Abstract
Insertion sequences (IS) are key players in bacterial genome plasticity and horizontal gene transfer. IS91 family members, belonging to the HUH superfamily of single-strand nucleases, are often linked with antibiotic resistance genes. Among these, the element IS91 is unique as it also carries a sequence called orf121, whose stop codon overlaps with the start codon of tnpA, a highly conserved feature of IS91 isoforms. We show that Orf121 serves as a dual regulator of IS91 transposition: Orf121 inhibits transposition activity of TnpA while facilitating accurate excision of IS91 single-strand circular intermediates. This accurate excision reduces one-ended transposition events, i.e., events arising when proper termination fails, leading to the co-mobilization of adjacent DNA. We also provide evidence that the bottom-stranded ssDNA circular intermediate is the functional substrate IS91. These findings highlight a sophisticated regulatory strategy balancing IS91 mobility and genetic stability.
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Acknowledgements
A. Fauconnier acknowledges the French ministère de l’Enseignement Supérieur, de la Recherche (MESR) for his doctoral training grant. This work was supported by funding from the French research institute Inserm and MESR. The authors thank Emilie Pinault from the BISCEm unit (Univ. Limoges, UAR 2015 CNRS, US 42 Inserm, CHU Limoges) for technical support regarding mass spectrometry. The authors are grateful to Céline Loot (Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75724 Paris, France) and Vincent Burrus (Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada) for critical review of the manuscript. The authors dedicate this publication to our colleague, Cécile Pasternak (last author), who left us during the final phase of this work.
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Aurélien Fauconnier [A.F.]: Conceptualization; Methodology; Investigation; Data curation; Formal analysis; Validation; Visualization; Writing – original draft; Writing – review & editing. Sandra Da Re [S.D.R.]: Conceptualization; Data curation; Validation; Visualization; Supervision; Writing – original draft; Writing – review & editing. Margaux Gaschet [M.G.]: Investigation; Data curation; Formal analysis; Validation. Thomas Jové [T.J.]: Conceptualization; Methodology; Investigation; Data curation; Formal analysis; Validation; Supervision. Marie-Cécile Ploy [M.C.P.]: Conceptualization; Resources; Data curation; Formal analysis; Validation; Supervision; Project administration; Funding acquisition; Writing – original draft; Writing – review & editing. Cécile Pasternak [C.P.]: Conceptualization; Methodology; Investigation; Resources; Data curation; Formal analysis; Validation; Visualization; Supervision; Project administration; Funding acquisition; Writing – original draft. All authors reviewed and approved the final manuscript.
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Fauconnier, A., Da Re, S., Gaschet, M. et al. Dual regulatory role of IS91-encoded Orf121 in IS91 transposition. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09874-7
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DOI: https://doi.org/10.1038/s42003-026-09874-7
