ArticleGenome biology2004
Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.
Article in Genome biology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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77 citing papers in PubMed, 40 citations in OpenAlex.
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- Biochemical and structural characterization of the BioZ enzyme engaged in bacterial biotin synthesis pathway.Nature communications · 2021Article
- Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris.The ISME journal · 2020Article
- Comparative Genomics Guides Elucidation of Vitamin BApplied and environmental microbiology · 2020Article
- Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China.International journal of environmental research and public health · 2019Article
- TheInfection and immunity · 2019Article
- Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.Acta crystallographica. Section D, Structural biology · 2019Article
- Function of Biohydrogen Metabolism and Related Microbial Communities in Environmental Bioremediation.Frontiers in microbiology · 2019Review
- Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide.Scientific reports · 2017Article
- Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes.MicrobiologyOpen · 2017Article
- Long-Range Interactions in Riboswitch Control of Gene Expression.Annual review of biophysics · 2017Review
- Contribution of riboflavin supply pathways toGut pathogens · 2017Article
- Different Types of Dietary Fibers Trigger Specific Alterations in Composition and Predicted Functions of Colonic Bacterial Communities in BALB/c Mice.Frontiers in microbiology · 2017Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRelatively 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.
resultsIn 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.
conclusionsPhylogenetically 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 in large-scale functional genomic characterization of Desulfovibrio species will provide a unique opportunity to test and expand our predictions.
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