Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers.
Identifieur interne : 000142 ( Main/Curation ); précédent : 000141; suivant : 000143Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers.
Auteurs : Ian J. Campbell [États-Unis] ; George N. Bennett [États-Unis] ; Jonathan J. Silberg [États-Unis]Source :
- Frontiers in energy research [ 2296-598X ] ; 2019.
Abstract
Proteins from the ferredoxin (Fd) and flavodoxin (Fld) families function as low potential electrical transfer hubs in cells, at times mediating electron transfer between overlapping sets of oxidoreductases. To better understand protein electron carrier (PEC) use across the domains of life, we evaluated the distribution of genes encoding [4Fe-4S] Fd, [2Fe-2S] Fd, and Fld electron carriers in over 7,000 organisms. Our analysis targeted genes encoding small PEC genes encoding proteins having ≤200 residues. We find that the average number of small PEC genes per Archaea (~13), Bacteria (~8), and Eukarya (~3) genome varies, with some organisms containing as many as 54 total PEC genes. Organisms fall into three groups, including those lacking genes encoding low potential PECs (3%), specialists with a single PEC gene type (20%), and generalists that utilize multiple PEC types (77%). Mapping PEC gene usage onto an evolutionary tree highlights the prevalence of [4Fe-4S] Fds in ancient organisms that are deeply rooted, the expansion of [2Fe-2S] Fds with the advent of photosynthesis and a concomitant decrease in [4Fe-4S] Fds, and the expansion of Flds in organisms that inhabit low-iron host environments. Surprisingly, [4Fe-4S] Fds present a similar abundance in aerobes as [2Fe-2S] Fds. This bioinformatic study highlights understudied PECs whose structure, stability, and partner specificity should be further characterized.
DOI: 10.3389/fenrg.2019.00079
PubMed: 32095484
PubMed Central: PMC7039249
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Campbell</name><affiliation wicri:level="1"><nlm:affiliation>Biochemistry and Cell Biology Graduate Program, Rice University, Houston, TX, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biochemistry and Cell Biology Graduate Program, Rice University, Houston, TX</wicri:regionArea></affiliation></author><author><name sortKey="Bennett, George N" sort="Bennett, George N" uniqKey="Bennett G" first="George N" last="Bennett">George N. Bennett</name><affiliation wicri:level="1"><nlm:affiliation>Department of BioSciences, Rice University, Houston, TX, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of BioSciences, Rice University, Houston, TX</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX</wicri:regionArea></affiliation></author><author><name sortKey="Silberg, Jonathan J" sort="Silberg, Jonathan J" uniqKey="Silberg J" first="Jonathan J" last="Silberg">Jonathan J. Silberg</name><affiliation wicri:level="1"><nlm:affiliation>Department of BioSciences, Rice University, Houston, TX, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of BioSciences, Rice University, Houston, TX</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Bioengineering, Rice University Houston, TX, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, Rice University Houston, TX</wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in energy research</title><idno type="eISSN">2296-598X</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Proteins from the ferredoxin (Fd) and flavodoxin (Fld) families function as low potential electrical transfer hubs in cells, at times mediating electron transfer between overlapping sets of oxidoreductases. To better understand protein electron carrier (PEC) use across the domains of life, we evaluated the distribution of genes encoding [4Fe-4S] Fd, [2Fe-2S] Fd, and Fld electron carriers in over 7,000 organisms. Our analysis targeted genes encoding small PEC genes encoding proteins having ≤200 residues. We find that the average number of small PEC genes per Archaea (~13), Bacteria (~8), and Eukarya (~3) genome varies, with some organisms containing as many as 54 total PEC genes. Organisms fall into three groups, including those lacking genes encoding low potential PECs (3%), specialists with a single PEC gene type (20%), and generalists that utilize multiple PEC types (77%). Mapping PEC gene usage onto an evolutionary tree highlights the prevalence of [4Fe-4S] Fds in ancient organisms that are deeply rooted, the expansion of [2Fe-2S] Fds with the advent of photosynthesis and a concomitant decrease in [4Fe-4S] Fds, and the expansion of Flds in organisms that inhabit low-iron host environments. Surprisingly, [4Fe-4S] Fds present a similar abundance in aerobes as [2Fe-2S] Fds. This bioinformatic study highlights understudied PECs whose structure, stability, and partner specificity should be further characterized.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32095484</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">2296-598X</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><PubDate><Year>2019</Year></PubDate></JournalIssue><Title>Frontiers in energy research</Title><ISOAbbreviation>Front Energy Res</ISOAbbreviation></Journal><ArticleTitle>Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.3389/fenrg.2019.00079</ELocationID><Abstract><AbstractText>Proteins from the ferredoxin (Fd) and flavodoxin (Fld) families function as low potential electrical transfer hubs in cells, at times mediating electron transfer between overlapping sets of oxidoreductases. To better understand protein electron carrier (PEC) use across the domains of life, we evaluated the distribution of genes encoding [4Fe-4S] Fd, [2Fe-2S] Fd, and Fld electron carriers in over 7,000 organisms. Our analysis targeted genes encoding small PEC genes encoding proteins having ≤200 residues. We find that the average number of small PEC genes per Archaea (~13), Bacteria (~8), and Eukarya (~3) genome varies, with some organisms containing as many as 54 total PEC genes. Organisms fall into three groups, including those lacking genes encoding low potential PECs (3%), specialists with a single PEC gene type (20%), and generalists that utilize multiple PEC types (77%). Mapping PEC gene usage onto an evolutionary tree highlights the prevalence of [4Fe-4S] Fds in ancient organisms that are deeply rooted, the expansion of [2Fe-2S] Fds with the advent of photosynthesis and a concomitant decrease in [4Fe-4S] Fds, and the expansion of Flds in organisms that inhabit low-iron host environments. Surprisingly, [4Fe-4S] Fds present a similar abundance in aerobes as [2Fe-2S] Fds. This bioinformatic study highlights understudied PECs whose structure, stability, and partner specificity should be further characterized.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Campbell</LastName><ForeName>Ian J</ForeName><Initials>IJ</Initials><AffiliationInfo><Affiliation>Biochemistry and Cell Biology Graduate Program, Rice University, Houston, TX, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bennett</LastName><ForeName>George N</ForeName><Initials>GN</Initials><AffiliationInfo><Affiliation>Department of BioSciences, Rice University, Houston, TX, United States.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Silberg</LastName><ForeName>Jonathan J</ForeName><Initials>JJ</Initials><AffiliationInfo><Affiliation>Department of BioSciences, Rice University, Houston, TX, United States.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Bioengineering, Rice University Houston, TX, United States.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>80NSSC18M0093</GrantID><Acronym>ImNASA</Acronym><Agency>Intramural NASA</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>08</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Energy Res</MedlineTA><NlmUniqueID>101638683</NlmUniqueID><ISSNLinking>2296-598X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">electron transfer</Keyword><Keyword MajorTopicYN="N">evolution</Keyword><Keyword MajorTopicYN="N">ferredoxin</Keyword><Keyword MajorTopicYN="N">flavin mononucleotide</Keyword><Keyword MajorTopicYN="N">flavodoxin</Keyword><Keyword MajorTopicYN="N">iron-sulfur cluster</Keyword><Keyword MajorTopicYN="N">oxidative stress</Keyword><Keyword MajorTopicYN="N">oxidoreductase</Keyword></KeywordList><CoiStatement>Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>26</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32095484</ArticleId><ArticleId IdType="doi">10.3389/fenrg.2019.00079</ArticleId><ArticleId IdType="pmc">PMC7039249</ArticleId><ArticleId IdType="mid">NIHMS1553086</ArticleId></ArticleIdList><pmc-dir>nihms</pmc-dir>
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