PMC

Phage A118 integration reaction and the subfamily of serine recombinases with large C-terminal domains. (A) Schematic representation of phage A118 integrative recombination, where attP on the phage genome recombines with attB within comK in the Listeria monocytogenes chromosome to form the two junction recombination sites attL and attR. (B) Phylogenetic tree of representative serine recombinases with large C-terminal domains (ClustalW2). (C) Sequence (56 bp) surrounding the A118 attP and attB loci. Palindromic sequences within each att site are denoted with arrows, and identical nucleotides between the two recombination sites are marked with dots. We show in this work that the central GG nucleotides define the crossover sites.

Programmed translational frameshifts near the 3′ ends of the genes result in synthesis of two different-length products for Cps and Tsh major structural proteins in the two Listeria phages A118 and A500. (A) The −1 frameshift in cps of A118, leading to an extended version of the Cps. (B) The +1 frameshift in the sequence coding for the Tsh of phage A118. (C and D) Similar to A118, the Cps-L product of phage A500 is made as the result of a −1 frameshift, whereas the Tsh-L of phage A500 is produced through a +1 decoding event.

Genomic comparison. (a) The A. baumannii A118 optical map was compared to the A. baumannii strain AB0057 and AYE NcoI restriction maps obtained in silico around the location of the AbaR-type resistance island region using the MapSolver software. The white regions represent DNA fragments missing in strain A118. The AbaR3 and AbaR1 regions are the genomic islands present in strains AB0057 and AYE (1, 14). Vertical lines represent NcoI restriction sites. (b) Diagram showing the point of insertion of AbaR genomic islands within the comM gene, which was shown to be intact in A. baumannii A118 by sequencing an amplicon generated using total DNA as the template and the primers 5′-TCCATTTTACCGCCACTTTC and 5′-AATCGATGCGGTCGAGTAAC (36). Nucleotides shown in red are directly repeated in those strains where AbaR has been inserted.

Genomic comparison. Comparison of the A. baumannii A118 optical map with the A. baumannii strain ATCC 17978, ACICU, AB307-0294, AB0057, and AYE NcoI restriction maps obtained in silico at a fragment of the pbp2 gene using the MapSolver software. White fragments represent putative missing/inserted fragments. The locations of relevant NcoI sites are shown. The numbers indicate the coordinates of NcoI sites or the locations of the specified genes in the GenBank entries for each strain.