Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit.
Saved in:
| Title: | Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit. |
|---|---|
| Authors: | Mansfeldt, Cresten B.1, Rowe, Annette R.2, Heavner, Gretchen L. W.1, Zinder, Stephen H.2, Richardson, Ruth E.1 rer26@cornell.edu |
| Source: | Applied & Environmental Microbiology. Oct2014, Vol. 80 Issue 19, p6062-6072. 11p. |
| Subjects: | Antisense DNA, DNA microarrays, Dehalococcoides, Gene expression, Oxidoreductases |
| Abstract: | A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through principal component analysis. The first two principal components separated the experiments into those with slow (1.6 ± 0.6 μ,M Cl~/h)- and fast (22.9 ± 9.6 μM Cl- /h)-respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (n = 53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup and Hym and the formate dehydrogenase-like oxidoreductase (DET0186-DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all Dehalococcoides strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112). [ABSTRACT FROM AUTHOR] |
| Copyright of Applied & Environmental Microbiology is the property of American Society for Microbiology and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
|---|---|
| Header | DbId: egs DbLabel: Engineering Source An: 98386747 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Mansfeldt%2C+Cresten+B%2E%22">Mansfeldt, Cresten B.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Rowe%2C+Annette+R%2E%22">Rowe, Annette R.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Heavner%2C+Gretchen+L%2E+W%2E%22">Heavner, Gretchen L. W.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Zinder%2C+Stephen+H%2E%22">Zinder, Stephen H.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Richardson%2C+Ruth+E%2E%22">Richardson, Ruth E.</searchLink><relatesTo>1</relatesTo><i> rer26@cornell.edu</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Applied+%26+Environmental+Microbiology%22">Applied & Environmental Microbiology</searchLink>. Oct2014, Vol. 80 Issue 19, p6062-6072. 11p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Antisense+DNA%22">Antisense DNA</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+microarrays%22">DNA microarrays</searchLink><br /><searchLink fieldCode="DE" term="%22Dehalococcoides%22">Dehalococcoides</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+expression%22">Gene expression</searchLink><br /><searchLink fieldCode="DE" term="%22Oxidoreductases%22">Oxidoreductases</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through principal component analysis. The first two principal components separated the experiments into those with slow (1.6 ± 0.6 μ,M Cl~/h)- and fast (22.9 ± 9.6 μM Cl- /h)-respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (n = 53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup and Hym and the formate dehydrogenase-like oxidoreductase (DET0186-DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all Dehalococcoides strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112). [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Applied & Environmental Microbiology is the property of American Society for Microbiology and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
| PLink | https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=98386747 |
| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1128/AEM.02130-14 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 11 StartPage: 6062 Subjects: – SubjectFull: Antisense DNA Type: general – SubjectFull: DNA microarrays Type: general – SubjectFull: Dehalococcoides Type: general – SubjectFull: Gene expression Type: general – SubjectFull: Oxidoreductases Type: general Titles: – TitleFull: Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Mansfeldt, Cresten B. – PersonEntity: Name: NameFull: Rowe, Annette R. – PersonEntity: Name: NameFull: Heavner, Gretchen L. W. – PersonEntity: Name: NameFull: Zinder, Stephen H. – PersonEntity: Name: NameFull: Richardson, Ruth E. IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 10 Text: Oct2014 Type: published Y: 2014 Identifiers: – Type: issn-print Value: 00992240 Numbering: – Type: volume Value: 80 – Type: issue Value: 19 Titles: – TitleFull: Applied & Environmental Microbiology Type: main |
| ResultId | 1 |
