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Title: Reconstruction Of Regulatory And Metabolic Pathways InMetal-Reducing delta-Proteobacteria

Reconstruction Of Regulatory And Metabolic Pathways InMetal-Reducing delta-Proteobacteria 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. In the genomes of delta-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. Phylogenetically diverse delta-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 more » in large-scale functional genomic characterization of Desulfovibrio species will provide a unique opportunity to test and expand our predictions. « less
Authors: ; ; ; ;
Publication Date:
OSTI Identifier:OSTI ID: 859740
Report Number(s):LBNL--57935
R&D Project: VGTLID; BnR: KP1102010; TRN: US200524%%31
DOE Contract Number:DE-AC02-05CH11231
Resource Type:Journal Article
Resource Relation:Journal Name: Genome Biology; Journal Volume: 5; Journal Issue: 11; Related Information: Journal Publication Date: 10/22/2004
Research Org:Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
Sponsoring Org:USDOE Director. Office of Science. Office of Biological andEnvironmental Research; Howard Hughes Medical Institute 55000309, RussianFund of Basic Research 04-04-49361, Russian Academy ofScience
Country of Publication:United States
Language:English
Subject: 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; AVAILABILITY; BACTERIA; BIOLOGICAL PATHWAYS; BIOSYNTHESIS; DESULFOVIBRIO; DETECTION; FUNCTIONALS; GENES; GENETICS; HOMEOSTASIS; METABOLISM; PHYSIOLOGY; SPECIFICITY; TRANSCRIPTION FACTORS Evolution Microbiology and parasitology Bioinformatics