A family of small cyclic amphipathic peptides (SCAmpPs) genes in citrus
Identifieur interne : 000578 ( Pmc/Curation ); précédent : 000577; suivant : 000579A family of small cyclic amphipathic peptides (SCAmpPs) genes in citrus
Auteurs : William R. Belknap [États-Unis] ; Kent F. Mccue [États-Unis] ; Leslie A. Harden [États-Unis] ; William H. Vensel [États-Unis] ; Michael G. Bausher [États-Unis] ; Ed Stover [États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2015.
Abstract
Citrus represents a crop of global importance both in economic impact and significance to nutrition. Citrus production worldwide is threatened by the disease Huanglongbing (HLB), caused by the phloem-limited pathogen
A gene family of Small Cyclic Amphipathic Peptides (SCAmpPs) in citrus is described. The citrus genomes contain 100–150 SCAmpPs genes, approximately 50 of which are represented in the citrus EST database. These genes encode small ~50 residue precursor proteins that are post-translationally processed, releasing 5–10 residue cyclic peptides. The structures of the SCAmpPs genes are highly conserved, with the small coding domains interrupted by a single intron and relatively extended untranslated regions. Some family members are very highly transcribed in specific citrus tissues, as determined by representation in tissue-specific cDNA libraries. Comparison of the ESTs of related SCAmpPs revealed an unexpected evolutionary profile, consistent with targeted mutagenesis of the predicted cyclic peptide domain. The SCAmpPs genes are displayed in clusters on the citrus chromosomes, with apparent association with receptor leucine-rich repeat protein arrays. This study focused on three SCAmpPs family members with high constitutive expression in citrus phloem. Unexpectedly high sequence conservation was observed in the promoter region of two phloem-expressed SCAmpPs that encode very distinct predicted cyclic products. The processed cyclic product of one of these phloem SCAmpPs was characterized by LC-MS-MS analysis of phloem tissue, revealing properties consistent with a K+ ionophore.
The SCAmpPs amino acid composition, protein structure, expression patterns, evolutionary profile and chromosomal distribution are consistent with designation as ribosomally synthesized defense-related peptides.
The online version of this article (doi:10.1186/s12864-015-1486-4) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-1486-4
PubMed: 25887227
PubMed Central: 4409773
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A family of small cyclic amphipathic peptides (SCAmpPs) genes in citrus</title><author><name sortKey="Belknap, William R" sort="Belknap, William R" uniqKey="Belknap W" first="William R" last="Belknap">William R. Belknap</name><affiliation wicri:level="2"><nlm:aff id="Aff1">USDA-ARS, Western Regional Research Center, Albany, CA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>USDA-ARS, Western Regional Research Center, Albany</wicri:cityArea></affiliation></author><author><name sortKey="Mccue, Kent F" sort="Mccue, Kent F" uniqKey="Mccue K" first="Kent F" last="Mccue">Kent F. Mccue</name><affiliation wicri:level="2"><nlm:aff id="Aff1">USDA-ARS, Western Regional Research Center, Albany, CA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>USDA-ARS, Western Regional Research Center, Albany</wicri:cityArea></affiliation></author><author><name sortKey="Harden, Leslie A" sort="Harden, Leslie A" uniqKey="Harden L" first="Leslie A" last="Harden">Leslie A. Harden</name><affiliation wicri:level="2"><nlm:aff id="Aff1">USDA-ARS, Western Regional Research Center, Albany, CA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>USDA-ARS, Western Regional Research Center, Albany</wicri:cityArea></affiliation></author><author><name sortKey="Vensel, William H" sort="Vensel, William H" uniqKey="Vensel W" first="William H" last="Vensel">William H. Vensel</name><affiliation wicri:level="2"><nlm:aff id="Aff1">USDA-ARS, Western Regional Research Center, Albany, CA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>USDA-ARS, Western Regional Research Center, Albany</wicri:cityArea></affiliation></author><author><name sortKey="Bausher, Michael G" sort="Bausher, Michael G" uniqKey="Bausher M" first="Michael G" last="Bausher">Michael G. Bausher</name><affiliation wicri:level="2"><nlm:aff id="Aff2">USDA-ARS, U. S. Horticultural Research Laboratory, Fort Pierce, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>USDA-ARS, U. S. Horticultural Research Laboratory, Fort Pierce</wicri:cityArea></affiliation></author><author><name sortKey="Stover, Ed" sort="Stover, Ed" uniqKey="Stover E" first="Ed" last="Stover">Ed Stover</name><affiliation wicri:level="2"><nlm:aff id="Aff2">USDA-ARS, U. S. Horticultural Research Laboratory, Fort Pierce, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>USDA-ARS, U. S. Horticultural Research Laboratory, Fort Pierce</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25887227</idno><idno type="pmc">4409773</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409773</idno><idno type="RBID">PMC:4409773</idno><idno type="doi">10.1186/s12864-015-1486-4</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000579</idno><idno type="wicri:Area/Pmc/Curation">000578</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A family of small cyclic amphipathic peptides (SCAmpPs) genes in citrus</title><author><name sortKey="Belknap, William R" sort="Belknap, William R" uniqKey="Belknap W" first="William R" last="Belknap">William R. Belknap</name><affiliation wicri:level="2"><nlm:aff id="Aff1">USDA-ARS, Western Regional Research Center, Albany, CA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>USDA-ARS, Western Regional Research Center, Albany</wicri:cityArea></affiliation></author><author><name sortKey="Mccue, Kent F" sort="Mccue, Kent F" uniqKey="Mccue K" first="Kent F" last="Mccue">Kent F. Mccue</name><affiliation wicri:level="2"><nlm:aff id="Aff1">USDA-ARS, Western Regional Research Center, Albany, CA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>USDA-ARS, Western Regional Research Center, Albany</wicri:cityArea></affiliation></author><author><name sortKey="Harden, Leslie A" sort="Harden, Leslie A" uniqKey="Harden L" first="Leslie A" last="Harden">Leslie A. Harden</name><affiliation wicri:level="2"><nlm:aff id="Aff1">USDA-ARS, Western Regional Research Center, Albany, CA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>USDA-ARS, Western Regional Research Center, Albany</wicri:cityArea></affiliation></author><author><name sortKey="Vensel, William H" sort="Vensel, William H" uniqKey="Vensel W" first="William H" last="Vensel">William H. Vensel</name><affiliation wicri:level="2"><nlm:aff id="Aff1">USDA-ARS, Western Regional Research Center, Albany, CA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>USDA-ARS, Western Regional Research Center, Albany</wicri:cityArea></affiliation></author><author><name sortKey="Bausher, Michael G" sort="Bausher, Michael G" uniqKey="Bausher M" first="Michael G" last="Bausher">Michael G. Bausher</name><affiliation wicri:level="2"><nlm:aff id="Aff2">USDA-ARS, U. S. Horticultural Research Laboratory, Fort Pierce, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>USDA-ARS, U. S. Horticultural Research Laboratory, Fort Pierce</wicri:cityArea></affiliation></author><author><name sortKey="Stover, Ed" sort="Stover, Ed" uniqKey="Stover E" first="Ed" last="Stover">Ed Stover</name><affiliation wicri:level="2"><nlm:aff id="Aff2">USDA-ARS, U. S. Horticultural Research Laboratory, Fort Pierce, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>USDA-ARS, U. S. Horticultural Research Laboratory, Fort Pierce</wicri:cityArea></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Citrus represents a crop of global importance both in economic impact and significance to nutrition. Citrus production worldwide is threatened by the disease Huanglongbing (HLB), caused by the phloem-limited pathogen <italic>Candidatus</italic> Liberibacter spp.. As a source of stable HLB-resistance has yet to be identified, there is considerable interest in characterization of novel disease-associated citrus genes.</p></sec><sec><title>Results</title><p>A gene family of Small Cyclic Amphipathic Peptides (SCAmpPs) in citrus is described. The citrus genomes contain 100–150 SCAmpPs genes, approximately 50 of which are represented in the citrus EST database. These genes encode small ~50 residue precursor proteins that are post-translationally processed, releasing 5–10 residue cyclic peptides. The structures of the SCAmpPs genes are highly conserved, with the small coding domains interrupted by a single intron and relatively extended untranslated regions. Some family members are very highly transcribed in specific citrus tissues, as determined by representation in tissue-specific cDNA libraries. Comparison of the ESTs of related SCAmpPs revealed an unexpected evolutionary profile, consistent with targeted mutagenesis of the predicted cyclic peptide domain. The SCAmpPs genes are displayed in clusters on the citrus chromosomes, with apparent association with receptor leucine-rich repeat protein arrays. This study focused on three SCAmpPs family members with high constitutive expression in citrus phloem. Unexpectedly high sequence conservation was observed in the promoter region of two phloem-expressed SCAmpPs that encode very distinct predicted cyclic products. The processed cyclic product of one of these phloem SCAmpPs was characterized by LC-MS-MS analysis of phloem tissue, revealing properties consistent with a K<sup>+</sup> ionophore.</p></sec><sec><title>Conclusions</title><p>The SCAmpPs amino acid composition, protein structure, expression patterns, evolutionary profile and chromosomal distribution are consistent with designation as ribosomally synthesized defense-related peptides.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1486-4) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Marmiroli, N" uniqKey="Marmiroli N">N Marmiroli</name></author><author><name sortKey="Maestri, E" uniqKey="Maestri E">E Maestri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grill, E" uniqKey="Grill E">E 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genomics</journal-id><journal-id journal-id-type="iso-abbrev">BMC Genomics</journal-id><journal-title-group><journal-title>BMC Genomics</journal-title></journal-title-group><issn pub-type="epub">1471-2164</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25887227</article-id><article-id pub-id-type="pmc">4409773</article-id><article-id pub-id-type="publisher-id">1486</article-id><article-id pub-id-type="doi">10.1186/s12864-015-1486-4</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>A family of small cyclic amphipathic peptides (SCAmpPs) genes in citrus</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Belknap</surname><given-names>William R</given-names></name><address><email>william.belknap@ars.usda.gov</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>McCue</surname><given-names>Kent F</given-names></name><address><email>kent.mccue@ars.usda.gov</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Harden</surname><given-names>Leslie A</given-names></name><address><email>leslie.harden@ars.usda.gov</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Vensel</surname><given-names>William H</given-names></name><address><email>william.vensel@ars.usda.gov</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Bausher</surname><given-names>Michael G</given-names></name><address><email>michael.bausher@ars.usda.gov</email></address><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Stover</surname><given-names>Ed</given-names></name><address><email>ed.stover@ars.usda.gov</email></address><xref ref-type="aff" rid="Aff2"></xref></contrib><aff id="Aff1"><label></label>USDA-ARS, Western Regional Research Center, Albany, CA USA</aff><aff id="Aff2"><label></label>USDA-ARS, U. S. Horticultural Research Laboratory, Fort Pierce, FL USA</aff></contrib-group><pub-date pub-type="epub"><day>16</day><month>4</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>16</day><month>4</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>16</volume><issue>1</issue><elocation-id>303</elocation-id><history><date date-type="received"><day>8</day><month>10</month><year>2014</year></date><date date-type="accepted"><day>25</day><month>3</month><year>2015</year></date></history><permissions><copyright-statement>© Belknap et al.; licensee BioMed Central. 2015</copyright-statement><license license-type="open-access"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>Citrus represents a crop of global importance both in economic impact and significance to nutrition. Citrus production worldwide is threatened by the disease Huanglongbing (HLB), caused by the phloem-limited pathogen <italic>Candidatus</italic> Liberibacter spp.. As a source of stable HLB-resistance has yet to be identified, there is considerable interest in characterization of novel disease-associated citrus genes.</p></sec><sec><title>Results</title><p>A gene family of Small Cyclic Amphipathic Peptides (SCAmpPs) in citrus is described. The citrus genomes contain 100–150 SCAmpPs genes, approximately 50 of which are represented in the citrus EST database. These genes encode small ~50 residue precursor proteins that are post-translationally processed, releasing 5–10 residue cyclic peptides. The structures of the SCAmpPs genes are highly conserved, with the small coding domains interrupted by a single intron and relatively extended untranslated regions. Some family members are very highly transcribed in specific citrus tissues, as determined by representation in tissue-specific cDNA libraries. Comparison of the ESTs of related SCAmpPs revealed an unexpected evolutionary profile, consistent with targeted mutagenesis of the predicted cyclic peptide domain. The SCAmpPs genes are displayed in clusters on the citrus chromosomes, with apparent association with receptor leucine-rich repeat protein arrays. This study focused on three SCAmpPs family members with high constitutive expression in citrus phloem. Unexpectedly high sequence conservation was observed in the promoter region of two phloem-expressed SCAmpPs that encode very distinct predicted cyclic products. The processed cyclic product of one of these phloem SCAmpPs was characterized by LC-MS-MS analysis of phloem tissue, revealing properties consistent with a K<sup>+</sup> ionophore.</p></sec><sec><title>Conclusions</title><p>The SCAmpPs amino acid composition, protein structure, expression patterns, evolutionary profile and chromosomal distribution are consistent with designation as ribosomally synthesized defense-related peptides.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1486-4) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd><italic>Citrus sinensis</italic></kwd><kwd><italic>Citrus clementina</italic></kwd><kwd><italic>Poncirus trifoliata</italic></kwd><kwd>Ribosomally synthesized</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2015</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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