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Mapping of genotype-phenotype diversity among clinical isolates of mycobacterium tuberculosis by sequence-based transcriptional profiling.

Rose G, Cortes T, Comas I, Coscolla M, Gagneux S, Young DB - Genome Biol Evol (2013)

Bottom Line: First, lineage-specific changes in amino acid sequence of transcriptional regulators were associated with alterations in their ability to control gene expression.Second, changes in nucleotide sequence were associated with alteration of promoter activity and generation of novel transcriptional start sites in intergenic regions and within coding sequences.Taken together, these findings advance our understanding of mycobacterial evolution, contribute to a systems level understanding of this important human pathogen, and more broadly demonstrate the application of state-of-the-art techniques to provide novel insight into mechanisms by which intergenic and silent mutations contribute to diversity.

View Article: PubMed Central - PubMed

Affiliation: MRC National Institute for Medical Research, Mill Hill, London, United Kingdom.

ABSTRACT
Genome sequencing has identified an extensive repertoire of single nucleotide polymorphisms among clinical isolates of Mycobacterium tuberculosis, but the extent to which these differences influence phenotypic properties of the bacteria remains to be elucidated. To determine whether these polymorphisms give rise to phenotypic diversity, we have integrated genome data sets with RNA sequencing to assess their impact on the comparative transcriptome profiles of strains belonging to M. tuberculosis Lineages 1 and 2. We observed clear correlations between genotype and transcriptional phenotype. These arose by three mechanisms. First, lineage-specific changes in amino acid sequence of transcriptional regulators were associated with alterations in their ability to control gene expression. Second, changes in nucleotide sequence were associated with alteration of promoter activity and generation of novel transcriptional start sites in intergenic regions and within coding sequences. We show that in some cases this mechanism is expected to generate functionally active truncated proteins involved in innate immune recognition. Finally, genes showing lineage-specific patterns of differential expression not linked directly to primary mutations were characterized by a striking overrepresentation of toxin-antitoxin pairs. Taken together, these findings advance our understanding of mycobacterial evolution, contribute to a systems level understanding of this important human pathogen, and more broadly demonstrate the application of state-of-the-art techniques to provide novel insight into mechanisms by which intergenic and silent mutations contribute to diversity.

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Related in: MedlinePlus

Examples of SNP-associated TSS. For each example, the main panels show total transcriptome profiles for the six strains; insets in the top right show TSS mapping for strain N0145 (Lineage 2) and N0153 (Lineage 1). Lineage-specific SNPs are indicated with an asterisk. (A) Intergenic TSS: Lineage 1 SNP (T 2017560 A) is associated with a new TSS and increased expression of malQ in the respective strains. (B) Internal coding TSS: Lineage 1 SNP (C 2309356 T) within ppm1 is associated with a new TSS and upregulation of ppm1 transcription. A second internal TSS present in all strains also indicated in the TSS mapping inset. (C) Internal coding TSS and 3′ antisense: SNP-associated TSS in 3′ region of umaA in Lineage 1 strains is associated with higher umaA expression and pcaA antisense expression. (D) Internal coding TSS and antisense: SNP within deaD in all Lineage 2 strains is associated with a new TSS and increased antisense transcription. The SNP also creates a -10 consensus on the forward strand; this is associated with a new TSS but has no significant impact on the level of sense transcription.
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evt138-F3: Examples of SNP-associated TSS. For each example, the main panels show total transcriptome profiles for the six strains; insets in the top right show TSS mapping for strain N0145 (Lineage 2) and N0153 (Lineage 1). Lineage-specific SNPs are indicated with an asterisk. (A) Intergenic TSS: Lineage 1 SNP (T 2017560 A) is associated with a new TSS and increased expression of malQ in the respective strains. (B) Internal coding TSS: Lineage 1 SNP (C 2309356 T) within ppm1 is associated with a new TSS and upregulation of ppm1 transcription. A second internal TSS present in all strains also indicated in the TSS mapping inset. (C) Internal coding TSS and 3′ antisense: SNP-associated TSS in 3′ region of umaA in Lineage 1 strains is associated with higher umaA expression and pcaA antisense expression. (D) Internal coding TSS and antisense: SNP within deaD in all Lineage 2 strains is associated with a new TSS and increased antisense transcription. The SNP also creates a -10 consensus on the forward strand; this is associated with a new TSS but has no significant impact on the level of sense transcription.

Mentions: For three of the differentially expressed genes (malQ, Rv3680, and PE_PGRS62), the new TSS was located upstream of the predicted translational start, either within an intergenic region or the adjacent gene (fig. 3A). The remaining six new TSSs (umaA, mgtA, Rv0724A, ppm1, Rv2765, and spoU) were located within the differentially expressed gene itself and, if translated, would give rise to truncated protein products. In some cases, truncated proteins may retain biological function. Ppm1 (Rv2051c) is a bifunctional protein created by fusion of polyprenyl phosphomannose synthase and apolipoprotein N-acyltransferase activities (Gurcha et al. 2002). The C 2309356 T SNP in Lineage 1 is associated with a novel internal transcript that includes the intact C-terminal polyprenyl phosphomannose synthase domain and at the same time introduces a T467I mutation that is predicted by SIFT analysis to impair the function of the N-terminal N-acyl transferase domain (fig. 3B). A second internal ppm1 TSS is present in all strains at position 2309159; the resulting transcript again provides the option of dissociating the two enzymatic activities.Fig. 3.—


Mapping of genotype-phenotype diversity among clinical isolates of mycobacterium tuberculosis by sequence-based transcriptional profiling.

Rose G, Cortes T, Comas I, Coscolla M, Gagneux S, Young DB - Genome Biol Evol (2013)

Examples of SNP-associated TSS. For each example, the main panels show total transcriptome profiles for the six strains; insets in the top right show TSS mapping for strain N0145 (Lineage 2) and N0153 (Lineage 1). Lineage-specific SNPs are indicated with an asterisk. (A) Intergenic TSS: Lineage 1 SNP (T 2017560 A) is associated with a new TSS and increased expression of malQ in the respective strains. (B) Internal coding TSS: Lineage 1 SNP (C 2309356 T) within ppm1 is associated with a new TSS and upregulation of ppm1 transcription. A second internal TSS present in all strains also indicated in the TSS mapping inset. (C) Internal coding TSS and 3′ antisense: SNP-associated TSS in 3′ region of umaA in Lineage 1 strains is associated with higher umaA expression and pcaA antisense expression. (D) Internal coding TSS and antisense: SNP within deaD in all Lineage 2 strains is associated with a new TSS and increased antisense transcription. The SNP also creates a -10 consensus on the forward strand; this is associated with a new TSS but has no significant impact on the level of sense transcription.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3814196&req=5

evt138-F3: Examples of SNP-associated TSS. For each example, the main panels show total transcriptome profiles for the six strains; insets in the top right show TSS mapping for strain N0145 (Lineage 2) and N0153 (Lineage 1). Lineage-specific SNPs are indicated with an asterisk. (A) Intergenic TSS: Lineage 1 SNP (T 2017560 A) is associated with a new TSS and increased expression of malQ in the respective strains. (B) Internal coding TSS: Lineage 1 SNP (C 2309356 T) within ppm1 is associated with a new TSS and upregulation of ppm1 transcription. A second internal TSS present in all strains also indicated in the TSS mapping inset. (C) Internal coding TSS and 3′ antisense: SNP-associated TSS in 3′ region of umaA in Lineage 1 strains is associated with higher umaA expression and pcaA antisense expression. (D) Internal coding TSS and antisense: SNP within deaD in all Lineage 2 strains is associated with a new TSS and increased antisense transcription. The SNP also creates a -10 consensus on the forward strand; this is associated with a new TSS but has no significant impact on the level of sense transcription.
Mentions: For three of the differentially expressed genes (malQ, Rv3680, and PE_PGRS62), the new TSS was located upstream of the predicted translational start, either within an intergenic region or the adjacent gene (fig. 3A). The remaining six new TSSs (umaA, mgtA, Rv0724A, ppm1, Rv2765, and spoU) were located within the differentially expressed gene itself and, if translated, would give rise to truncated protein products. In some cases, truncated proteins may retain biological function. Ppm1 (Rv2051c) is a bifunctional protein created by fusion of polyprenyl phosphomannose synthase and apolipoprotein N-acyltransferase activities (Gurcha et al. 2002). The C 2309356 T SNP in Lineage 1 is associated with a novel internal transcript that includes the intact C-terminal polyprenyl phosphomannose synthase domain and at the same time introduces a T467I mutation that is predicted by SIFT analysis to impair the function of the N-terminal N-acyl transferase domain (fig. 3B). A second internal ppm1 TSS is present in all strains at position 2309159; the resulting transcript again provides the option of dissociating the two enzymatic activities.Fig. 3.—

Bottom Line: First, lineage-specific changes in amino acid sequence of transcriptional regulators were associated with alterations in their ability to control gene expression.Second, changes in nucleotide sequence were associated with alteration of promoter activity and generation of novel transcriptional start sites in intergenic regions and within coding sequences.Taken together, these findings advance our understanding of mycobacterial evolution, contribute to a systems level understanding of this important human pathogen, and more broadly demonstrate the application of state-of-the-art techniques to provide novel insight into mechanisms by which intergenic and silent mutations contribute to diversity.

View Article: PubMed Central - PubMed

Affiliation: MRC National Institute for Medical Research, Mill Hill, London, United Kingdom.

ABSTRACT
Genome sequencing has identified an extensive repertoire of single nucleotide polymorphisms among clinical isolates of Mycobacterium tuberculosis, but the extent to which these differences influence phenotypic properties of the bacteria remains to be elucidated. To determine whether these polymorphisms give rise to phenotypic diversity, we have integrated genome data sets with RNA sequencing to assess their impact on the comparative transcriptome profiles of strains belonging to M. tuberculosis Lineages 1 and 2. We observed clear correlations between genotype and transcriptional phenotype. These arose by three mechanisms. First, lineage-specific changes in amino acid sequence of transcriptional regulators were associated with alterations in their ability to control gene expression. Second, changes in nucleotide sequence were associated with alteration of promoter activity and generation of novel transcriptional start sites in intergenic regions and within coding sequences. We show that in some cases this mechanism is expected to generate functionally active truncated proteins involved in innate immune recognition. Finally, genes showing lineage-specific patterns of differential expression not linked directly to primary mutations were characterized by a striking overrepresentation of toxin-antitoxin pairs. Taken together, these findings advance our understanding of mycobacterial evolution, contribute to a systems level understanding of this important human pathogen, and more broadly demonstrate the application of state-of-the-art techniques to provide novel insight into mechanisms by which intergenic and silent mutations contribute to diversity.

Show MeSH
Related in: MedlinePlus