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Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria

Dmitry A Rodionov1*, Inna Dubchak2, Adam Arkin345, Eric Alm3 and Mikhail S Gelfand16

Author Affiliations

1 Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny per. 19, Moscow 127994, Russia

2 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

3 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

4 Howard Hughes Medical Institute, Berkeley, CA 94720, USA

5 University of California, Berkeley, CA 94720, USA

6 State Scientific Center GosniiGenetika, 1st Dorozhny pr. 1, Moscow 117545, Russia

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Genome Biology 2004, 5:R90  doi:10.1186/gb-2004-5-11-r90

Published: 22 October 2004

Abstract

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.