MTS1338, a distinctive small RNA in pathogenic mycobacteria, plays a crucial role in host-pathogen interactions during infection. Mycobacterial cells encounter heterogeneous stresses in macrophages, which highly upregulate MTS1338. A dormancy regulatory factor DosR regulates the intracellular abundance of MTS1338. Herein, we investigated the interplay of DosR and a low pH-inducible gene regulator PhoP binding to the MTS1338 promoter. We identified that DosR strongly binds to two regions upstream of the MTS1338 gene. The proximal region possesses a threefold higher affinity than the distal site, but the presence of both regions increased the affinity for DosR by > 10-fold. PhoP did not bind to the MTS1338 gene but binds to the DosR-bound MTS1338 gene, suggesting a concerted mechanism for MTS1338 expression.
Arnvig K and Young D (2012) Non‐coding RNA and its potential role in Mycobacterium tuberculosis pathogenesis. RNA Biol 9, 427–436.
Ostrik AA, Azhikina TL and Salina EG (2021) Small noncoding RNAs and their role in the pathogenesis of Mycobacterium tuberculosis infection. Biochemistry 86, S109–S119.
Schwenk S and Arnvig KB (2018) Regulatory RNA in Mycobacterium tuberculosis, back to basics. Path Dis 76, 1–12.
Taneja S and Dutta T (2019) On a stake‐out: mycobacterial small RNA identification and regulation. Noncoding RNA Res 4, 86–95.
Arnvig KB, Comas I, Thomson NR, Houghton J, Boshoff HI, Croucher NJ and Young DB (2011) Sequence‐based analysis uncovers an abundance of non‐coding RNA in the total transcriptome of Mycobacterium tuberculosis. PLoS Path 7, e1002342.
Ignatov DV, Timoshina OY, Logunova NN, Skvortsov TA and Azhikina TL (2014) Expression of small RNAs of Mycobacterium tuberculosis in murine models of tuberculosis infection. Russian J Bioorg Chem 40, 233–235.
Salina EG, Grigorov A, Skvortsova Y, Majorov K, Bychenko O, Ostrik A and 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. Front Cell Infect Microbiol 9, 405.
Moores A, Riesco AB, Schwenk S and Arnvig KB (2017) Expression, maturation and turnover of DrrS, an unusually stable, DosR regulated small RNA in Mycobacterium tuberculosis. PLoS ONE 12, e0174079.
Gerrick ER, Barbier T, Chase MR, Xu R, François J, Lin VH and Fortune SM (2018) Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response. Proc Natl Acad Sci USA 115, 6464–6469.
Singh S, Nirban R and Dutta T (2021) MTS1338 in Mycobacterium tuberculosis promotes detoxification of reactive oxygen species under oxidative stress. Tuberculosis 131, 102142.
Shepelkova G, Evstifeev V, Averbakch M Jr, Sivokozov I, Ergeshov A, Azhikina T and Yeremeev V (2021) Small noncoding RNAs MTS0997 and MTS1338 affect the adaptation and virulence of Mycobacterium tuberculosis. Microbiol Res 12, 186–195.
Bychenko O, Skvortsova Y, Ziganshin R, Grigorov A, Aseev L, Ostrik A and Azhikina T (2021) Mycobacterium tuberculosis small RNA MTS1338 confers pathogenic properties to non‐pathogenic mycobacterium smegmatis. Microorganisms 9, 414.
Ostrik AA, Salina EG, Skvortsova YV, Grigorov AS, Bychenko OS, Kaprelyants AS and Azhikina TL (2020) Small RNAs of Mycobacterium tuberculosis in adaptation to host‐like stress conditions in vitro. Appl Biochem Microbiol 56, 381–386.
Roberts DM, Liao RP, Wisedchaisri G, Hol WG and Sherman DR (2004) Two sensor kinases contribute to the hypoxic response of Mycobacterium tuberculosis. J Biol Chem 279, 23082–23087.
Mehra S, Foreman TW, Didier PJ, Ahsan MH, Hudock TA, Kissee R and Kaushal D (2015) The DosR regulon modulates adaptive immunity and is essential for Mycobacterium tuberculosis persistence. Am J Respir Crit Care Med 191, 1185–1196.
Sharma S and Tyagi JS (2016) Mycobacterium tuberculosis DevR/DosR dormancy regulator activation mechanism: dispensability of phosphorylation, cooperativity and essentiality of α10 helix. PLoS ONE 11, e0160723.
Pedrosa J, Saunders BM, Appelberg R, Orme IM, Silva MT and Cooper AM (2000) Neutrophils play a protective nonphagocytic role in systemic Mycobacterium tuberculosis infection of mice. Infect Immun 68, 577–583.
Wisedchaisri G, Wu M, Rice AE, Roberts DM, Sherman DR and Hol WG (2005) Structures of Mycobacterium tuberculosis DosR and DosR–DNA complex involved in gene activation during adaptation to hypoxic latency. J Mol Biol 354, 630–641.
Vashist A, Malhotra V, Sharma G, Tyagi JS and Clark‐Curtiss JE (2018) Interplay of PhoP and DevR response regulators defines expression of the dormancy regulon in virulent Mycobacterium tuberculosis. J Biol Chem 293, 16413–16425.
Malhotra V, Agrawal R, Duncan TR, Saini DK and Clark‐Curtiss JE (2015) Mycobacterium tuberculosis response regulators, DevR and NarL, interact in vivo and co‐regulate gene expression during aerobic nitrate metabolism. J Biol Chem 290, 8294–8309.
Bretl DJ, He H, Demetriadou C, White MJ, Penoske RM, Salzman NH and Zahrt TC (2012) MprA and DosR coregulate a Mycobacterium tuberculosis virulence operon encoding Rv1813c and Rv1812c. Infect Immun 80, 3018–3033.
Goyal R, Das AK, Singh R, Singh PK, Korpole S and Sarkar D (2011) Phosphorylation of PhoP protein plays direct regulatory role in lipid biosynthesis of Mycobacterium tuberculosis. J Biol Chem 286, 45197–45208.
He X and Wang S (2014) DNA consensus sequence motif for binding response regulator PhoP, a virulence regulator of Mycobacterium tuberculosis. Biochemistry 53, 8008–8020.
Lee JS, Krause R, Schreiber J, Mollenkopf HJ, Kowall J, Stein R and Kaufmann SH (2008) Mutation in the transcriptional regulator PhoP contributes to avirulence of Mycobacterium tuberculosis H37Ra strain. Cell Host Microbe 3, 97–103.
Bansal R, Anil Kumar V, Sevalkar RR, Singh PR and Sarkar D (2017) Mycobacterium tuberculosis virulence‐regulator PhoP interacts with alternative sigma factor SigE during acid‐stress response. Mol Microbiol 104, 400–411.
Salina EG, Grigorov AS, Bychenko OS, Skvortsova YV, Mamedov IZ, Azhikina TL and Kaprelyants AS (2019) Resuscitation of dormant “non‐culturable” Mycobacterium tuberculosis is characterized by immediate transcriptional burst. Front Cell Infect Microbiol 9, 272.
Chauhan S, Sharma D, Singh A, Surolia A and Tyagi JS (2011) Comprehensive insights into Mycobacterium tuberculosis DevR (DosR) regulon activation switch. Nucleic Acids Res 39, 7400–7414.
Lun DS, Sherrid A, Weiner B, Sherman DR and Galagan JE (2009) A blind deconvolution approach to high‐resolution mapping of transcription factor binding sites from ChIP‐seq data. Genome Biol 10, R142.
Siddiqui N, Gupta AK and Dutta T (2022) PhoP induces RyjB expression under acid stress in Escherichia coli. J Biochem 171, 277–285.
Wisedchaisri G, Wu M, Sherman DR and Hol WG (2008) Crystal structures of the response regulator DosR from Mycobacterium tuberculosis suggest a helix rearrangement mechanism for phosphorylation activation. J Mol Biol 378, 227–242.
Dutta T and Srivastava S (2018) Small RNA‐mediated regulation in bacteria: a growing palette of diverse mechanisms. Gene 656, 60–72.
Solans L, Gonzalo‐Asensio J, Sala C, Benjak A, Uplekar S, Rougemont J and Cole ST (2014) The PhoP‐dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis. PLoS Path 10, e1004183.
