Open AccessGenome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis
Author(s) -
Paolo Miotto,
Francesca Forti,
Alessandro Ambrosi,
Danilo Pellin,
Diogo F. Veiga,
Gábor Balázsi,
Maria Laura Gennaro,
Clelia Di Serio,
Daniela Ghisotti,
Daniela María Cirillo
Publication year - 2012
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0051950
Subject(s) - biology , transfer rna , genetics , rna , genome , gene , mycobacterium tuberculosis , terminator (solar) , primer extension , sigma factor , promoter , non coding rna , dna microarray , antisense rna , computational biology , gene expression , tuberculosis , medicine , ionosphere , physics , pathology , astronomy
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.