Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention II.
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.
Sridhar
Jayavel
J
Centre of Excellence in Bioinformatics, Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India.
Kumar
Sivasankaran Sathesh
SS
Rafi
Ziauddin Ahamed
ZA
D004755:Enterobacteriaceae / Q000235:genetics*; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D022661:RNA, Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA; D026801:Synteny
D022661:RNA, Untranslated