Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Nov 20;9(11):e113714.
doi: 10.1371/journal.pone.0113714. eCollection 2014.

Comparative Genomics of Transcriptional Regulation of Methionine Metabolism in Proteobacteria

Affiliations
Free PMC article

Comparative Genomics of Transcriptional Regulation of Methionine Metabolism in Proteobacteria

Semen A Leyn et al. PLoS One. .
Free PMC article

Abstract

Methionine metabolism and uptake genes in Proteobacteria are controlled by a variety of RNA and DNA regulatory systems. We have applied comparative genomics to reconstruct regulons for three known transcription factors, MetJ, MetR, and SahR, and three known riboswitch motifs, SAH, SAM-SAH, and SAM_alpha, in ∼ 200 genomes from 22 taxonomic groups of Proteobacteria. We also identified two novel regulons: a SahR-like transcription factor SamR controlling various methionine biosynthesis genes in the Xanthomonadales group, and a potential RNA regulatory element with terminator-antiterminator mechanism controlling the metX or metZ genes in beta-proteobacteria. For each analyzed regulator we identified the core, taxon-specific and genome-specific regulon members. By analyzing the distribution of these regulators in bacterial genomes and by comparing their regulon contents we elucidated possible evolutionary scenarios for the regulation of the methionine metabolism genes in Proteobacteria.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Methionine metabolism and its conserved regulation in Proteobacteria.
Genes encoding enzymes for respective reactions are shown in boxes. The Enzyme Commission numbers (EC numbers) of these reactions are shown. Genes encoding transporters of methionine, methylmethionine, and methylthioribose are shown in rounded boxes. Alternative isoenzymes or transporters are shown in different boxes attached to the same arrow. Core regulon members for TFs and riboswitches are shown by colored circles and squares, respectively. The taxonomic distributions of these regulatory interactions are shown in Figure 7.
Figure 2
Figure 2. Conservation of regulatory interactions in the reconstructed MetJ regulons.
The core regulon, taxon- and genome-specific regulon members are highlighted and listed along with their average conservation scores and functional annotations in Table S2.
Figure 3
Figure 3. Conservation of regulatory interactions in the reconstructed MetR regulons.
The core regulon, taxon- and genome-specific regulon members are highlighted and listed along with their average conservation scores and functional annotations in Table S2.
Figure 4
Figure 4. Conservation of regulatory interactions in the reconstructed SahR regulons.
The core regulon, taxon- and genome-specific regulon members are highlighted and listed along with their average conservation scores and functional annotations in Table S2.
Figure 5
Figure 5. Conservation of regulatory interactions in the reconstructed SAH riboswitch regulons.
The core regulon, taxon- and genome-specific regulon members are highlighted and listed along with their average conservation scores and functional annotations in Table S2.
Figure 6
Figure 6. Conservation of regulatory interactions in the reconstructed SAM_alpha riboswitch regulons.
The core regulon, taxon- and genome-specific regulon members are highlighted and listed along with their average conservation scores and functional annotations in Table S2.
Figure 7
Figure 7. Distribution of regulatory interactions for core members of methionine regulons in Proteobacteria.
The presence or absence of gene orthologs in at least one studied genome in a taxonomic group is shown by light green or gray background, respectively. Regulation of at least one gene ortholog within each taxonomic group is shown by colored circles and squares as in Figure 1.
Figure 8
Figure 8. Alternative secondary structures of candidate metXZ RNA element.
Regions 1–6 shown in yellow boxes are conserved sequences found in the multiple alignment of leader regions of 34 metX and metZ genes from β-proteobacteria (Figure S2). In the consensus RNA sequence, N denotes any nucleotide, and M stands for A or C. Possible secondary structures formed by the interaction between the conserved regions are shown by yellow lines.

Similar articles

See all similar articles

Cited by 7 articles

See all "Cited by" articles

References

    1. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS (2004) Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res 32: 3340–3353. - PMC - PubMed
    1. Novichkov PS, Li X, Kuehl JV, Deutschbauer AM, Arkin AP, et al. (2014) Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environ Microbiol 16: 1–8. - PubMed
    1. Liu M, Prakash C, Nauta A, Siezen RJ, Francke C (2012) Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria. J Bacteriol 194: 3522–3533. - PMC - PubMed
    1. Rowbury RJ, Woods DD (1964) O-Succinylhomoserine as an Intermediate in the Synthesis of Cystathionine by Escherichia coli . J Gen Microbiol 36: 341–358. - PubMed
    1. Foglino M, Borne F, Bally M, Ball G, Patte JC (1995) A direct sulfhydrylation pathway is used for methionine biosynthesis in Pseudomonas aeruginosa . Microbiology 141 (Pt 2): 431–439. - PubMed

Publication types

MeSH terms

Grant support

This research was supported by the Russian Science Foundation via grants 14-14-00289 (to S.A.L and D.A.R.) and 14-24-00155 (to I.A.S. and M.S.G.). This research was also partially supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), and U.S. Department of Energy (DOE), and is a contribution of the Pacific Northwest National Laboratory (PNNL) Foundational Scientific Focus Area. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Feedback