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Comparative Study
. 2013 Jun;195(11):2463-73.
doi: 10.1128/JB.00140-13. Epub 2013 Mar 15.

Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus Subtilis

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Free PMC article
Comparative Study

Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus Subtilis

Semen A Leyn et al. J Bacteriol. .
Free PMC article

Abstract

The adaptation of microorganisms to their environment is controlled by complex transcriptional regulatory networks (TRNs), which are still only partially understood even for model species. Genome scale annotation of regulatory features of genes and TRN reconstruction are challenging tasks of microbial genomics. We used the knowledge-driven comparative-genomics approach implemented in the RegPredict Web server to infer TRN in the model Gram-positive bacterium Bacillus subtilis and 10 related Bacillales species. For transcription factor (TF) regulons, we combined the available information from the DBTBS database and the literature with bioinformatics tools, allowing inference of TF binding sites (TFBSs), comparative analysis of the genomic context of predicted TFBSs, functional assignment of target genes, and effector prediction. For RNA regulons, we used known RNA regulatory motifs collected in the Rfam database to scan genomes and analyze the genomic context of new RNA sites. The inferred TRN in B. subtilis comprises regulons for 129 TFs and 24 regulatory RNA families. First, we analyzed 66 TF regulons with previously known TFBSs in B. subtilis and projected them to other Bacillales genomes, resulting in refinement of TFBS motifs and identification of novel regulon members. Second, we inferred motifs and described regulons for 28 experimentally studied TFs with previously unknown TFBSs. Third, we discovered novel motifs and reconstructed regulons for 36 previously uncharacterized TFs. The inferred collection of regulons is available in the RegPrecise database (http://regprecise.lbl.gov/) and can be used in genetic experiments, metabolic modeling, and evolutionary analysis.

Figures

Fig 1
Fig 1
Phylogenetic tree and distribution of TFs in the studied bacteria from the order Bacillales. The hatched bars show total numbers of TFs per genome. The crosshatched bars show numbers of orthologs of B. subtilis TFs. The tree was built using phylogenetic analysis of the concatenated 16S-23S rRNA sequences from the studied genomes.
Fig 2
Fig 2
Novel reconstructed regulons for rhamnose metabolism in Bacillales. The genes in each regulated operon are shown by arrows; TF genes are in black, ABC transporters are in dark gray, catabolic enzymes and other genes present in B. subtilis are in light gray, and genes lacking orthologs in B. subtilis are in white. TF binding sites are shown by circles (RhaR) (A), triangles (RhgR) (B), and squares (RmgR) (C). Regulons upregulated by growth on type I rhamnogalacturonan are marked with asterisks.
Fig 3
Fig 3
Interconnections between inferred TF regulons for inositol metabolism in the Bacillales. Genes from each regulon are shown by arrows; TF genes are in blue and black, predicted inositol transporters are in pink, and inositol dehydrogenases are in green; orthologous genes are marked by the same letter inside arrows. TF binding sites of IolR, IolR1, and IolR2 are shown by triangles, circles, and squares, respectively. The functional roles of the regulated genes in B. subtilis are as follows: iolS, oxidoreductase; iolA, methylmalonate-semialdehyde dehydrogenase; iolB, 5-deoxy-glucuronate isomerase; iolC, 5-keto-2-deoxygluconokinase; iolD, 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase; iolE, inosose dehydratase; iolF, myo-inositol transporter; iolG, myo-inositol 2-dehydrogenase; iolH, putative sugar-phosphate epimerase; iolI, inosose isomerase; iolJ, 5-keto-2-deoxy-d-gluconate-6 phosphate aldolase; iolX, scyllo-inositol 2-dehydrogenase; yrbE, predicted inositol derivative dehydrogenase.
Fig 4
Fig 4
Regulatory cascades in B. subtilis TRN. TFs are shown as circles. The directions of regulatory interactions are shown by arrows. TF autoregulation is shown by curved arrows.

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