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The genus  Marinomonas  comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of  Marinomonas fungiae  JCM 18476 T  (ICE Mfu Ind1a and ICE Mfu Ind1b) and in  Marinomonas profundimaris  strain D104 (ICE Mpr Chn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICE Mfu Ind1b and ICE Mpr Chn1 were inserted into the genome at 5′-end of an typical host  prfC  gene, while ICE Mfu Ind1a was inserted at 5′-end of an atypical  hipA -like gene. Despite their coexistence, the ICE Mfu Ind1a and ICE Mfu Ind1b were not present in a tandem fashion in the genome of  M. fungiae.  Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their evolution from a common SXT ancestor. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE into the  M. fungiae  genome due to mutations. Our analysis showed the presence of 16, 25, and 27 variable genes in the hotspots of ICE Mfu Ind1a, ICE Mfu Ind1b, and ICE Mpr Chn1, respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hotspot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from  M. fungiae  but were present within a transposon cassette in the HS-1 of the ICE Mpr Chn1 from  M. profundimaris.  Finally, our data provided information on the genetic diversity and predicted functions encoded by variable genes present in the hotspot regions of these new ICEs.

frontiers in microbiology

Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICEMfuInd1a and ICEMfuInd1b, and ICEMprChn1 Identified in the Genomes of Marinomonas fungiae JCM 18476T and Marinomonas profundimaris Strain D104