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Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae)
BACKGROUND: Gamma-proteobacteria, such as Escherichia coli, can use a variety of respiratory substrates employing numerous aerobic and anaerobic respiratory systems controlled by multiple transcription regulators. Thus, in E. coli, global control of respiration is mediated by four transcription fact...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805755/ https://www.ncbi.nlm.nih.gov/pubmed/17313674 http://dx.doi.org/10.1186/1471-2164-8-54 |
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author | Ravcheev, Dmitry A Gerasimova, Anna V Mironov, Andrey A Gelfand, Mikhail S |
author_facet | Ravcheev, Dmitry A Gerasimova, Anna V Mironov, Andrey A Gelfand, Mikhail S |
author_sort | Ravcheev, Dmitry A |
collection | PubMed |
description | BACKGROUND: Gamma-proteobacteria, such as Escherichia coli, can use a variety of respiratory substrates employing numerous aerobic and anaerobic respiratory systems controlled by multiple transcription regulators. Thus, in E. coli, global control of respiration is mediated by four transcription factors, Fnr, ArcA, NarL and NarP. However, in other Gamma-proteobacteria the composition of global respiration regulators may be different. RESULTS: In this study we applied a comparative genomic approach to the analysis of three global regulatory systems, Fnr, ArcA and NarP. These systems were studied in available genomes containing these three regulators, but lacking NarL. So, we considered several representatives of Pasteurellaceae, Vibrionaceae and Yersinia spp. As a result, we identified new regulon members, functioning in respiration, central metabolism (glycolysis, gluconeogenesis, pentose phosphate pathway, citrate cicle, metabolism of pyruvate and lactate), metabolism of carbohydrates and fatty acids, transcriptional regulation and transport, in particular: the ATP synthase operon atpIBEFHAGCD, Na(+)-exporting NADH dehydrogenase operon nqrABCDEF, the D-amino acids dehydrogenase operon dadAX. Using an extension of the comparative technique, we demonstrated taxon-specific changes in regulatory interactions and predicted taxon-specific regulatory cascades. CONCLUSION: A comparative genomic technique was applied to the analysis of global regulation of respiration in ten gamma-proteobacterial genomes. Three structurally different but functionally related regulatory systems were described. A correlation between the regulon size and the position of a transcription factor in regulatory cascades was observed: regulators with larger regulons tend to occupy top positions in the cascades. On the other hand, there is no obvious link to differences in the species' lifestyles and metabolic capabilities. |
format | Text |
id | pubmed-1805755 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-18057552007-03-01 Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) Ravcheev, Dmitry A Gerasimova, Anna V Mironov, Andrey A Gelfand, Mikhail S BMC Genomics Research Article BACKGROUND: Gamma-proteobacteria, such as Escherichia coli, can use a variety of respiratory substrates employing numerous aerobic and anaerobic respiratory systems controlled by multiple transcription regulators. Thus, in E. coli, global control of respiration is mediated by four transcription factors, Fnr, ArcA, NarL and NarP. However, in other Gamma-proteobacteria the composition of global respiration regulators may be different. RESULTS: In this study we applied a comparative genomic approach to the analysis of three global regulatory systems, Fnr, ArcA and NarP. These systems were studied in available genomes containing these three regulators, but lacking NarL. So, we considered several representatives of Pasteurellaceae, Vibrionaceae and Yersinia spp. As a result, we identified new regulon members, functioning in respiration, central metabolism (glycolysis, gluconeogenesis, pentose phosphate pathway, citrate cicle, metabolism of pyruvate and lactate), metabolism of carbohydrates and fatty acids, transcriptional regulation and transport, in particular: the ATP synthase operon atpIBEFHAGCD, Na(+)-exporting NADH dehydrogenase operon nqrABCDEF, the D-amino acids dehydrogenase operon dadAX. Using an extension of the comparative technique, we demonstrated taxon-specific changes in regulatory interactions and predicted taxon-specific regulatory cascades. CONCLUSION: A comparative genomic technique was applied to the analysis of global regulation of respiration in ten gamma-proteobacterial genomes. Three structurally different but functionally related regulatory systems were described. A correlation between the regulon size and the position of a transcription factor in regulatory cascades was observed: regulators with larger regulons tend to occupy top positions in the cascades. On the other hand, there is no obvious link to differences in the species' lifestyles and metabolic capabilities. BioMed Central 2007-02-21 /pmc/articles/PMC1805755/ /pubmed/17313674 http://dx.doi.org/10.1186/1471-2164-8-54 Text en Copyright © 2007 Ravcheev et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Ravcheev, Dmitry A Gerasimova, Anna V Mironov, Andrey A Gelfand, Mikhail S Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) |
title | Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) |
title_full | Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) |
title_fullStr | Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) |
title_full_unstemmed | Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) |
title_short | Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) |
title_sort | comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (enterobacteriaceae, pasteurellaceae, vibrionaceae) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805755/ https://www.ncbi.nlm.nih.gov/pubmed/17313674 http://dx.doi.org/10.1186/1471-2164-8-54 |
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