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Noncoding RNA in Mycobacteria

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  • Authors: Kristine B. Arnvig1, Teresa Cortes2, Douglas B. Young3
  • Editors: Graham F. Hatfull4, William R. Jacobs Jr.5
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: National Institute for Medical Research, Mycobacterial Research Division, London, NW7 1AA, United Kingdom; 2: National Institute for Medical Research, Mycobacterial Research Division, London, NW7 1AA, United Kingdom; 3: National Institute for Medical Research, Mycobacterial Research Division, London, NW7 1AA, United Kingdom; 4: University of Pittsburgh, Pittsburgh, PA; 5: Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, NY
    • Source: microbiolspec March 2014 vol. 2 no. 2 doi:10.1128/microbiolspec.MGM2-0029-2013
  • Received 17 August 2013 Accepted 25 September 2013 Published 14 March 2014
  • KB Arnvig, [email protected]
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  • Abstract:

    Efforts to understand the molecular basis of mycobacterial gene regulation are dominated by a protein-centric view. However, there is a growing appreciation that noncoding RNA, i.e., RNA that is not translated, plays a role in a wide variety of molecular mechanisms. Noncoding RNA comprises rRNA, tRNA, 4.5S RNA, RnpB, and transfer-messenger RNA, as well as a vast population of regulatory RNA, often dubbed “the dark matter of gene regulation.” The regulatory RNA species comprise 5′ and 3′ untranslated regions and a rapidly expanding category of transcripts with the ability to base-pair with mRNAs or to interact with proteins. Regulatory RNA plays a central role in the bacterium's response to changes in the environment, and in this article we review emerging information on the presence and abundance of different types of noncoding RNA in mycobacteria.

  • Citation: Arnvig K, Cortes T, Young D. 2014. Noncoding RNA in Mycobacteria. Microbiol Spectrum 2(2):MGM2-0029-2013. doi:10.1128/microbiolspec.MGM2-0029-2013.

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/content/journal/microbiolspec/10.1128/microbiolspec.MGM2-0029-2013
2014-03-14
2019-06-16

Abstract:

Efforts to understand the molecular basis of mycobacterial gene regulation are dominated by a protein-centric view. However, there is a growing appreciation that noncoding RNA, i.e., RNA that is not translated, plays a role in a wide variety of molecular mechanisms. Noncoding RNA comprises rRNA, tRNA, 4.5S RNA, RnpB, and transfer-messenger RNA, as well as a vast population of regulatory RNA, often dubbed “the dark matter of gene regulation.” The regulatory RNA species comprise 5′ and 3′ untranslated regions and a rapidly expanding category of transcripts with the ability to base-pair with mRNAs or to interact with proteins. Regulatory RNA plays a central role in the bacterium's response to changes in the environment, and in this article we review emerging information on the presence and abundance of different types of noncoding RNA in mycobacteria.

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Noncoding RNA in Mycobacteria
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Citation: Arnvig K, Cortes T, Young D. 2014. Noncoding rna in mycobacteria. microbiolspec 2(2): doi:10.1128/microbiolspec.MGM2-0029-2013
/content/microbiolspec/10.1128/microbiolspec.MGM2-0029-2013.fig1
FIGURE 1
Venn diagram illustrating how the (nomenclature of) different types of ncRNA and regulatory RNAs overlap and, in particular, how sRNAs can be assigned to more than one category. The sRNA subcategories shown are sRNA (purely regulatory function), sRNA (dual function, i.e., regulatory potential as well as encoding small peptide), sRNA (purely coding, i.e., no function as ribo-regulator). Thus, sRNAs can be coding or noncoding, regulatory or not regulatory. Figure modified from reference 15 .
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FIGURE 1

Venn diagram illustrating how the (nomenclature of) different types of ncRNA and regulatory RNAs overlap and, in particular, how sRNAs can be assigned to more than one category. The sRNA subcategories shown are sRNA (purely regulatory function), sRNA (dual function, i.e., regulatory potential as well as encoding small peptide), sRNA (purely coding, i.e., no function as ribo-regulator). Thus, sRNAs can be coding or noncoding, regulatory or not regulatory. Figure modified from reference 15 .

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FIGURE 2
Transcription termination in mycobacteria. The top panel illustrates the consensus sequence and structure of the mycobacterial terminator, TRIT (tuberculosis rho-independent terminator). TRIT is a novel rho-independent terminator with high sequence conservation identified in and specific for mycobacteria ( 29 ). The bottom panel illustrates the expression of two converging genes in , according to RNA-seq and visualized in the Artemis genome browser; blue represents expression from the forward strand (), and red represents expression from the reverse strand (); the height of the trace represents the normalized expression level (reads) over the entire region. The traces demonstrate the termination efficiency exerted by TRIT between the two converging genes.
microbiolspec/2/2/MGM2-0029-2013-fig2_thmb.gif
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FIGURE 2

Transcription termination in mycobacteria. The top panel illustrates the consensus sequence and structure of the mycobacterial terminator, TRIT (tuberculosis rho-independent terminator). TRIT is a novel rho-independent terminator with high sequence conservation identified in and specific for mycobacteria ( 29 ). The bottom panel illustrates the expression of two converging genes in , according to RNA-seq and visualized in the Artemis genome browser; blue represents expression from the forward strand (), and red represents expression from the reverse strand (); the height of the trace represents the normalized expression level (reads) over the entire region. The traces demonstrate the termination efficiency exerted by TRIT between the two converging genes.

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FIGURE 3
Ribo-regulation associated with methionine biosynthesis in . At least three enzymes synthesize methionine in ; the expression of two of these is regulated by riboswitches. expression is regulated by a SAM-IV riboswitch, and the MetC enzyme uses homoserine as substrate. expression is regulated by a B riboswitch, and the MetE enzyme uses homocysteine as substrate. The third enzyme, MetH, is a B-dependent isoform of MetE, and MetH also uses homocysteine as substrate; the mRNA of this gene belongs to the category of naturally leaderless mRNAs, which are unusually widespread in ( 16 ). Riboswitch ligands and enzyme cofactors are shown as “stars,” genes are shown in blue, and enzymes are shown as green/yellow “clouds.”
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FIGURE 3

Ribo-regulation associated with methionine biosynthesis in . At least three enzymes synthesize methionine in ; the expression of two of these is regulated by riboswitches. expression is regulated by a SAM-IV riboswitch, and the MetC enzyme uses homoserine as substrate. expression is regulated by a B riboswitch, and the MetE enzyme uses homocysteine as substrate. The third enzyme, MetH, is a B-dependent isoform of MetE, and MetH also uses homocysteine as substrate; the mRNA of this gene belongs to the category of naturally leaderless mRNAs, which are unusually widespread in ( 16 ). Riboswitch ligands and enzyme cofactors are shown as “stars,” genes are shown in blue, and enzymes are shown as green/yellow “clouds.”

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FIGURE 4
Magnesium-sensing riboswitches in . The figure illustrates the genomic context of the two identified Mboxes (magnesium-sensing riboswitches) in . Genes shown in green are conserved hypotheticals, those in orange are information pathways, gray represents PE-PPE genes, and genes in blue are cell wall associated. Black arrows indicate relevant transcription start sites.
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FIGURE 4

Magnesium-sensing riboswitches in . The figure illustrates the genomic context of the two identified Mboxes (magnesium-sensing riboswitches) in . Genes shown in green are conserved hypotheticals, those in orange are information pathways, gray represents PE-PPE genes, and genes in blue are cell wall associated. Black arrows indicate relevant transcription start sites.

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FIGURE 5
The RNA is highly expressed during exponential growth and significantly downregulated in stationary phase in H37Rv. The RNA is expressed in the majority of lineage 4 strains (here represented by H37Rv) and in some lineage 1 strains (represented by N0157), but not in other lineages (N0052—lineage 2—has been shown for comparison). RNA-seq data is visualized in Artemis. All reads are normalized to total reads and adjusted to the same scale.
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FIGURE 5

The RNA is highly expressed during exponential growth and significantly downregulated in stationary phase in H37Rv. The RNA is expressed in the majority of lineage 4 strains (here represented by H37Rv) and in some lineage 1 strains (represented by N0157), but not in other lineages (N0052—lineage 2—has been shown for comparison). RNA-seq data is visualized in Artemis. All reads are normalized to total reads and adjusted to the same scale.

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FIGURE 6
-encoded RNAs with -regulating potential. A transcript encoded opposite (antisense) to the gene (ASpks) shows high complementarity to three other mRNAs, namely , , and . The figure illustrates the predicted base-pairing between ASpks and the three mRNAs. From reference 8 .
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FIGURE 6

-encoded RNAs with -regulating potential. A transcript encoded opposite (antisense) to the gene (ASpks) shows high complementarity to three other mRNAs, namely , , and . The figure illustrates the predicted base-pairing between ASpks and the three mRNAs. From reference 8 .

Source: microbiolspec March 2014 vol. 2 no. 2 doi:10.1128/microbiolspec.MGM2-0029-2013
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FIGURE 7
RNA-seq data (visualized in Artemis) of the CRISPR locus. The upper trace records TSS mapping (i.e., enriched for primary transcripts) from the right-hand side of the CRISPR locus, showing overlapping start sites for the Rv2816c antisense transcript (forward direction in blue) and the single CRISPR-RNA (crRNA) transcript (reverse, in red). The lower trace records sequencing of total RNA, showing the antisense transcript covering Rv2816c and Rv2817c (blue) and illustrating how the single crRNA transcript is processed into a series of mature, smaller crRNAs (red). A similar crRNA profile is seen on the left-hand side of the CRISPR locus, upstream of the Rv2614c/Rv2615c IS6110 insertion sequence (not shown).
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microbiolspec/2/2/MGM2-0029-2013-fig7.gif
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FIGURE 7

RNA-seq data (visualized in Artemis) of the CRISPR locus. The upper trace records TSS mapping (i.e., enriched for primary transcripts) from the right-hand side of the CRISPR locus, showing overlapping start sites for the Rv2816c antisense transcript (forward direction in blue) and the single CRISPR-RNA (crRNA) transcript (reverse, in red). The lower trace records sequencing of total RNA, showing the antisense transcript covering Rv2816c and Rv2817c (blue) and illustrating how the single crRNA transcript is processed into a series of mature, smaller crRNAs (red). A similar crRNA profile is seen on the left-hand side of the CRISPR locus, upstream of the Rv2614c/Rv2615c IS6110 insertion sequence (not shown).

Source: microbiolspec March 2014 vol. 2 no. 2 doi:10.1128/microbiolspec.MGM2-0029-2013
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Tables

Noncoding RNA in Mycobacteria
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Citation: Arnvig K, Cortes T, Young D. 2014. Noncoding rna in mycobacteria. microbiolspec 2(2): doi:10.1128/microbiolspec.MGM2-0029-2013
/content/microbiolspec/10.1128/microbiolspec.MGM2-0029-2013.T1
TABLE 1
Intergenic sRNAs
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TABLE 1

Intergenic sRNAs

Source: microbiolspec March 2014 vol. 2 no. 2 doi:10.1128/microbiolspec.MGM2-0029-2013

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