The second IR another was located between the lipoprotein-encoding gene, lip, and a putative Acyl-CoA acyltransferase-encoding gene, acf, designated IR2 here. The third IR was adjacent to orf39, part of the core chromosome of S. haemolyticus, designated IR3 here (Figure 1). This 40-kb region was actually bracketed by two IR, IR1 and IR3, resembling the remnant of a SCC-like element but without ccr genes. In light of the presence of an internal
IR, IR2, this ccr-absent large region was a remnant of a composite SCC element or comprised remnants of multiple SCC NVP-LDE225 elements. The 3.7-kb region between orfX and Proteasome inhibitor the IS431-1 was designated R1 (representing region 1) and contained genes encoding ADP-ribosylglycohydrolase, permease and ribokinase. R1 was almost identical to the counterpart (loci SERP2216 to SERP2218) of the integrative plasmid vSe1 on the chromosome of S. epidermidis RP62a (GenBank accession no. CP000029) JNK inhibitor but was absent from S. haemolyticus JCSC1435, suggesting a foreign origin. Of note, the ribokinase-encoding gene, rbk, was truncated at the 3′ end by the
insertion of IS431, leaving a 920 bp remnant of the 939 bp gene. The region between the IS431-1 and IR2 was designated R2. As mentioned above, Tn6191 was inserted into the spacer between arsR and copA in R2. Besides Tn6191, R2 also contained a few genes, the cadXD operon mediating resistance to cadmium and the ars operon required for detoxifying arsenate. In R2, the sequence from the IS431-1 to arsB was closest (99.9% similarity) to the counterpart in the type IX SCCmec Demeclocycline of S. aureus strain JCSC6943 (GenBank accession no. AB505628), while that from arsB to IR2 excluding Tn6191 was almost identical to the corresponding region in the type X SCCmec of S. aureus JCSC6945 (GenBank accession no. AB505630). This suggests that R2 might have resulted from homologous recombination between the ars operons of the type IX and X SCCmec. R1 and R2 had different origins
and were separated by a single copy of IS431, suggesting that IS431 served as a joining point that brought the two regions together. The large region between IR2 and IR3 was designated R3. The two genes, acf and orf27 (putatively encoding a type I restriction endonuclease), adjacent to IR2 had 96.8% identities to the counterparts of a SCC element on the chromosome of S. haemolyticus JCSC1435. At the other end of R3, there was a second copy of the ars operon, which was closest to those on a few S. aureus plasmids, e.g. pI258 (GenBank accession no. GQ900378) and pK59 (GenBank accession no. GQ900488) with 92.0% identity and had only 86.4% identity with the first ars operon in R2 of WCH1. The intervening genetic components in R3 had lower than 80% identity with the closest matches identified by BLAST and were absent from the chromosome of S. haemolyticus JCSC1435. All above findings suggest that all genetic components in R3 had origins other than S. haemolyticus.