MTS1338 MTB000077

ncRNA Putative small regulatory RNA

This is an RNA, not a coding gene: it belongs to a separate track and carries none of the protein evidence layers.

Location

1960667–1960783 (+ strand), 117 nt, on H37Rv (NC_000962.3). Overlaps: Rv1734c. Upstream neighbour Rv1733c (180 bp). Downstream neighbour Rv1735c (508 bp).

Intra-MTBC variation

Coverage control

Variant density inside this RNA: 93.2 sites/100 bp, versus 75.3 in the flanking ±500 bp (GC 61.5 %). The flanks act as an internal witness: if variants are called normally around the RNA but none becomes widespread inside it, the constraint is real rather than a sequencing gap.

Verdict: n/a (a des variants communs)

Predicted secondary structure

63.2 % of bases are paired in the minimum-free-energy fold (74 paired, 43 unpaired). Folded in isolation; the in vivo structure may differ (partners, co-transcriptional folding).

Literature characterised

Virulence-associated sRNA, actively studied 2019-2026 (12 papers): regulates transcriptional shifts for dormancy entry and macrophage survival (Salina et al. 2019); confers pathogenic properties on non-pathogenic M. smegmatis; detoxifies reactive oxygen species under oxidative stress; transcriptionally activated by DosR and PhoP; posttranscriptionally regulated by ribonuclease YbeY; binds the cold-shock protein CspB; and activates the ABC transporter CydC for rifampicin efflux (2024).

Read with care. The atlas track still carried only the 2011 discovery description ('putative small regulatory RNA', Arnvig et al.) — the gene has been under active functional study for seven years since.

• Salina EG, Grigorov A, Skvortsova Y, Majorov K, Bychenko O, Ostrik A, Logunova N, Ignatov D, Kaprelyants A, Apt A, Azhikina T (2019) MTS1338, A Small Mycobacterium tuberculosis RNA, Regulates Transcriptional Shifts Consistent With Bacterial Adaptation for Entering Into Dormancy and Survival Within Host Macrophages. Frontiers in Cellular and Infection Microbiology. doi:10.3389/fcimb.2019.00405, PMID 30733920.
• Salina EG, et al. (2024) A virulence-associated small RNA MTS1338 activates an ABC transporter CydC for rifampicin efflux in Mycobacterium tuberculosis. Frontiers in Microbiology. doi:10.3389/fmicb.2024.1469280.

Sweep: tbmonitor TB corpus (~330k PubMed abstracts), single grouped UNION-ALL sweep of 2026-08-17 over the 72 ncRNA never previously searched; positive controls MTS2823 (6 papers), mcr11 (3), mcr7 (2) all returned their known hits, so a zero here is a measured absence and not a broken query.

Legacy record

MTS1338, putative small regulatory RNA (See Arnvig et al., 2011), 5'-end mapped by RLM-RACE, alternate 5'-end at position 1960601, ~100 bp band detected by Northern blot.

Sources

• Descriptive record (locus, name, product, comment, coordinates): Mycobrowser v5, stable RNAs (Kapopoulou et al. 2011, doi:10.1016/j.tube.2010.09.006).
• Intra-MTBC variation and coverage control: computed for this atlas over 145,209 genomes.
• Secondary structure: ViennaRNA 2.7.2, MFE fold.

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