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Relaxed selection drives a noisy noncoding transcriptome in members of the Mycobacterium tuberculosis complex.

Dinan AM, Tong P, Lohan AJ, Conlon KM, Miranda-CasoLuengo AA, Malone KM, Gordon SV, Loftus BJ - MBio (2014)

Bottom Line: A small number of studies have compared the primary transcriptomes of different bacterial species, but few have compared closely related species with clearly divergent evolutionary histories.We show that a species population history is reflected in its transcriptome and posit relaxed selection as the main driver of an abundance of canonical -10 promoter sites in M. bovis relative to M. marinum.Finally, through comparison of M. bovis and M. tuberculosis, we illustrate that single nucleotide polymorphism (SNP)-driven promoter differences likely underpin many of the transcriptional differences between M. tuberculosis complex lineages.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Cell Biology Centre, The University of Edinburgh, Edinburgh, United Kingdom.

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(A) Pie chart distribution of consensus −10 box motifs detected within the promoters across each TSS class between M. marinum and M. bovis. (B) Comparison of SigA consensus −10 box motif densities along the genomes of both species. Forward strand genes are indicated in purple, and reverse strand genes are in green.
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fig2: (A) Pie chart distribution of consensus −10 box motifs detected within the promoters across each TSS class between M. marinum and M. bovis. (B) Comparison of SigA consensus −10 box motif densities along the genomes of both species. Forward strand genes are indicated in purple, and reverse strand genes are in green.

Mentions: A striking feature of the TSS maps of M. marinum and M. bovis is the divergence in TSS distribution, with M. bovis manifesting a much larger proportion of its assigned TSSs in all categories except the primary TSS (Fig. 1A). Additionally, in marked contrast to the relatively high conservation of pTSSs, other categories displayed an almost complete lack of conservation, with just 50 iTSSs and 49 asTSSs in total shared between the species, based on the best reciprocal alignment of the promoter sequences (see Table S2 in the supplemental material). A comparison of the contributing motifs across the different TSS classes reveals that the elevated distribution of nonprimary TSSs in M. bovis is driven by an expanded representation of −10 box consensus promoters in these classes relative to M. marinum (Fig. 2A).


Relaxed selection drives a noisy noncoding transcriptome in members of the Mycobacterium tuberculosis complex.

Dinan AM, Tong P, Lohan AJ, Conlon KM, Miranda-CasoLuengo AA, Malone KM, Gordon SV, Loftus BJ - MBio (2014)

(A) Pie chart distribution of consensus −10 box motifs detected within the promoters across each TSS class between M. marinum and M. bovis. (B) Comparison of SigA consensus −10 box motif densities along the genomes of both species. Forward strand genes are indicated in purple, and reverse strand genes are in green.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4128351&req=5

fig2: (A) Pie chart distribution of consensus −10 box motifs detected within the promoters across each TSS class between M. marinum and M. bovis. (B) Comparison of SigA consensus −10 box motif densities along the genomes of both species. Forward strand genes are indicated in purple, and reverse strand genes are in green.
Mentions: A striking feature of the TSS maps of M. marinum and M. bovis is the divergence in TSS distribution, with M. bovis manifesting a much larger proportion of its assigned TSSs in all categories except the primary TSS (Fig. 1A). Additionally, in marked contrast to the relatively high conservation of pTSSs, other categories displayed an almost complete lack of conservation, with just 50 iTSSs and 49 asTSSs in total shared between the species, based on the best reciprocal alignment of the promoter sequences (see Table S2 in the supplemental material). A comparison of the contributing motifs across the different TSS classes reveals that the elevated distribution of nonprimary TSSs in M. bovis is driven by an expanded representation of −10 box consensus promoters in these classes relative to M. marinum (Fig. 2A).

Bottom Line: A small number of studies have compared the primary transcriptomes of different bacterial species, but few have compared closely related species with clearly divergent evolutionary histories.We show that a species population history is reflected in its transcriptome and posit relaxed selection as the main driver of an abundance of canonical -10 promoter sites in M. bovis relative to M. marinum.Finally, through comparison of M. bovis and M. tuberculosis, we illustrate that single nucleotide polymorphism (SNP)-driven promoter differences likely underpin many of the transcriptional differences between M. tuberculosis complex lineages.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Cell Biology Centre, The University of Edinburgh, Edinburgh, United Kingdom.

Show MeSH
Related in: MedlinePlus