Abstract
Only few small RNAs (sRNAs) have been characterized in Mycobacterium tuberculosis and their role in regulatory networks is still poorly understood. Here we report a genome-wide characterization of sRNAs in M. tuberculosis integrating experimental and computational analyses. Global RNA-seq analysis of exponentially growing cultures of M. tuberculosis H37Rv had previously identified 1373 sRNA species. In the present report we show that 258 (19%) of these were also identified by microarray expression. This set included 22 intergenic sRNAs, 84 sRNAs mapping within 5′/3′ UTRs, and 152 antisense sRNAs. Analysis of promoter and terminator consensus sequences identified sigma A promoter consensus sequences for 121 sRNAs (47%), terminator consensus motifs for 22 sRNAs (8.5%), and both motifs for 35 sRNAs (14%). Additionally, 20/23 candidates were visualized by Northern blot analysis and 5′ end mapping by primer extension confirmed the RNA-seq data. We also used a computational approach utilizing functional enrichment to identify the pathways targeted by sRNA regulation. We found that antisense sRNAs preferentially regulated transcription of membrane-bound proteins. Genes putatively regulated by novel cis-encoded sRNAs were enriched for two-component systems and for functional pathways involved in hydrogen transport on the membrane.
Highlights
Regulatory RNA species can modulate transcription, translation, mRNA stability, DNA maintenance, and gene silencing
Genome-wide Expression Profiling of small RNAs (sRNAs) in Mycobacterium tuberculosis (MTB) To identify sRNAs in MTB, we performed microarray expression analysis on small-size RNA enriched fraction extracted from exponentially growing cultures of M. tuberculosis H37Rv
We used a set of 1373 sRNA species previously identified by RNA sequencing (RNA-seq) (Type A candidates, [22]), which was updated to reflect changes in annotation in the genome of MTB
Summary
Regulatory RNA species can modulate transcription, translation, mRNA stability, DNA maintenance, and gene silencing. They function through a variety of mechanisms, including changes in RNA conformation, protein binding, base pairing with other RNAs, and interaction with DNA [1,2,3]. The prototype of a bacterial sRNA is a non-coding RNA of 50– 300 nucleotides (nt) in length that acts by imperfect base pairing with trans encoded RNA target(s). Recent research has shed some light on the relevance of sRNAs in bacterial pathogenesis, including modulation of expression of virulence factors in response to environmental and host signals [2,8,9,10,11,12,13,14]. Understanding how sRNAs control bacterial virulence may open a new prospective in the fight against tuberculosis (TB) and contribute to the goal of TB eradication [15,16,17,18]
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