Abstract: Genome evolution in prokaryotes is assisted by integration of gene
pools from phages and plasmids. Regions downstream of tRNAs and
tmRNAs are considered as hot spots for the integration of these gene pools or
genomic islands. Till date, genomic islands have been identified only at
tRNA/tmRNA genes in the enterobacterial genomes. Present work reports 10
distinct small RNAs as potent integration sites for genomic islands. A known
tool tRNAcc 1.0 has been used to identify genomic islands associated with small
RNAs c0362, oxyS, ryaA, rybB, rybD, ryeB,
ryeE, rtT, sraE and tmRNA. The coordinates of 25 such
small RNA associated genomic islands in three E. coli (strains: CFT073,
EDL933 and K12) and Shigella flexneri (strain: 301) genomes are
presented. Moreover cross-verification of the genomic sequences encoded within
the identified genomic islands in horizontal gene transfer database, GenBank
annotation features and atypical sequence compositions support our results.
Again, all of the identified 25 genomic integration sites do exhibit genomic
block rearrangements with respect to the associated small RNA. Similar to
tRNAs/tmRNAs, the downstream regions of the small RNAs are found to be
hotspots of integration.
Keywords: sRNA, genomic islands, genomic blocks, integration sites, phage elements
