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

Abstract

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 18476T (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). 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 ICEMfuInd1b and ICEMprChn1 were inserted into the genome at 5′-end of an typical host prfC gene, while ICEMfuInd1a was inserted at 5′-end of an atypical hipA-like gene. Despite their coexistence, the ICEMfuInd1a and ICEMfuInd1b 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 ICEMfuInd1a, ICEMfuInd1b, and ICEMprChn1, 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 ICEMprChn1 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.

Distribution and Genetic Characteristics of SXT/R391 Integrative Conjugative Elements in Shewanella spp. From China

“…Until now, SXT/R391 ICEs have been investigated in the genera Vibrio ( Wang et al, 2016 ), Providencia ( Coetzee et al, 1972 ), Photobacterium ( Nonaka et al, 2012 ), Proteus ( Lei et al, 2016 ; Li et al, 2016 ), Alteromonas ( Badhai and Das, 2016 ), Enterovibrio ( Taviani et al, 2009 ; Song et al, 2013 ; Luo et al, 2016 ), and Shewanella . S. putrefaciens , S. haliotis , and S. fidelis in the genus Shewanella , which were obtained from the Pacific Ocean, Portugal, and Japan, respectively, were reported to harbor SXT/R391 elements ( Pembroke and Piterina, 2006 ; Rodriguez-Blanco et al, 2012 ; Nonaka et al, 2014 ).…”

Analysis and Comparative Genomics of the SXT/R391 Family ICE, pMERPH

“…All other genes were found in the hotspots and variable regions of the pMERPH genome ( Figure 1). pMERPH Hotspot 1 (HS1) contains the same 18 gene insertion as previously reported in HS1 of ICEMprChn1 (orf32 to orf47) (showing 94% to 100% nucleotide identity across all genes) [23]. The functions of most of these genes are unknown but predicted to encode hypothetical genes with no known functional homologs.…”

A Novel Arsenate-Resistant Determinant Associated with ICEpMERPH, a Member of the SXT/R391 Group of Mobile Genetic Elements

“…All other genes were found in the hotspots and variable regions of the ICEpMERPH genome ( Figure 1). ICEpMERPH hotspot 1 (HS1) contains the same 18-gene insertion as previously found in HS1 in ICEMprChn1 (orf32 to orf47), showing 94% to 100% nucleotide identity across all genes [8]. Most of these genes encode hypothetical proteins of unknown functions that have been conserved only in these type of elements.…”