Dynamic proteomic analysis of Phanerochaete chrysosporium under copper stress.
Identifieur interne : 000033 ( Main/Exploration ); précédent : 000032; suivant : 000034Dynamic proteomic analysis of Phanerochaete chrysosporium under copper stress.
Auteurs : Sezer Okay [Turquie] ; Volkan Yildirim [Turquie] ; Knut Büttner [Allemagne] ; Dörte Becher [Allemagne] ; Gülay Özcengiz [Turquie]Source :
- Ecotoxicology and environmental safety [ 1090-2414 ] ; 2020.
Abstract
The model white rot fungus Phanerochaete chrysosporium is frequently preferred for heavy metal accumulation studies due to its high resistance to heavy metals, including copper (Cu). Here, the response of P. chrysosporium under Cu stress at different time points was investigated for the first time by a detailed proteomic analysis using 2DE MALDI-TOF/MS and nanoLC-MS/MS techniques. A total of 123 Cu-responsive protein spots were determined using 2DE approach, and 104 of them were corresponded to 73 distinct open reading frames (ORFs). Of identified ones, 88 spots were over-, and 16 spots were underrepresented. The majority of these proteins showed to the strongest response at 8th h of Cu exposure. Using nanoLC-MS/MS analysis, a total of 167 differentially produced proteins were identified from Cu-exposed cultures after enrichment of the membrane proteins followed by SILAC. Seventy four, 66, and 69 overrepresented, and 56, 71, and 64 underrepresented proteins were identified at 2 h, 4 h, and 8 h of Cu exposure, respectively. The bioinformatic analysis of these proteins revealed that intracellular trafficking proteins such as Ran GTPase and a p24 family protein, and certain proteins involved in posttranslational modification, protein turnover and folding were Cu-responsive. Three important transcription factors (TFs), NAC, BTF3, and homeobox TFs, 40S and 60S ribosomal proteins, chaperones such as Hsp26/Hsp42 and mortalin, as well as 20S proteasome, 14-3-3 proteins and Hsp90 involve in Cu-stress response of P. chrysosporium. Moreover, certain elements of translation machinery, the proteins related with aspartate, methionine, and pyruvate metabolisms, transketolase, and trehalase related with carbohydrate metabolism, citrate synthase, fumarase, V-ATPase, and F0F1-type ATPase playing role in energy production and conversion, transport proteins such as multidrug resistance and p24 family proteins as well as actin-related proteins involved in cytoskeleton remodeling were determined to be Cu-responsive. The present proteome analysis revealed that P. chrysosporium mainly regulates translational and posttranslational processes, certain transport processes, many metabolic pathways and cytoskeleton to overcome the Cu-induced oxidative stress.
DOI: 10.1016/j.ecoenv.2020.110694
PubMed: 32388186
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Dynamic proteomic analysis of Phanerochaete chrysosporium under copper stress.</title><author><name sortKey="Okay, Sezer" sort="Okay, Sezer" uniqKey="Okay S" first="Sezer" last="Okay">Sezer Okay</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara</wicri:regionArea><wicri:noRegion>Ankara</wicri:noRegion></affiliation></author><author><name sortKey="Yildirim, Volkan" sort="Yildirim, Volkan" uniqKey="Yildirim V" first="Volkan" last="Yildirim">Volkan Yildirim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Biology, Faculty of Science, Atatürk University, Erzurum, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Biology, Faculty of Science, Atatürk University, Erzurum</wicri:regionArea><wicri:noRegion>Erzurum</wicri:noRegion></affiliation></author><author><name sortKey="Buttner, Knut" sort="Buttner, Knut" uniqKey="Buttner K" first="Knut" last="Büttner">Knut Büttner</name><affiliation wicri:level="1"><nlm:affiliation>Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald</wicri:regionArea><wicri:noRegion>Greifswald</wicri:noRegion><wicri:noRegion>Greifswald</wicri:noRegion><wicri:noRegion>Greifswald</wicri:noRegion></affiliation></author><author><name sortKey="Becher, Dorte" sort="Becher, Dorte" uniqKey="Becher D" first="Dörte" last="Becher">Dörte Becher</name><affiliation wicri:level="1"><nlm:affiliation>Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald</wicri:regionArea><wicri:noRegion>Greifswald</wicri:noRegion><wicri:noRegion>Greifswald</wicri:noRegion><wicri:noRegion>Greifswald</wicri:noRegion></affiliation></author><author><name sortKey="Ozcengiz, Gulay" sort="Ozcengiz, Gulay" uniqKey="Ozcengiz G" first="Gülay" last="Özcengiz">Gülay Özcengiz</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. Electronic address: ozcengiz@metu.edu.tr.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Biological Sciences, Middle East Technical University, Ankara</wicri:regionArea><wicri:noRegion>Ankara</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32388186</idno><idno type="pmid">32388186</idno><idno type="doi">10.1016/j.ecoenv.2020.110694</idno><idno type="wicri:Area/Main/Corpus">000018</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000018</idno><idno type="wicri:Area/Main/Curation">000018</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000018</idno><idno type="wicri:Area/Main/Exploration">000018</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Dynamic proteomic analysis of Phanerochaete chrysosporium under copper stress.</title><author><name sortKey="Okay, Sezer" sort="Okay, Sezer" uniqKey="Okay S" first="Sezer" last="Okay">Sezer Okay</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara</wicri:regionArea><wicri:noRegion>Ankara</wicri:noRegion></affiliation></author><author><name sortKey="Yildirim, Volkan" sort="Yildirim, Volkan" uniqKey="Yildirim V" first="Volkan" last="Yildirim">Volkan Yildirim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Biology, Faculty of Science, Atatürk University, Erzurum, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Biology, Faculty of Science, Atatürk University, Erzurum</wicri:regionArea><wicri:noRegion>Erzurum</wicri:noRegion></affiliation></author><author><name sortKey="Buttner, Knut" sort="Buttner, Knut" uniqKey="Buttner K" first="Knut" last="Büttner">Knut Büttner</name><affiliation wicri:level="1"><nlm:affiliation>Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald</wicri:regionArea><wicri:noRegion>Greifswald</wicri:noRegion><wicri:noRegion>Greifswald</wicri:noRegion><wicri:noRegion>Greifswald</wicri:noRegion></affiliation></author><author><name sortKey="Becher, Dorte" sort="Becher, Dorte" uniqKey="Becher D" first="Dörte" last="Becher">Dörte Becher</name><affiliation wicri:level="1"><nlm:affiliation>Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald</wicri:regionArea><wicri:noRegion>Greifswald</wicri:noRegion><wicri:noRegion>Greifswald</wicri:noRegion><wicri:noRegion>Greifswald</wicri:noRegion></affiliation></author><author><name sortKey="Ozcengiz, Gulay" sort="Ozcengiz, Gulay" uniqKey="Ozcengiz G" first="Gülay" last="Özcengiz">Gülay Özcengiz</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. Electronic address: ozcengiz@metu.edu.tr.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Biological Sciences, Middle East Technical University, Ankara</wicri:regionArea><wicri:noRegion>Ankara</wicri:noRegion></affiliation></author></analytic><series><title level="j">Ecotoxicology and environmental safety</title><idno type="eISSN">1090-2414</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The model white rot fungus Phanerochaete chrysosporium is frequently preferred for heavy metal accumulation studies due to its high resistance to heavy metals, including copper (Cu). Here, the response of P. chrysosporium under Cu stress at different time points was investigated for the first time by a detailed proteomic analysis using 2DE MALDI-TOF/MS and nanoLC-MS/MS techniques. A total of 123 Cu-responsive protein spots were determined using 2DE approach, and 104 of them were corresponded to 73 distinct open reading frames (ORFs). Of identified ones, 88 spots were over-, and 16 spots were underrepresented. The majority of these proteins showed to the strongest response at 8th h of Cu exposure. Using nanoLC-MS/MS analysis, a total of 167 differentially produced proteins were identified from Cu-exposed cultures after enrichment of the membrane proteins followed by SILAC. Seventy four, 66, and 69 overrepresented, and 56, 71, and 64 underrepresented proteins were identified at 2 h, 4 h, and 8 h of Cu exposure, respectively. The bioinformatic analysis of these proteins revealed that intracellular trafficking proteins such as Ran GTPase and a p24 family protein, and certain proteins involved in posttranslational modification, protein turnover and folding were Cu-responsive. Three important transcription factors (TFs), NAC, BTF3, and homeobox TFs, 40S and 60S ribosomal proteins, chaperones such as Hsp26/Hsp42 and mortalin, as well as 20S proteasome, 14-3-3 proteins and Hsp90 involve in Cu-stress response of P. chrysosporium. Moreover, certain elements of translation machinery, the proteins related with aspartate, methionine, and pyruvate metabolisms, transketolase, and trehalase related with carbohydrate metabolism, citrate synthase, fumarase, V-ATPase, and F0F1-type ATPase playing role in energy production and conversion, transport proteins such as multidrug resistance and p24 family proteins as well as actin-related proteins involved in cytoskeleton remodeling were determined to be Cu-responsive. The present proteome analysis revealed that P. chrysosporium mainly regulates translational and posttranslational processes, certain transport processes, many metabolic pathways and cytoskeleton to overcome the Cu-induced oxidative stress.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32388186</PMID><DateRevised><Year>2020</Year><Month>05</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1090-2414</ISSN><JournalIssue CitedMedium="Internet"><Volume>198</Volume><PubDate><Year>2020</Year><Month>May</Month><Day>07</Day></PubDate></JournalIssue><Title>Ecotoxicology and environmental safety</Title><ISOAbbreviation>Ecotoxicol Environ Saf</ISOAbbreviation></Journal><ArticleTitle>Dynamic proteomic analysis of Phanerochaete chrysosporium under copper stress.</ArticleTitle><Pagination><MedlinePgn>110694</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0147-6513(20)30533-9</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ecoenv.2020.110694</ELocationID><Abstract><AbstractText>The model white rot fungus Phanerochaete chrysosporium is frequently preferred for heavy metal accumulation studies due to its high resistance to heavy metals, including copper (Cu). Here, the response of P. chrysosporium under Cu stress at different time points was investigated for the first time by a detailed proteomic analysis using 2DE MALDI-TOF/MS and nanoLC-MS/MS techniques. A total of 123 Cu-responsive protein spots were determined using 2DE approach, and 104 of them were corresponded to 73 distinct open reading frames (ORFs). Of identified ones, 88 spots were over-, and 16 spots were underrepresented. The majority of these proteins showed to the strongest response at 8th h of Cu exposure. Using nanoLC-MS/MS analysis, a total of 167 differentially produced proteins were identified from Cu-exposed cultures after enrichment of the membrane proteins followed by SILAC. Seventy four, 66, and 69 overrepresented, and 56, 71, and 64 underrepresented proteins were identified at 2 h, 4 h, and 8 h of Cu exposure, respectively. The bioinformatic analysis of these proteins revealed that intracellular trafficking proteins such as Ran GTPase and a p24 family protein, and certain proteins involved in posttranslational modification, protein turnover and folding were Cu-responsive. Three important transcription factors (TFs), NAC, BTF3, and homeobox TFs, 40S and 60S ribosomal proteins, chaperones such as Hsp26/Hsp42 and mortalin, as well as 20S proteasome, 14-3-3 proteins and Hsp90 involve in Cu-stress response of P. chrysosporium. Moreover, certain elements of translation machinery, the proteins related with aspartate, methionine, and pyruvate metabolisms, transketolase, and trehalase related with carbohydrate metabolism, citrate synthase, fumarase, V-ATPase, and F0F1-type ATPase playing role in energy production and conversion, transport proteins such as multidrug resistance and p24 family proteins as well as actin-related proteins involved in cytoskeleton remodeling were determined to be Cu-responsive. The present proteome analysis revealed that P. chrysosporium mainly regulates translational and posttranslational processes, certain transport processes, many metabolic pathways and cytoskeleton to overcome the Cu-induced oxidative stress.</AbstractText><CopyrightInformation>Copyright © 2020 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Okay</LastName><ForeName>Sezer</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara, Turkey.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yildirim</LastName><ForeName>Volkan</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Biology, Faculty of Science, Atatürk University, Erzurum, Turkey.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Büttner</LastName><ForeName>Knut</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Becher</LastName><ForeName>Dörte</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Özcengiz</LastName><ForeName>Gülay</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. Electronic address: ozcengiz@metu.edu.tr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>05</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Ecotoxicol Environ Saf</MedlineTA><NlmUniqueID>7805381</NlmUniqueID><ISSNLinking>0147-6513</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Copper</Keyword><Keyword MajorTopicYN="N">Metal toxicity</Keyword><Keyword MajorTopicYN="N">Phanerochaete chrysosporium</Keyword><Keyword MajorTopicYN="N">Proteome</Keyword><Keyword MajorTopicYN="N">Stress response</Keyword></KeywordList><CoiStatement>Declaration of competing interest The authors declare that there is no conflict of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>02</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>04</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>04</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>5</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>5</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>5</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32388186</ArticleId><ArticleId IdType="pii">S0147-6513(20)30533-9</ArticleId><ArticleId IdType="doi">10.1016/j.ecoenv.2020.110694</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li><li>Turquie</li></country></list><tree><country name="Turquie"><noRegion><name sortKey="Okay, Sezer" sort="Okay, Sezer" uniqKey="Okay S" first="Sezer" last="Okay">Sezer Okay</name></noRegion><name sortKey="Ozcengiz, Gulay" sort="Ozcengiz, Gulay" uniqKey="Ozcengiz G" first="Gülay" last="Özcengiz">Gülay Özcengiz</name><name sortKey="Yildirim, Volkan" sort="Yildirim, Volkan" uniqKey="Yildirim V" first="Volkan" last="Yildirim">Volkan Yildirim</name></country><country name="Allemagne"><noRegion><name sortKey="Buttner, Knut" sort="Buttner, Knut" uniqKey="Buttner K" first="Knut" last="Büttner">Knut Büttner</name></noRegion><name sortKey="Becher, Dorte" sort="Becher, Dorte" uniqKey="Becher D" first="Dörte" last="Becher">Dörte Becher</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PhanerochaeteV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000033 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000033 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PhanerochaeteV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:32388186
|texte= Dynamic proteomic analysis of Phanerochaete chrysosporium under copper stress.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:32388186" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PhanerochaeteV1
| This area was generated with Dilib version V0.6.37. |  |