Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria

Desmila Idola; Hiroshi Mori; Yuji Nagata; Lisa Nonaka; Hirokazu Yano

doi:10.1186/s13100-023-00295-5

Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria

Mob DNA. 2023 May 26;14(1):7. doi: 10.1186/s13100-023-00295-5.

Authors

Desmila Idola¹, Hiroshi Mori², Yuji Nagata¹, Lisa Nonaka³, Hirokazu Yano^{4

5}

Affiliations

¹ Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan.
² Department of Informatics, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan.
³ Faculty of Human Life Sciences, Shokei University, 2-6-78 Kuhonji, Kumamoto, 862-8678, Japan.
⁴ Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan. h-yano@niid.go.jp.
⁵ Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 4-2-1 Aobacho, Higashimurayama, Tokyo, 189-0002, Japan. h-yano@niid.go.jp.

Abstract

Background: The strand-biased circularizing integrative elements (SEs) are putatively non-mobilizable integrative elements for transmitting antimicrobial resistance genes. The transposition mode and the prevalence of SEs in prokaryotes remain vague.

Results: To corroborate the transposition mode and the prevalence of SEs, hypothetical transposition intermediates of an SE were searched for in genomic DNA fractions of an SE host. Then, the SE core genes were defined based on gene knockout experiments, and the synteny blocks of their distant homologs were searched for in the RefSeq complete genome sequence database using PSI-BLAST. A genomic DNA fractionation experiment revealed that SE copies are present in a double-stranded nicked circular form in vivo. Operonic structure of three conserved coding sequences (intA, tfp, intB) and srap located at the left end of SEs were identified as essential for attL × attR recombination. The synteny blocks of tfp and srap homologs were detected in 3.6% of the replicons of Gammaproteobacteria but not in other taxa, implying that SE movement is host-dependent. SEs have been discovered most frequently in the orders Vibrionales (19% of replicons), Pseudomonadales (18%), Alteromonadales (17%), and Aeromonadales (12%). Genomic comparisons revealed 35 new SE members with identifiable termini. SEs are present at 1 to 2 copies per replicon and have a median length of 15.7 kb. Three newly identified SE members carry antimicrobial resistance genes, like tmexCD-toprJ, mcr-9, and bla_GMA-1. Further experiments validated that three new SE members possess the strand-biased attL × attR recombination activity.

Conclusions: This study suggested that transposition intermediates of SEs are double-stranded circular DNA. The main hosts of SEs are a subset of free-living Gammaproteobacteria; this represents a rather narrow host range compared to those of mobile DNA element groups discovered to date. As the host range, genetic organization, and movements are unique among the mobile DNA elements, SEs provide a new model system for host-mobile DNA element coevolution studies.

Keywords: Copy-out; GInt; ICE; IME; Integrase; MexCD-OprJ; RIT; SE; Transposon; mcr-9.