Mycobacterium Tuberculosis 6C SRNA Binds Multiple MRNA Targets Via C-rich Loops Independent of RNA Chaperones

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 Mar 2

PMID 30820540

Citations 23

Authors

Juntao Mai

Chitong Rao

Jacqueline Watt

Xian Sun

Chen Lin

Lu Zhang

Jun Liu

Affiliations

Soon will be listed here.

Abstract

Bacterial small regulatory RNAs (sRNAs) are the most abundant class of post-transcriptional regulators and have been well studied in Gram-negative bacteria. Little is known about the functions and mechanisms of sRNAs in high GC Gram-positive bacteria including Mycobacterium and Streptomyces. Here, we performed an in-depth study of 6C sRNA of Mycobacterium tuberculosis, which is conserved among high GC Gram-positive bacteria. Forty-seven genes were identified as possible direct targets of 6C sRNA and 15 of them were validated using an in vivo translational lacZ fusion system. We found that 6C sRNA plays a pleotropic role and regulates genes involved in various cellular processes, including DNA replication and protein secretion. Mapping the interactions of 6C sRNA with mRNA targets panD and dnaB revealed that the C-rich loops of 6C sRNA act as direct binding sites to mRNA targets. Unlike in Gram-negative bacteria where RNA binding proteins Hfq and ProQ are required, the interactions of 6C sRNA with mRNAs appear to be independent of RNA chaperones. Our findings suggest that the multiple G-C pairings between single stranded regions are sufficient to establish stable interactions between 6C sRNA and mRNA targets, providing a mechanism for sRNAs in high GC Gram-positive bacteria.

Citing Articles

Involvement of Mycobacterium smegmatis small noncoding RNA B11 in triacylglycerol accumulation and altered cell wall permeability.

Wu Z, Liu W, Tan Q, Chen Y, Lai X, Hong J BMC Microbiol. 2025; 25(1):124.

PMID: 40057673 PMC: 11889869. DOI: 10.1186/s12866-025-03826-7.

Transcriptome analysis and molecular characterization of novel small RNAs in Mycobacterium tuberculosis Lineage 1.

Jumat M, Chin K World J Microbiol Biotechnol. 2024; 40(9):279.

PMID: 39048776 DOI: 10.1007/s11274-024-04089-6.

The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence.

Bar-Oz M, Martini M, Alonso M, Meir M, Lore N, Miotto P PLoS Pathog. 2023; 19(8):e1011575.

PMID: 37603560 PMC: 10470900. DOI: 10.1371/journal.ppat.1011575.

Small RNA MTS1338 Configures a Stress Resistance Signature in .

Martini B, Grigorov A, Skvortsova Y, Bychenko O, Salina E, Azhikina T Int J Mol Sci. 2023; 24(9).

PMID: 37175635 PMC: 10178195. DOI: 10.3390/ijms24097928.

The stationary phase-specific sRNA FimR2 is a multifunctional regulator of bacterial motility, biofilm formation and virulence.

Raad N, Tandon D, Hapfelmeier S, Polacek N Nucleic Acids Res. 2022; 50(20):11858-11875.

PMID: 36354005 PMC: 9723502. DOI: 10.1093/nar/gkac1025.

References

Arnvig K, Young D . Identification of small RNAs in Mycobacterium tuberculosis. Mol Microbiol. 2009; 73(3):397-408. PMC: 2764107. DOI: 10.1111/j.1365-2958.2009.06777.x. View

Smirnov A, Forstner K, Holmqvist E, Otto A, Gunster R, Becher D . Grad-seq guides the discovery of ProQ as a major small RNA-binding protein. Proc Natl Acad Sci U S A. 2016; 113(41):11591-11596. PMC: 5068311. DOI: 10.1073/pnas.1609981113. View

Gey van Pittius N, Gamieldien J, Hide W, Brown G, Siezen R, Beyers A . The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2001; 2(10):RESEARCH0044. PMC: 57799. DOI: 10.1186/gb-2001-2-10-research0044. View

Vockenhuber M, Sharma C, Statt M, Schmidt D, Xu Z, Dietrich S . Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol. 2011; 8(3):468-77. PMC: 3218513. DOI: 10.4161/rna.8.3.14421. View

Robinson M, McCarthy D, Smyth G . edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009; 26(1):139-40. PMC: 2796818. DOI: 10.1093/bioinformatics/btp616. View

Storz G, Vogel J, Wassarman K . Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell. 2011; 43(6):880-91. PMC: 3176440. DOI: 10.1016/j.molcel.2011.08.022. View

Mahairas G, Sabo P, Hickey M, Singh D, Stover C . Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J Bacteriol. 1996; 178(5):1274-82. PMC: 177799. DOI: 10.1128/jb.178.5.1274-1282.1996. View

Sambandamurthy V, Wang X, Chen B, Russell R, Derrick S, Collins F . A pantothenate auxotroph of Mycobacterium tuberculosis is highly attenuated and protects mice against tuberculosis. Nat Med. 2002; 8(10):1171-4. DOI: 10.1038/nm765. View

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

10.

Abdallah A, Gey van Pittius N, Champion P, Cox J, Luirink J, Vandenbroucke-Grauls C . Type VII secretion--mycobacteria show the way. Nat Rev Microbiol. 2007; 5(11):883-91. DOI: 10.1038/nrmicro1773. View

11.

Greendyke R, Rajagopalan M, Parish T, Madiraju M . Conditional expression of Mycobacterium smegmatis dnaA, an essential DNA replication gene. Microbiology (Reading). 2002; 148(Pt 12):3887-3900. DOI: 10.1099/00221287-148-12-3887. View

12.

Hor J, Gorski S, Vogel J . Bacterial RNA Biology on a Genome Scale. Mol Cell. 2018; 70(5):785-799. DOI: 10.1016/j.molcel.2017.12.023. View

13.

Blasco B, Chen J, Hartkoorn R, Sala C, Uplekar S, Rougemont J . Virulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein. PLoS Pathog. 2012; 8(3):e1002621. PMC: 3315491. DOI: 10.1371/journal.ppat.1002621. View

14.

Lorenz R, Bernhart S, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler P . ViennaRNA Package 2.0. Algorithms Mol Biol. 2011; 6:26. PMC: 3319429. DOI: 10.1186/1748-7188-6-26. View

15.

Frigui W, Bottai D, Majlessi L, Monot M, Josselin E, Brodin P . Control of M. tuberculosis ESAT-6 secretion and specific T cell recognition by PhoP. PLoS Pathog. 2008; 4(2):e33. PMC: 2242835. DOI: 10.1371/journal.ppat.0040033. View

16.

Klann A, Belanger A, Lee J, Hatfull G . Characterization of the dnaG locus in Mycobacterium smegmatis reveals linkage of DNA replication and cell division. J Bacteriol. 1998; 180(1):65-72. PMC: 106850. DOI: 10.1128/JB.180.1.65-72.1998. View

17.

Langmead B, Trapnell C, Pop M, Salzberg S . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):R25. PMC: 2690996. DOI: 10.1186/gb-2009-10-3-r25. View

18.

Cortes T, Schubert O, Rose G, Arnvig K, Comas I, Aebersold R . Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis. Cell Rep. 2013; 5(4):1121-31. PMC: 3898074. DOI: 10.1016/j.celrep.2013.10.031. View

19.

Heueis N, Vockenhuber M, Suess B . Small non-coding RNAs in streptomycetes. RNA Biol. 2014; 11(5):464-9. PMC: 4152355. DOI: 10.4161/rna.28262. View

20.

Moores A, Riesco A, Schwenk S, Arnvig K . Expression, maturation and turnover of DrrS, an unusually stable, DosR regulated small RNA in Mycobacterium tuberculosis. PLoS One. 2017; 12(3):e0174079. PMC: 5360333. DOI: 10.1371/journal.pone.0174079. View