General stress response or adaptation to rapid growth in Aspergillus nidulans?
Identifieur interne : 000118 ( Main/Exploration ); précédent : 000117; suivant : 000119General stress response or adaptation to rapid growth in Aspergillus nidulans?
Auteurs : Károly Antal [Hongrie] ; Barnabás Cs Gila [Hongrie] ; István P Csi [Hongrie] ; Tamás Emri [Hongrie]Source :
- Fungal biology [ 1878-6146 ] ; 2020.
Abstract
Genome-wide transcriptional changes in Aspergillus nidulans induced by nine different stress conditions were evaluated to reveal the general environmental stress response gene set showing unidirectional expressional changes under various types of stress. Clustering the genes by their transcriptional changes was a useful technique for identifying large groups of co-regulated genes. Altogether, 1642 co-upregulated and 3916 co-downregulated genes were identified. Nevertheless, the co-regulated genes describe the difference between the transcriptomes recorded under the stress conditions tested and one chosen reference culture condition which is designated as the "unstressed" condition. Obviously, the corresponding transcriptional differences may be attributed to either the general stress response or the reference condition. Accordingly, reduced growth and increased transcription of certain antioxidative enzymes observed under stress may be interpreted as elements of the general stress response or as a feature of the "optimal growth" reference condition and decreased antioxidative protection due to "rapid growth" stress. Reversing the many to one comparison underlying the identification of co-regulated gene sets allows the same procedure to highlight changes under a single condition with respect to a set of other "background" conditions. As an example, we compared menadione treatment to our other conditions and identified downregulation of endoplasmic reticulum dependent processes and upregulation of iron-sulfur cluster assembly as well as glutathione-S-transferase genes as changes characteristic of MSB-treated cultures. Deletion of the atfA gene markedly altered the co-regulated gene sets primarily by changing the reference transcriptome; not by changing the stress responsiveness of genes. The functional characterization of AtfA-dependent co-regulated genes demonstrated the involvement of AtfA in the regulation of both vegetative growth and conidiogenesis in untreated cultures. Our data also suggested that the diverse effects of atfA gene deletion on the transcriptome under different stress conditions were the consequence of the altered transcription of several phosphorelay signal transduction system genes, including fphA, nikA, phkA, srrB, srrC, sskA and tcsB. Hopefully, this study will draw further attention to the importance of the proper selection of reference cultures in fungal transcriptomics studies especially when elements of specific stress responses are mapped.
DOI: 10.1016/j.funbio.2019.10.009
PubMed: 32389300
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">General stress response or adaptation to rapid growth in Aspergillus nidulans?</title><author><name sortKey="Antal, Karoly" sort="Antal, Karoly" uniqKey="Antal K" first="Károly" last="Antal">Károly Antal</name><affiliation wicri:level="1"><nlm:affiliation>Department of Zoology, Eszterházy Károly University, Eszterházy tér 1, Eger, 3300, Hungary.</nlm:affiliation><country xml:lang="fr">Hongrie</country><wicri:regionArea>Department of Zoology, Eszterházy Károly University, Eszterházy tér 1, Eger, 3300</wicri:regionArea><wicri:noRegion>3300</wicri:noRegion></affiliation></author><author><name sortKey="Gila, Barnabas Cs" sort="Gila, Barnabas Cs" uniqKey="Gila B" first="Barnabás Cs" last="Gila">Barnabás Cs Gila</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary; University of Debrecen, Doctoral School of Nutrition and Food Sciences, Egyetem tér 1, Debrecen, 4032, Hungary.</nlm:affiliation><country xml:lang="fr">Hongrie</country><wicri:regionArea>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary; University of Debrecen, Doctoral School of Nutrition and Food Sciences, Egyetem tér 1, Debrecen, 4032</wicri:regionArea><wicri:noRegion>4032</wicri:noRegion></affiliation></author><author><name sortKey="P Csi, Istvan" sort="P Csi, Istvan" uniqKey="P Csi I" first="István" last="P Csi">István P Csi</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.</nlm:affiliation><country xml:lang="fr">Hongrie</country><wicri:regionArea>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032</wicri:regionArea><wicri:noRegion>4032</wicri:noRegion></affiliation></author><author><name sortKey="Emri, Tamas" sort="Emri, Tamas" uniqKey="Emri T" first="Tamás" last="Emri">Tamás Emri</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary. Electronic address: emri.tamas@science.unideb.hu.</nlm:affiliation><country xml:lang="fr">Hongrie</country><wicri:regionArea>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032</wicri:regionArea><wicri:noRegion>4032</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32389300</idno><idno type="pmid">32389300</idno><idno type="doi">10.1016/j.funbio.2019.10.009</idno><idno type="wicri:Area/Main/Corpus">000096</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000096</idno><idno type="wicri:Area/Main/Curation">000096</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000096</idno><idno type="wicri:Area/Main/Exploration">000096</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">General stress response or adaptation to rapid growth in Aspergillus nidulans?</title><author><name sortKey="Antal, Karoly" sort="Antal, Karoly" uniqKey="Antal K" first="Károly" last="Antal">Károly Antal</name><affiliation wicri:level="1"><nlm:affiliation>Department of Zoology, Eszterházy Károly University, Eszterházy tér 1, Eger, 3300, Hungary.</nlm:affiliation><country xml:lang="fr">Hongrie</country><wicri:regionArea>Department of Zoology, Eszterházy Károly University, Eszterházy tér 1, Eger, 3300</wicri:regionArea><wicri:noRegion>3300</wicri:noRegion></affiliation></author><author><name sortKey="Gila, Barnabas Cs" sort="Gila, Barnabas Cs" uniqKey="Gila B" first="Barnabás Cs" last="Gila">Barnabás Cs Gila</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary; University of Debrecen, Doctoral School of Nutrition and Food Sciences, Egyetem tér 1, Debrecen, 4032, Hungary.</nlm:affiliation><country xml:lang="fr">Hongrie</country><wicri:regionArea>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary; University of Debrecen, Doctoral School of Nutrition and Food Sciences, Egyetem tér 1, Debrecen, 4032</wicri:regionArea><wicri:noRegion>4032</wicri:noRegion></affiliation></author><author><name sortKey="P Csi, Istvan" sort="P Csi, Istvan" uniqKey="P Csi I" first="István" last="P Csi">István P Csi</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.</nlm:affiliation><country xml:lang="fr">Hongrie</country><wicri:regionArea>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032</wicri:regionArea><wicri:noRegion>4032</wicri:noRegion></affiliation></author><author><name sortKey="Emri, Tamas" sort="Emri, Tamas" uniqKey="Emri T" first="Tamás" last="Emri">Tamás Emri</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary. Electronic address: emri.tamas@science.unideb.hu.</nlm:affiliation><country xml:lang="fr">Hongrie</country><wicri:regionArea>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032</wicri:regionArea><wicri:noRegion>4032</wicri:noRegion></affiliation></author></analytic><series><title level="j">Fungal biology</title><idno type="ISSN">1878-6146</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">Genome-wide transcriptional changes in Aspergillus nidulans induced by nine different stress conditions were evaluated to reveal the general environmental stress response gene set showing unidirectional expressional changes under various types of stress. Clustering the genes by their transcriptional changes was a useful technique for identifying large groups of co-regulated genes. Altogether, 1642 co-upregulated and 3916 co-downregulated genes were identified. Nevertheless, the co-regulated genes describe the difference between the transcriptomes recorded under the stress conditions tested and one chosen reference culture condition which is designated as the "unstressed" condition. Obviously, the corresponding transcriptional differences may be attributed to either the general stress response or the reference condition. Accordingly, reduced growth and increased transcription of certain antioxidative enzymes observed under stress may be interpreted as elements of the general stress response or as a feature of the "optimal growth" reference condition and decreased antioxidative protection due to "rapid growth" stress. Reversing the many to one comparison underlying the identification of co-regulated gene sets allows the same procedure to highlight changes under a single condition with respect to a set of other "background" conditions. As an example, we compared menadione treatment to our other conditions and identified downregulation of endoplasmic reticulum dependent processes and upregulation of iron-sulfur cluster assembly as well as glutathione-S-transferase genes as changes characteristic of MSB-treated cultures. Deletion of the atfA gene markedly altered the co-regulated gene sets primarily by changing the reference transcriptome; not by changing the stress responsiveness of genes. The functional characterization of AtfA-dependent co-regulated genes demonstrated the involvement of AtfA in the regulation of both vegetative growth and conidiogenesis in untreated cultures. Our data also suggested that the diverse effects of atfA gene deletion on the transcriptome under different stress conditions were the consequence of the altered transcription of several phosphorelay signal transduction system genes, including fphA, nikA, phkA, srrB, srrC, sskA and tcsB. Hopefully, this study will draw further attention to the importance of the proper selection of reference cultures in fungal transcriptomics studies especially when elements of specific stress responses are mapped.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32389300</PMID><DateRevised><Year>2020</Year><Month>11</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1878-6146</ISSN><JournalIssue CitedMedium="Internet"><Volume>124</Volume><Issue>5</Issue><PubDate><Year>2020</Year><Month>05</Month></PubDate></JournalIssue><Title>Fungal biology</Title><ISOAbbreviation>Fungal Biol</ISOAbbreviation></Journal><ArticleTitle>General stress response or adaptation to rapid growth in Aspergillus nidulans?</ArticleTitle><Pagination><MedlinePgn>376-386</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1878-6146(19)30150-3</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.funbio.2019.10.009</ELocationID><Abstract><AbstractText>Genome-wide transcriptional changes in Aspergillus nidulans induced by nine different stress conditions were evaluated to reveal the general environmental stress response gene set showing unidirectional expressional changes under various types of stress. Clustering the genes by their transcriptional changes was a useful technique for identifying large groups of co-regulated genes. Altogether, 1642 co-upregulated and 3916 co-downregulated genes were identified. Nevertheless, the co-regulated genes describe the difference between the transcriptomes recorded under the stress conditions tested and one chosen reference culture condition which is designated as the "unstressed" condition. Obviously, the corresponding transcriptional differences may be attributed to either the general stress response or the reference condition. Accordingly, reduced growth and increased transcription of certain antioxidative enzymes observed under stress may be interpreted as elements of the general stress response or as a feature of the "optimal growth" reference condition and decreased antioxidative protection due to "rapid growth" stress. Reversing the many to one comparison underlying the identification of co-regulated gene sets allows the same procedure to highlight changes under a single condition with respect to a set of other "background" conditions. As an example, we compared menadione treatment to our other conditions and identified downregulation of endoplasmic reticulum dependent processes and upregulation of iron-sulfur cluster assembly as well as glutathione-S-transferase genes as changes characteristic of MSB-treated cultures. Deletion of the atfA gene markedly altered the co-regulated gene sets primarily by changing the reference transcriptome; not by changing the stress responsiveness of genes. The functional characterization of AtfA-dependent co-regulated genes demonstrated the involvement of AtfA in the regulation of both vegetative growth and conidiogenesis in untreated cultures. Our data also suggested that the diverse effects of atfA gene deletion on the transcriptome under different stress conditions were the consequence of the altered transcription of several phosphorelay signal transduction system genes, including fphA, nikA, phkA, srrB, srrC, sskA and tcsB. Hopefully, this study will draw further attention to the importance of the proper selection of reference cultures in fungal transcriptomics studies especially when elements of specific stress responses are mapped.</AbstractText><CopyrightInformation>Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Antal</LastName><ForeName>Károly</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Zoology, Eszterházy Károly University, Eszterházy tér 1, Eger, 3300, Hungary.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gila</LastName><ForeName>Barnabás Cs</ForeName><Initials>BC</Initials><AffiliationInfo><Affiliation>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary; University of Debrecen, Doctoral School of Nutrition and Food Sciences, Egyetem tér 1, Debrecen, 4032, Hungary.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pócsi</LastName><ForeName>István</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Emri</LastName><ForeName>Tamás</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary. Electronic address: emri.tamas@science.unideb.hu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>10</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Fungal Biol</MedlineTA><NlmUniqueID>101524465</NlmUniqueID></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">AtfA</Keyword><Keyword MajorTopicYN="Y">Co-regulated genes</Keyword><Keyword MajorTopicYN="Y">Environmental stress response</Keyword><Keyword MajorTopicYN="Y">Transcriptomics</Keyword></KeywordList><CoiStatement>Declaration of Competing Interest The authors declare that they have no conflict of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>08</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>10</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>10</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>5</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>5</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>5</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32389300</ArticleId><ArticleId IdType="pii">S1878-6146(19)30150-3</ArticleId><ArticleId IdType="doi">10.1016/j.funbio.2019.10.009</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Hongrie</li></country></list><tree><country name="Hongrie"><noRegion><name sortKey="Antal, Karoly" sort="Antal, Karoly" uniqKey="Antal K" first="Károly" last="Antal">Károly Antal</name></noRegion><name sortKey="Emri, Tamas" sort="Emri, Tamas" uniqKey="Emri T" first="Tamás" last="Emri">Tamás Emri</name><name sortKey="Gila, Barnabas Cs" sort="Gila, Barnabas Cs" uniqKey="Gila B" first="Barnabás Cs" last="Gila">Barnabás Cs Gila</name><name sortKey="P Csi, Istvan" sort="P Csi, Istvan" uniqKey="P Csi I" first="István" last="P Csi">István P Csi</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/IronSulferCluV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000118 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000118 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= IronSulferCluV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:32389300
|texte= General stress response or adaptation to rapid growth in Aspergillus nidulans?
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:32389300" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a IronSulferCluV1
| This area was generated with Dilib version V0.6.38. |  |