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Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria
BACKGROUND: Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of complete finished or draft-quality genome sequences for seven representatives allowed us to investigate the geneti...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2004
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC545781/ https://www.ncbi.nlm.nih.gov/pubmed/15535866 http://dx.doi.org/10.1186/gb-2004-5-11-r90 |
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author | Rodionov, Dmitry A Dubchak, Inna Arkin, Adam Alm, Eric Gelfand, Mikhail S |
author_facet | Rodionov, Dmitry A Dubchak, Inna Arkin, Adam Alm, Eric Gelfand, Mikhail S |
author_sort | Rodionov, Dmitry A |
collection | PubMed |
description | BACKGROUND: Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of complete finished or draft-quality genome sequences for seven representatives allowed us to investigate the genetic and regulatory factors in a number of key pathways involved in the biosynthesis of building blocks and cofactors, metal-ion homeostasis, stress response, and energy metabolism using a combination of regulatory sequence detection and analysis of genomic context. RESULTS: In the genomes of δ-proteobacteria, we identified candidate binding sites for four regulators of known specificity (BirA, CooA, HrcA, sigma-32), four types of metabolite-binding riboswitches (RFN-, THI-, B12-elements and S-box), and new binding sites for the FUR, ModE, NikR, PerR, and ZUR transcription factors, as well as for the previously uncharacterized factors HcpR and LysX. After reconstruction of the corresponding metabolic pathways and regulatory interactions, we identified possible functions for a large number of previously uncharacterized genes covering a wide range of cellular functions. CONCLUSIONS: Phylogenetically diverse δ-proteobacteria appear to have homologous regulatory components. This study for the first time demonstrates the adaptability of the comparative genomic approach to de novo reconstruction of a regulatory network in a poorly studied taxonomic group of bacteria. Recent efforts in large-scale functional genomic characterization of Desulfovibrio species will provide a unique opportunity to test and expand our predictions. |
format | Text |
id | pubmed-545781 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2004 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-5457812005-01-27 Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria Rodionov, Dmitry A Dubchak, Inna Arkin, Adam Alm, Eric Gelfand, Mikhail S Genome Biol Research BACKGROUND: Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of complete finished or draft-quality genome sequences for seven representatives allowed us to investigate the genetic and regulatory factors in a number of key pathways involved in the biosynthesis of building blocks and cofactors, metal-ion homeostasis, stress response, and energy metabolism using a combination of regulatory sequence detection and analysis of genomic context. RESULTS: In the genomes of δ-proteobacteria, we identified candidate binding sites for four regulators of known specificity (BirA, CooA, HrcA, sigma-32), four types of metabolite-binding riboswitches (RFN-, THI-, B12-elements and S-box), and new binding sites for the FUR, ModE, NikR, PerR, and ZUR transcription factors, as well as for the previously uncharacterized factors HcpR and LysX. After reconstruction of the corresponding metabolic pathways and regulatory interactions, we identified possible functions for a large number of previously uncharacterized genes covering a wide range of cellular functions. CONCLUSIONS: Phylogenetically diverse δ-proteobacteria appear to have homologous regulatory components. This study for the first time demonstrates the adaptability of the comparative genomic approach to de novo reconstruction of a regulatory network in a poorly studied taxonomic group of bacteria. Recent efforts in large-scale functional genomic characterization of Desulfovibrio species will provide a unique opportunity to test and expand our predictions. BioMed Central 2004 2004-10-22 /pmc/articles/PMC545781/ /pubmed/15535866 http://dx.doi.org/10.1186/gb-2004-5-11-r90 Text en Copyright © 2004 Rodionov et al.; licensee BioMed Central Ltd. |
spellingShingle | Research Rodionov, Dmitry A Dubchak, Inna Arkin, Adam Alm, Eric Gelfand, Mikhail S Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria |
title | Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria |
title_full | Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria |
title_fullStr | Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria |
title_full_unstemmed | Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria |
title_short | Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria |
title_sort | reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC545781/ https://www.ncbi.nlm.nih.gov/pubmed/15535866 http://dx.doi.org/10.1186/gb-2004-5-11-r90 |
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