-PexRD54 expressing cells to see if the vesicles we observed are peroxisomes. As you can clearly see in <xref ref-type="fig" rid="fig3s3">Figure 3—figure supplement 3</xref>, anti- catalase conjugated gold particles did not co-localize with GFP coated gold particles. We can now conclude that GFP-PexRD54 accumulates in vesicles that are not peroxisomes.</p><p>We have tried to do serial sectioning TEM using gold conjugated ATG8 antibodies. We used two different ATG8 antibodies: (i) AS14 2769 from Agrisera raised for <italic>Chlamydomanas</italic> ATG8; (ii) ab77003 from abcam raised for yeast ATG8 protein. These antibodies were suggested to us by members of the plant autophagy community. Unfortunately none of these antibodies were specific in TEM trials and we could not proceed further with these experiments. Nonetheless as we stated above, we believe we have several lines of evidence confirming that PexRD54 localize at ATG8CL labeled autophagosomes.</p><p>It was noted that the PexRD54 labeled vesicles are not surrounded by double membranes. Please note that membranes cannot be visualized in the TEM experiments we conducted because we have used high pressure freezing to get better immunogold labelling.</p><p>2) Biological relevance:</p><p>A weakness of the work is a lack of information about the relevance of autophagy for this pathosystem and the relevance of PexRD54 for virulence. We think these issues can be addressed by: (<xref rid="bib1" ref-type="bibr">1</xref>) silencing PexRD54 to address its role in virulence and its effect on autophagy during infection; and/or (<xref rid="bib2" ref-type="bibr">2</xref>) performing an experiment to test the importance of autophagy for this pathosystem.</p><p>To further demonstrate that autophagy is important for this pathosystem, we complemented the original experiments with silencing the autophagy cargo receptor, Joka2 and measured <italic>P. infestans</italic> colonization in silenced plants. Using two different silencing constructs we have shown that silencing of Joka2 enhances susceptibility to <italic>P. infestans</italic>. These results are now presented in <xref ref-type="fig" rid="fig7s1">Figure 7—figure supplement 1</xref>. Our silencing results are consistent with Joka2 overexpression phenotype presented in <xref ref-type="fig" rid="fig7">Figure 7</xref>, where we see enhanced resistance in Joka2 overexpressing leaves. These experiments clearly demonstrate the relevance of selective autophagy in the <italic>P. infestans</italic> pathosystem. Furthermore this is the first report demonstrating that selective autophagy and the cargo receptor Joka2 play a positive role in antimicrobial immunity in plants.</p><p>The reliance on in planta expression is a recurring issue in effector biology. Nonetheless, much progress has still been made in this field even with obligate pathogens where there is no chance of having knock-outs or knock-downs. Unfortunately, our <italic>P. infestans</italic> system is simply not reliable enough for gene silencing as detailed below. This is counteracted by using mutants of the effector that can genetically link various phenotypes, such as binding to a host interactor, effect on virulence, etc.</p><p>There are technical difficulties of gene silencing in <italic>P. infestans</italic>, which is also much harder to transform than a couple other <italic>Phytophthora</italic> spp. An important issue with <italic>P. infestans</italic> transformation is phenotypic variation between transformants, which confounds interpretation of the results. Transformants of the same construct are variable in virulence, growth and habit, and also are typically unstable. Even empty vector control transformants can show defects in virulence. Considering the expected quantitative phenotypes, this variation may mask the potential phenotype of PexRD54 silencing. Also, only a few labs managed to stably silence genes in <italic>P. infestans</italic> and results are typically not readily reproducible, even within individual labs. Recently, a new issue popped up because the changes in heterochromatin that are associated with gene silencing appear to affect other (linked or unlinked) genes. Yet, another argument against the robustness of the method. Although we are trying to improve our methods to manipulate <italic>P. infestans</italic> (CRISPR etc), so far we did not manage to get a reproducible knock-out/knock-down system.</p><p>To overcome this, we used the effector mutant “AIM2” as a control in every experiment. Although AIM2 mutant is only 2 amino acids different from PexRD54 and is equally stable, it lost its ability to bind its host target ATG8, failed to stimulate autophagy, and failed to subvert autophagy related defenses. We believe the AIM2 mutant ensures that the observed phenotypes are not artifacts of the transient expression system. This mutant was used as a negative control in ALL functional assays and provided a genetic link between multiple experimental readouts. We feel using effector mutants is a critical check in effector biology to ensure the validity of the interactors and other readouts.</p><p>Note also that in most systems (even with <italic>Pseudomonas syringae</italic> and animal pathogens, see for example Galán J. Cell Host Microbe.5, 571, 2009), knock outs of effector genes typically do not reveal phenotype probably due to redundancy. Thus PexRD54 silencing is unlikely to yield mechanistic insights on manipulation of autophagy by <italic>P. infestans</italic>.</p><p>Additional critique:</p><p>You should address the following comments:</p><p>3) <xref ref-type="fig" rid="fig3s4">Figure 3—figure supplement 4</xref> shows expression of GFP-ATG8CL, with only about 50 puncta/10,000 µm^2, while <xref ref-type="fig" rid="fig4">Figure 4A</xref> counts about 10 puncta/10,000 µm^2 (with EV control). Please explain the discrepancy. It is important to address this as you claim that PexRD54 enhances autophagy activity based on the ATG8CL counts (about 40 puncta/10,000 µm^2 in <xref ref-type="fig" rid="fig4">Figure 4</xref>).</p><p>We thank the reviewers for raising this point and we are sorry for the confusion. As we wrote in the Materials and methods part (Chemical treatments), in the 3-MA treatment we boosted the number of autophagosomes by coexpressing GFP:PexRD54 and GFP:ATG8CL with RFP:ATG8CL and RFP:PexRD54, respectively, to make sure that the phenotype we are observing with the inhibitor treatment is more clear. We have now modified the figure and figure legend to make this clear.</p><p>4) Can you assay for autophagy flux biochemically to bolster your conclusion thatPexRD54 is affecting autophagy flux?</p><p>Actually we did not conclude that PexRD54 affects autophagic flux:</p><p>“Next we set out to determine the effect of PexRD54 on autophagic flux. […] PexRD54 did not alter the accumulation of GFP:ATG8IL or control GFP protein, confirming that PexRD54 increases ATG8CL protein accumulation specifically (<xref ref-type="fig" rid="fig5">Figure 5C</xref>).“</p><p>5) <xref ref-type="fig" rid="fig2">Figure 2</xref> – it seems that AVRBlb2 interacts weakly with ATG8IL. Does it have an AIM domain or is ATG8IL a bit sticky? Can you please quantify binding in the protein blot?</p><p>We thank the reviewers for carefully investigating our results. The band that we see in GFP-IP RFP WB is an unspecific band, because the size of AVRBlb2 is smaller than PexRD54. Also for RFP-IP, we only see a band in saturated exposure conditions and we believe it is not specific. Also, this weak band is not visible in replicate experiments. Additionally there is no predicted AIM motif in AVRBlb2.</p><p>6) All experiments are performed using transient overexpression in Nicotiana. Please comment on the caveats with this approach and consider doing some validation using native promoters to validate findings in a more biologically relevant context.</p><p>This is a standard approach in effector biology. As we discussed above the use of mutants as negative controls is an important check for linking the different readouts. All experiments used effector mutants as additional controls (in addition to empty vector controls) and we carefully quantified the relative differences based on multiple experimental readouts.</p><p>7) Since PexRD54 can stimulate the formation of ATG8CL-marked autophagosomes, you suggest that PexRD54 can activate autophagy for the pathogen's own benefit (Pro-death?). You conclude at the same time that PexRD54 counteracts the positive role of Joka2-mediated selective autophagy in pathogen defense (Pro-survival?). Is it either or both? Please clarify.</p><p>We thank the reviewers for the detailed analysis of our results. Please note that we do not know whether there is a link between ATG8CL/JOKA2-mediated selective autophagy and cell death. We believe these terms are not necessarily applicable to our findings but indeed by reviewers’ definition PexRD54 has both pro-death and pro-survival roles.</p><p>[Editors' note: further revisions were requested prior to acceptance, as described below.]</p><p>The work is substantially improved. An EM expert has suggested a number of improvements that we would like you to implement (none of which require additional experimentation):</p><p>1) About <xref ref-type="fig" rid="fig3s3">Figure 3—figure supplement 3</xref>:</p><p>The upper and lower photos seem to have different magnification. Please add size bars in the upper images.</p><p>We thank the reviewers for pointing this out. We have added the scale bars.</p><p>Legends: "Vesicles labelled with GFP antibody were different than the vesicles labelled with catalase antibody, confirming that PexRD54 labelled vesicles are not peroxisomes." Please do not use the term "vesicles" here, since it is not sure that they are not vesicles. Instead, the description can be considered as: high electron dense regions (structures)</p><p>Also the statement: "Stars indicate vesicular structures that are labelled by gold particles in the other image" is improper. The stars in two images obviously indicate different structures- the upper image indicates electron-dense structure and the lower image indicates peroxisomes (organelle). It is better to use different labels.</p><p>We thank the reviewers for coming up with “electron dense structures” term. This is a much better definition for the localization that we are seeing. We have made the changes in the legends and text as suggested by the reviewer. Here is the main text part where we mention electron microscopy data: Immunogold labelling in transmission electron micrographs of cells expressing GFP:PexRD54 revealed a strong signal in electron dense structures that are not peroxisomes (<xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2</xref>–<xref ref-type="fig" rid="fig3s3">3</xref>, Figure 3—source data 1).</p><p>Here is the new legend of <xref ref-type="fig" rid="fig3s3">Figure 3—figure supplement 3</xref>:</p><p>“<xref ref-type="fig" rid="fig3s3">Figure 3—figure supplement 3</xref>. PexRD54 labelled high electron dense structures that are not peroxisomes. Serial sections of <italic>N. benthamiana</italic> leaves transiently expressing GFP:PexRD54 were collected three days post infiltration and probed with Anti-GFP and Anti-Catalase antibodies conjugated to gold particles. High electron dense structures labelled with GFP antibody were different than the regions labelled with catalase antibody, confirming that PexRD54 labelled structures are not peroxisomes. Stars indicate regions that are labelled by gold particles in the other image. Scale bar=500nm”.</p><p>For anti-GFP, the upper image indicates that gold particles were labeled in the electron-dense portion, which was neither associated with vesicle-like structures nor peroxisomes.</p><p>We thank the reviewers. We now define this localization pattern as electron dense structures.</p><p>2) About <xref ref-type="fig" rid="fig3s3">Figure 3—figure supplement 3</xref>:</p><p>Based on the total set of supplemental EM images which authors provided, <xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2A</xref> seems not to be a typical image. Since most of images do not have vesicle like structures, the photo of number 11 seems to represent the total set of images.</p><p>We thank the reviewers for carefully investigating our images. We have replaced the old image with Image 11 from the raw data set.</p><p>3) Methods – Electron Microscopy and Immunogold labelling:</p><p>Since authors used high pressure freezing to get immunogold labelling, the authors need to describe the process in the Methods. I think authors may have cited the wrong reference (Liu, Schiff and Dinesh-Kumar et al., 2002), please check it.</p><p>In your revision, please include your archive of EM images as supplemental material so that readers can see the whole range of data.</p><p>We are already presenting all the images as a supplemental data set (Figure 3—source data 1). It will be available to the readers.</p></body></sub-article></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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