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

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 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.

Conclusions: 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 in large-scale functional genomic characterization of Desulfovibrio species will provide a unique opportunity to test and expand our predictions.

Figure 1

Genomic organization of the biotin biosynthetic genes and regulatory elements. DV (Desulfovibrio vulgaris); DD (Desulfovibrio desulfuricans G20); GM (Geobacter metallireducens); GS (Geobacter sulfurreducens PCA); DA (Desulfuromonas species); DP (Desulfotalea psychrophila).

Figure 2

Genomic organization of the thiamin biosynthetic genes and regulatory THI-elements (yellow structures). See Figure 1 legend for abbreviations.

Figure 3

Genomic organization of the cobalamin biosynthetic genes and regulatory B12-elements (yellow cloverleaf-type structures). Genes of the first part of the pathway, involved in the corrin ring synthesis are shown as yellow arrows, the genes required for the attachment of the aminopropanol arm and assembly of the nucleotide loop in vitamin B₁₂ are in green. Cobalt transporters and chelatases used for the insertion of cobalt ions into the corrin ring are shown in pink and orange, respectively. ABC transport systems for vitamin B₁₂ are shown in blue. See Figure 1 legend for abbreviations.

Figure 4

Genomic organization of the methionine biosynthetic genes and regulatory S-boxes (yellow cloverleaf-type structures). See Figure 1 legend for abbreviations.

Figure 5

Genomic organization of the predicted iron-regulated genes and FUR-binding sites (small black rectangles). *Name introduced in this study. See Figure 1 legend for abbreviations.

Figure 6

Genomic organization of the nickel-regulated genes and NikR-binding sites (small blue arrows). See Figure 1 legend for abbreviations.

Figure 7

Genomic organization of predicted zinc ABC transporters and ZUR-binding sites. The black oval and blue box represent two different types of ZUR-binding site. See Figure 1 legend for abbreviations.

Figure 8

Genomic organization of predicted molybdate ABC transporters and ModE-binding sites (small ovals). The black and blue ovals represent two different types of ModE-binding site. See Figure 1 legend for abbreviations.

Figure 9

Genomic organization of genes involved in oxidative stress response. Dots of various colors represent predicted PerR-binding sites with different consensus sequences. See Figure 1 legend for abbreviations.

Figure 10

Maximum-likelihood phylogenetic tree of the FUR/ZUR/PerR family of transcriptional regulators. Consensus sequences of binding sites predicted in this study are underlined. See Figure 1 legend for abbreviations.

Figure 11

Pairwise sequence alignment of upstream regions of the perR-rbr-roo operons from Geobacter species. Conserved palindromic signal, that is the candidate PerR-box, is highlighted in gray. Predicted SD-boxes and start codons of the perR genes are in bold. Predicted -10 and -35 promoter boxes are underlined. *Conserved position of alignment. See Figure 1 legend for abbreviations.

Figure 12

Genomic organization of genes predicted to be regulated by two transcription factors from the CRP/FNR-family. Black circles denote operators for the CO-responsive regulator CooA. Blue circles and squares denote predicted sites of the hypothetical transcriptional factor HcpR with two different consensus sequences, respectively. w, HcpR site with a weak score; ..., a set of gene names that are not shown. See Figure 1 legend for abbreviations.

Figure 13

Pairwise sequence alignment of upstream regions of the predicted HcpR-regulated operons from Desulfovibrio species. (a) sat; (b) apsAB; (c) 206515-206516. Candidate HcpR sites are highlighted in gray. Predicted SD-boxes and start codons of the first genes in the operons are in bold. Predicted '-10' and '-35' promoter boxes are underlined. *Conserved position of alignment. See Figure 1 legend for abbreviations.