G51ST25 and G51acb carry the rtcA and rntZ
genes, encoding the RNA 3′-terminal phosphate cyclase see more and the RNAseZ, respectively. The cyclase catalyzes the ATP-dependent conversion of the 3′-phosphate to the 2′, 3′-cyclic phosphodiester at the end of various RNA substrates ; RNAseZ is responsible for the maturation of the 3′-end of a large family of transfer RNAs . In E. coli the 3′-terminal phosphate cyclase rtcA gene forms an operon with the upstream rtcB gene. Expression of rtcAB is regulated by rtcR, a gene positioned upstream of rtcAB, but transcribed in the opposite direction, encoding a sigma54-dependent regulator . rtcBA and rtcR genes are conserved in both G51ST25 and G51acb islands, separated by rntZ. Interestingly, only rntZ is present at the corresponding chromosomal position in strains lacking G51. In type I restriction systems the three subunits S, M and R, which may variably associate to form a HM781-36B purchase modification methylase or a restriction endonuclease, are encoded by hsd (host specificity of DNA) genes.
Alternative hsd genes reside in G13ST25 and G13ST78. The former are clustered in one operon, whereas hsdSM and hsdR genes in G13ST78 are at distance, as frequently found in other species. Homologs of a cytosine DNA methyltransferase and a restriction endonuclease, which may constitute a type II restriction modification system, are encoded by genes residing in G38ST78. The G55 islands found in strains 4190, AB0057 and AYE are closely related, and all include a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) block, flanked by a cas (CRISPR-associated) gene cluster. CRISPRs are repeated DNA sequence blocks found in
the genomes of approximately crotamiton 40% of bacteria, often next to a cluster of cas genes. The CRISPR/Cas system provides a form of acquired immunity against exogenous DNA, foreign DNA sequences being first integrated at the CRISPR locus and eventually degraded by Cas proteins . Horizontal transfer of CRISPRs and associated genes among prokaryotes is documented . Gram-negative bacteria contain a variety of genes encoding proteins enriched in dipeptide motifs (valine-glycine repeats) hence called Vgr. Islands encoding Vgr-like proteins are found inserted at eight genome variable loci (loci 2, 7, 15, 17, 19, 25, 27 of Figure 2). Vgr proteins are associated with ligand-binding proteins at the bacterial surface , and are involved in biofilm formation and swarming and swimming motility in Burholderia . Intriguingly, Vgr proteins, along with Hcp (hemolysin co-regulated) proteins, are components of the type VI (T6SS) secretion apparatus, a transport system extensively conserved among Gram-negative bacteria . Secreted Vgr proteins assemble a cell-puncturing device analogous to phage tail spikes to deliver effector proteins, and are also able to covalently cross-link host cell actin contributing to T6SS pathogenicity .