Abstract
Bacterial small RNAs (sRNAs) are short transcripts that typically do not encode proteins and often act as regulators of gene expression through a variety of mechanisms. Regulatory sRNAs have been identified in many species, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Here, we use a computational algorithm to predict sRNA candidates in the mycobacterial species M. smegmatis and M. bovis BCG and confirmed the expression of many sRNAs using Northern blotting. Thus, we have identified 17 and 23 novel sRNAs in M. smegmatis and M. bovis BCG, respectively. We have also applied a high-throughput technique (Deep-RACE) to map the 5′ and 3′ ends of many of these sRNAs and identified potential regulators of sRNAs by analysis of existing ChIP-seq datasets. The sRNAs identified in this work likely contribute to the unique biology of mycobacteria.
Highlights
The genus Mycobacterium contains many clinically relevant pathogens, including Mycobacterium tuberculosis and Mycobacterium leprae, the etiologic agents of tuberculosis (TB) and leprosy, respectively
Prediction of sRNAs in silico using SIPHT Using SIPHT, we identified 93 candidate sRNAs in M. smegmatis (Table S3) and 144 candidate sRNAs in M. bovis BCG (Table S4)
Novel sRNAs Identified in Mycobacterium Smegmatis All 93 M. smegmatis sRNA candidates were tested by Northern blot using oligonucleotides in both orientations; expression was confirmed for 18 sRNA
Summary
The genus Mycobacterium contains many clinically relevant pathogens, including Mycobacterium tuberculosis and Mycobacterium leprae, the etiologic agents of tuberculosis (TB) and leprosy, respectively. SRNAs can originate from their own independent genes or through the processing of larger transcripts [3]. To exert their function, sRNAs typically base-pair with target messenger RNAs (mRNAs), resulting in altered transcription, mRNA stability, or translation [4]. RNA-seq has been widely applied to identify novel sRNA candidates in many bacterial species [6,7,8,9,10], including M. tuberculosis [11]. SRNAs have been identified in other mycobacterial species: 34 and 15 sRNAs have been experimentally validated in Mycobcaterium bovis BCG and Mycobacterium smegmatis, respectively [13] 63 sRNAs have been experimentally validated in M. tuberculosis. sRNAs have been identified in other mycobacterial species: 34 and 15 sRNAs have been experimentally validated in Mycobcaterium bovis BCG and Mycobacterium smegmatis, respectively [13]
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