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Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions.

Balhana RJ, Singla A, Sikder MH, Withers M, Kendall SL - BMC Genomics (2015)

Bottom Line: We examined genomic contexts of 663 of the conserved TFTRs and observed that the majority of TFTRs are separated by 200 bp or less from divergently oriented genes.Analyses of divergent genes indicated that the TFTRs control diverse biochemical functions not limited to efflux pumps.TFTRs typically bind to palindromic motifs and we identified 11 highly significant novel motifs in the upstream regions of divergently oriented TFTRs.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology and Pathogen Biology, The Royal Veterinary College, Royal College street, Camden, London, NW1 OTU, UK. r.balhana@surrey.ac.uk.

ABSTRACT

Background: Mycobacteria inhabit diverse niches and display high metabolic versatility. They can colonise both humans and animals and are also able to survive in the environment. In order to succeed, response to environmental cues via transcriptional regulation is required. In this study we focused on the TetR family of transcriptional regulators (TFTRs) in mycobacteria.

Results: We used InterPro to classify the entire complement of transcriptional regulators in 10 mycobacterial species and these analyses showed that TFTRs are the most abundant family of regulators in all species. We identified those TFTRs that are conserved across all species analysed and those that are unique to the pathogens included in the analysis. We examined genomic contexts of 663 of the conserved TFTRs and observed that the majority of TFTRs are separated by 200 bp or less from divergently oriented genes. Analyses of divergent genes indicated that the TFTRs control diverse biochemical functions not limited to efflux pumps. TFTRs typically bind to palindromic motifs and we identified 11 highly significant novel motifs in the upstream regions of divergently oriented TFTRs. The C-terminal ligand binding domain from the TFTR complement in M. tuberculosis showed great diversity in amino acid sequence but with an overall architecture common to other TFTRs.

Conclusion: This study suggests that mycobacteria depend on TFTRs for the transcriptional control of a number of metabolic functions yet the physiological role of the majority of these regulators remain unknown.

No MeSH data available.


Related in: MedlinePlus

Functional classification of the products encoded by the divergent neighbouring genes. Genes that were divergently oriented to TFTRs with an intergenic region of 200 bp or less in M. tuberculosis, M. marinum, M. avium paratuberculosis and M. smegmatis were analysed as described in the materials and methods. Gene products that were enzymes were classified according to class (EC 1 to EC 6). Non enzymatic products were classified into membrane proteins, other proteins (e.g. transcriptional regulators), and proteins of unassigned function
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Fig4: Functional classification of the products encoded by the divergent neighbouring genes. Genes that were divergently oriented to TFTRs with an intergenic region of 200 bp or less in M. tuberculosis, M. marinum, M. avium paratuberculosis and M. smegmatis were analysed as described in the materials and methods. Gene products that were enzymes were classified according to class (EC 1 to EC 6). Non enzymatic products were classified into membrane proteins, other proteins (e.g. transcriptional regulators), and proteins of unassigned function

Mentions: We examined the functions of the genes divergent to the TFTRs in the six mycobacterial genomes in order to determine the possible functions regulated. We only included those genes that were separated from their divergent TFTRs by 200 bp or less. 340 genes from four different genomes (M. tuberculosis, M. avium paratuberculosis, M. marinum M. ulcerans, M. gilvum and M. smegmatis) were analysed in total. The results are shown in Fig. 4.Fig. 4


Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions.

Balhana RJ, Singla A, Sikder MH, Withers M, Kendall SL - BMC Genomics (2015)

Functional classification of the products encoded by the divergent neighbouring genes. Genes that were divergently oriented to TFTRs with an intergenic region of 200 bp or less in M. tuberculosis, M. marinum, M. avium paratuberculosis and M. smegmatis were analysed as described in the materials and methods. Gene products that were enzymes were classified according to class (EC 1 to EC 6). Non enzymatic products were classified into membrane proteins, other proteins (e.g. transcriptional regulators), and proteins of unassigned function
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4482099&req=5

Fig4: Functional classification of the products encoded by the divergent neighbouring genes. Genes that were divergently oriented to TFTRs with an intergenic region of 200 bp or less in M. tuberculosis, M. marinum, M. avium paratuberculosis and M. smegmatis were analysed as described in the materials and methods. Gene products that were enzymes were classified according to class (EC 1 to EC 6). Non enzymatic products were classified into membrane proteins, other proteins (e.g. transcriptional regulators), and proteins of unassigned function
Mentions: We examined the functions of the genes divergent to the TFTRs in the six mycobacterial genomes in order to determine the possible functions regulated. We only included those genes that were separated from their divergent TFTRs by 200 bp or less. 340 genes from four different genomes (M. tuberculosis, M. avium paratuberculosis, M. marinum M. ulcerans, M. gilvum and M. smegmatis) were analysed in total. The results are shown in Fig. 4.Fig. 4

Bottom Line: We examined genomic contexts of 663 of the conserved TFTRs and observed that the majority of TFTRs are separated by 200 bp or less from divergently oriented genes.Analyses of divergent genes indicated that the TFTRs control diverse biochemical functions not limited to efflux pumps.TFTRs typically bind to palindromic motifs and we identified 11 highly significant novel motifs in the upstream regions of divergently oriented TFTRs.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology and Pathogen Biology, The Royal Veterinary College, Royal College street, Camden, London, NW1 OTU, UK. r.balhana@surrey.ac.uk.

ABSTRACT

Background: Mycobacteria inhabit diverse niches and display high metabolic versatility. They can colonise both humans and animals and are also able to survive in the environment. In order to succeed, response to environmental cues via transcriptional regulation is required. In this study we focused on the TetR family of transcriptional regulators (TFTRs) in mycobacteria.

Results: We used InterPro to classify the entire complement of transcriptional regulators in 10 mycobacterial species and these analyses showed that TFTRs are the most abundant family of regulators in all species. We identified those TFTRs that are conserved across all species analysed and those that are unique to the pathogens included in the analysis. We examined genomic contexts of 663 of the conserved TFTRs and observed that the majority of TFTRs are separated by 200 bp or less from divergently oriented genes. Analyses of divergent genes indicated that the TFTRs control diverse biochemical functions not limited to efflux pumps. TFTRs typically bind to palindromic motifs and we identified 11 highly significant novel motifs in the upstream regions of divergently oriented TFTRs. The C-terminal ligand binding domain from the TFTR complement in M. tuberculosis showed great diversity in amino acid sequence but with an overall architecture common to other TFTRs.

Conclusion: This study suggests that mycobacteria depend on TFTRs for the transcriptional control of a number of metabolic functions yet the physiological role of the majority of these regulators remain unknown.

No MeSH data available.


Related in: MedlinePlus