Biology subjects

Siguier, P.

Publications and source records attributed to Siguier, P..

5 recordsLinked to original sources

bioRxiv2026

Chromosomal integration of blaCTX-M redefines the evolutionary trajectory of antibiotic resistance in E. coli through lineage-structured expansion

The global CTX-M pandemic is considered a plasmid-driven phenomenon, yet chromosomal integration of blaCTX-M has been reported in various settings. Screening 451,174 publicly available E. coli genomes and retaining 2,269 CTX-M-E. coli long-read or hybrid assemblies, we found that 33.5% carried at least one chromosomally integrated blaCTX-M. Chromosomal integration was strongly structured by E. coli lineage and CTX-M variant, reaching 68.5% in ST38 and 43.9% in ST131. In the latter, integration rates varied between subclades with modelling, suggesting recent acceleration within the ST131-C2 subclade. Additional resistance genes were frequently co-integrated with blaCTX-M (33%), with architectures largely inherited from plasmid-borne structures. Integrations were mainly ISEcp1- or IS26-mediated (77.3% and 18.9%, respectively) and occurred across the entire E. coli chromosome without spared zones. blaCTX-M chromosomal integration is a widespread, lineage-structured component of the CTX-M pandemic, providing stable vertical inheritance that complements or may supplant plasmid-mediated dissemination in successful ESBL-E. coli clones.

microbiology↗

bioRxiv2024

Interplay between the Xer recombination system and the dissemination of antibioresistance in Acinetobacter baumannii

Antibiotic-resistant infections pose a pressing challenge in clinical settings. Plasmids are widely recognized for hastening the emergence of resistance by facilitating horizontal gene transfer of antibiotic resistance genes among bacteria. We explore this inquiry in Acinetobacter baumannii, a globally emerging nosocomial pathogen responsible for a wide array of infections with worrying accumulation of resistances, notably involving plasmids. In this specie, plasmids of the Rep_3 family harbor adaptive genes within variable regions edged by potential site-specific recombination sites recognized by the XerCD recombinase. We first show that the Xer system of Acinetobacter baumannii functions as described in Escherichia coli, resolving chromosome dimers at the dif site as well as recombining plasmid-borne sites. The multiple Xer recombination sites found in Rep_3 plasmids do not, however, allow excising plasmid fragments. They rather recombine to co-integrate plasmids, which may then further evolve to exchange genes. Co-integrates represent a significative part of the plasmid population and their formation is controlled by the sequence of the recombination sites determining their compatibility between the recombining sites. We conclude that plasmids frequently exchange genes in Acinetobacter baumannii using Xer recombination, allowing a high level yet controlled plasticity involved in the acquisition and combination of resistance genes.

microbiology↗

bioRxiv2022

A subclass of the IS1202 family of bacterial insertion sequences targets XerCD recombination sites

IS1202, originally isolated from Streptococcus pneumonia in the mid-1990s had been previously tagged as an emerging IS family in ISfinder. While searching for plasmid-associated Xer recombinase recombination sites (xrs) in Acinetobacter baumannii, we observed that some insertion sequences related to IS1202 were repeatedly found abutting these sites in a number of plasmids. The plasmids often carried repeated xrs thought to form a new type of mobile genetic element (MGE) which uses the chromosomally-encoded XerCD recombinase for mobility. The MGE (xrs cassette) consist of xrs flanking one or a small number of genes often including different clinically important carbapenemase-encoding bla-OXA. The IS1202- related IS are inserted with their left, transposase proximal extremity, IRL, five base pairs from xrs and include a characteristic 5bp flanking target duplication. Further searches revealed that many different plasmid- and chromosome-borne xrs can be targeted and that IS1202-xrs combinations are not limited to Acinetobacter baumannii but occur in other bacteria. In addition to 28 IS1202 group ISs in ISfinder and a number which had been subsequently submitted, we undertook a survey of the NCBI (February 2020) and identified 138 additional IS1202-related IS. These could be divided into 3 principal subgroups based on their transposase sequences and on the length of the DR generated on insertion: subgroup IS1202 27-28bp DR); ISTde1 (15-17bp); and ISAba32 (5-6bp). Members of each group which lacked DR were also found. But since other examples of most of these were subsequently identified having DR, those lacking DR may have been generated by intra-replicon recombination. Only members of the group which generate 5bp DR were found to target xrs. These were not only identified in plasmids but also occurred at some individual xrs sites, dif, located at the chromosome replication terminus and involved in post-replication chromosome segregation. Further analysis showed the presence of subgroup-specific indels in their transposases which may be responsible for the differences in their behavior. We propose that this collection of IS be classed as a new insertion sequence family: the IS1202 family composed of at three subfamilies, only one of which specifically targets plasmid-borne xrs. We discuss the implications of xrs targeting for gene mobility.

genomics↗

bioRxiv2022

Characterization of the DNA binding domain of StbA, a key protein of a new type of DNA segregation system

Low-copy-number plasmids require sophisticated genetic devices to achieve efficient segregation of plasmid copies during cell division. Plasmid R388 uses a unique segregation mechanism, based on StbA, a small multifunctional protein. StbA is the key protein in a segregation system not involving a plasmid-encoded NTPase partner, it regulates the expression of several plasmid operons, and it is the main regulator of plasmid conjugation. The mechanisms by which StbA, together with the centromere-like sequence stbS, achieves segregation, is largely uncharacterized. To better understand the molecular basis of R388 segregation, we determined the crystal structure of the conserved N-terminal domain of StbA to 1.9 [A] resolution. It folds into an HTH DNA-binding motif, structurally related to that of the PadR subfamily II of transcriptional regulators. StbA is organized in two domains. Its N-terminal domain carries the specific stbS DNA binding activity. A truncated version of StbA, deleted of its C-terminal domain, displays only partial activities in vivo, indicating that the non-conserved C-terminal domain is required for efficient segregation and subcellular plasmid positioning. The structure of StbA DNA-binding domain also provides some insight into how StbA monomers cooperate to repress transcription by binding to the stbDR and to form the segregation complex with stbS.

microbiology↗

bioRxiv2018

Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases

BackgroundSome mobile genetic elements target the lagging strand template during DNA replication. Bacterial examples are insertion sequences IS608 and ISDra2 (IS200/IS605 family members). They use obligatory single-stranded circular DNA intermediates for excision and insertion and encode a transposase, TnpAIS200, which recognizes subterminal secondary structures at the insertion sequence ends. Similar secondary structures, Repeated Extragenic Palindromes (REP), are present in many bacterial genomes. TnpAIS200-related proteins, TnpAREP, have been identified and could be responsible for REP sequence proliferation. These proteins share a conserved HuH/Tyrosine core domain responsible for catalysis and are involved in processes of ssDNA cleavage and ligation. Our goal is to characterize the diversity of these proteins collectively referred as the TnpAY1 family.\n\nResultsA genome-wide analysis of sequences similar to TnpAIS200 and TnpAREP in prokaryotes revealed a large number of family members with a wide taxonomic distribution. These can be arranged into three distinct classes and 12 subclasses based on sequence similarity. One subclass includes sequences similar to TnpAIS200. Proteins from other subclasses are not associated with typical insertion sequence features. These are characterized by specific additional domains possibly involved in protein/DNA or protein/protein interactions. Their genes are found in more than 25% of species analyzed. They exhibit a patchy taxonomic distribution consistent with dissemination by horizontal gene transfers followed by loss. The tnpAREP genes of five subclasses are flanked by typical REP sequences in a REPtron-like arrangement. Four distinct REP types were characterized with a subclass specific distribution. Other subclasses are not associated with REP sequences but have a large conserved domain located in C-terminal end of their sequence. This unexpected diversity suggests that, while most likely involved in processing single-strand DNA, proteins from different subfamilies may play a number of different roles.\n\nConclusionsWe established a detailed classification of TnpAY1 proteins, consolidated by the analysis of the conserved core domains and the characterization of additional domains. The data obtained illustrate the unexpected diversity of the TnpAY1 family and provide a strong framework for future evolutionary and functional studies. By their potential function in ssDNA edition, they may confer adaptive responses to host cell physiology and metabolism.

genomics↗