title: Identification of small RNAs in Mycobacterium smegmatis using heterologous Hfq.
abstract: Gene regulation by small RNAs (sRNAs) has been extensively studied in various bacteria. However, the presence and roles of sRNAs in mycobacteria remain largely unclear. Immunoprecipitation of RNA chaperone Hfq to enrich for sRNAs is one of the effective methods to isolate sRNAs. However, the lack of an identified mycobacterial hfq restricts the feasibility of this approach. We developed a novel method that takes advantage of the conserved inherent sRNAs-binding capability of heterologous Hfq from Escherichia coli to enrich sRNAs from Mycobacterium smegmatis, a model organism for studying Mycobacterium tuberculosis. We validated 12 trans-encoded and 12 cis-encoded novel sRNAs in M. smegmatis. Many of these sRNAs are differentially expressed at exponential phase compared with stationary phase, suggesting that sRNAs are involved in the growth of mycobacteria. Intriguingly, five of the cis-encoded novel sRNAs target known transposases. Phylogenetic conservation analysis shows that these sRNAs are pathogenicity dependent. We believe that our findings will serve as an important reference for future analysis of sRNAs regulation in mycobacteria and will contribute significantly to the development of sRNAs prediction programs. Moreover, this novel method of using heterologous Hfq for sRNAs enrichment can be of general use for the discovery of bacterial sRNAs in which no endogenous Hfq is identified.
authors.affiliation: Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR.
authors.forename: Sai-Kam
authors.initials: SK
authors.lastname: Li
authors.forename: Patrick Kwok-Shing
authors.initials: PK
authors.lastname: Ng
authors.forename: Hao
authors.initials: H
authors.lastname: Qin
authors.forename: Jeffrey Kwan-Yiu
authors.initials: JK
authors.lastname: Lau
authors.forename: Jonathan Pak-Yuen
authors.initials: JP
authors.lastname: Lau
authors.forename: Stephen Kwok-Wing
authors.initials: SK
authors.lastname: Tsui
authors.forename: Ting-Fung
authors.initials: TF
authors.lastname: Chan
authors.forename: Terrence Chi-Kong
authors.initials: TC
authors.lastname: Lau
mesh_terms: D029968:Escherichia coli Proteins / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics / Q000502:physiology; D035001:Host Factor 1 Protein / Q000378:metabolism*; D047468:Immunoprecipitation / Q000379:methods; D035683:MicroRNAs / Q000032:analysis / Q000235:genetics / Q000378:metabolism*; D018832:Molecular Chaperones / Q000032:analysis / Q000235:genetics / Q000378:metabolism*; D020102:Mycobacterium smegmatis / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D012329:RNA, Bacterial / Q000378:metabolism; D019895:Transposases / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; D035001:Host Factor 1 Protein; D035683:MicroRNAs; D018832:Molecular Chaperones; D012329:RNA, Bacterial; D019895:Transposases