Small RNA Identification in Enterobacteriaceae Using Synteny and Genomic Backbone Retention II

Abstract

Small RNAs are bacterial counterparts of noncoding RNAs. Increasing evidence being added in the literature indicates that these small RNAs play major roles in prokaryotes both at the transcriptome and proteome levels. Based on comparative genomic studies, we present manually curated small RNA regions in 25 recently completed genomes from Enterobacteriaceae. The study is a continuation of our earlier work that uses the presence of small RNAs sandwiched between specific conserved flanking genes retaining genomic backbone and gene synteny. Based on this study, a total of 931 identified sRNA/sRNA regions are reported. This data contains 498 small RNA homologs, 80 putative small RNA regions containing partial stretches of homologous sequences, and 353 putative nonhomologous sRNA regions. This homologs/partial homologs includes, 84 putative small RNA homologous regions retaining at least one of the conserved flanking genes pair which may possibly act as hotspots for genetic pool insertion/deletion in genomes. Nonhomologous CsrB sRNA region reported by us in Yersinia pseudotuberculosis IP32953 has been experimentally confirmed by Kulkarni's group and sraH and ryeE sRNAs from Erwinia carotovora subsp. atroseptica SCRI1043 recently added to the Rfam database are indicative proof of our positive approach.

The small RNA SraG participates in PNPase homeostasis

“…Potential SraG homologs located between the pnp and rpsO genes exist in various enterobacteria, such as Salmonella typhimurium, Shigella flexneri, and Klebsiella pneumoniae (Hershberg et al 2003;Sridhar et al 2009). All the Yersinia species exhibit the rpsO-pnp synteny (i.e., gene co-localization), but in Yersinia pestis an insertion element is annotated in the intergenic region of the rpsO-pnp operon.…”

Small non-coding RNA SraG regulates the operon YPK_1206-1205 in Yersinia pseudotuberculosis

“…Sequence analysis demonstrated that sraG also exists in several other enteric bacteria, e.g. Salmonella, Shigella, Klebsiella and Yersinia (Hershberg et al, 2003;Sridhar et al, 2009), and the intergenic location of sraG in these bacteria is the same as reported in E. coli (Sridhar et al, 2009). In Listeria monocytogenes, an sRNA gene named rliD is also located between pnpA and rpsO in a similar way to sraG, although their DNA sequences do not share high similarity (Mandin et al, 2007).…”

Yersinia pestis and Yersinia pseudotuberculosis infection: a regulatory RNA perspective

“…First reported in E. coli , SraG located between pnp (PNPase) and rpsO (30S ribosomal protein S15), is expressed preferentially at late-logarithmic phase, and activated by heat and cold shock treatments ( Argaman et al, 2001 ; Sridhar et al, 2009 ). A comparative sequence analysis with E. coli revealed a SraG homolog in Yersinia species ( Sridhar et al, 2009 ). In Y. pseudotuberculosis 16 proteins were identified as potential regulatory targets of SraG ( Lu et al, 2012 ).…”