Biology subjects

Jove, T.

Publications and source records attributed to Jove, T..

5 recordsLinked to original sources

bioRxiv2025

The bacterial SOS response promotes the expression of the transposase encoded by ISCR mobile genetic elements

Insertion sequences (IS) are widely involved in bacterial genomic plasticity by disrupting, adding, moving genomic sequences, or by activating or extinguishing gene expression. A specific family of IS, ISCR (for insertion sequence of Common Region), is thought to be involved in the dissemination of antibiotic resistance genes (ARG). While some ISCR members are commonly found in bacteria isolated in clinical settings and can contribute to downstream ARG expression, the mechanisms regulating the ISCR-encoded transposases expression have remained uncharacterized. Here, we investigated the expression of the transposase gene of ISCR1, ISCR2 and ISCR8, and its regulation in Escherichia coli. Using in silico analyses and in vitro experiments, we showed that expression levels were extremely low, as observed for most IS transposases. We further demonstrated the direct role of DNA damages and the key SOS response repressor, LexA, in controlling the activity of transposase promoter. These results provide evidence that the mobility of at least some ISCR elements may be promoted upon bacterial exposure to antibiotics inducing the SOS response. IMPORTANCEMobile genetic elements are the most prevalent cause of antibiotic resistance emergence. Among these mobile elements, insertion sequences (IS) are well known to allow the dissemination of antibiotic resistance genes through the action of their tranposase. Here, we studied the regulation of the transposase expression in a specific family of IS, the ISCR family, some members of which are known to be involved in antibiotic resistance. Characterizing the regulation of transposase expression is an important starting point for understanding how these IS can contribute, through their movement, to the spread and expression of antibiotic resistance. This knowledge is necessary if we are to hope to prevent this spread one day.

microbiology↗

bioRxiv2025

Dual regulatory role of IS91-encoded Orf121 in IS91 transposition

Prokaryotic insertion sequences (IS) are pivotal in the propagation of bacterial multidrug resistance, with IS91 notably linked to virulence and antibiotic resistance genes. However, the precise mechanism by which IS91 contributes to gene dissemination remains elusive. Unique among its family, IS91 features a small open reading frame (orf) upstream of the tnpA transposase gene, potentially encoding a 121-amino acid protein, orf121, which may be translationally coupled with tnpA. Using a genetic system based on the mating-out assay in Escherichia coli, we explored the role of orf121 in the in vivo transposition of IS91. Our findings indicate that the overlap between orf121 and tnpA is crucial for tnpA transcription, with both being primarily transcribed as bicistronic mRNAs from the Porf121 promoter. Additionally, the expression of orf121 (whether in cis or trans) significantly reduces the frequency of IS91 transposition and the rate of one-ended transposition. Furthermore, only the single-stranded DNA circles of IS91 intermediates can integrate into new target sequences, and Orf121 negatively influences this insertion step. In summary, orf121 acts as a negative regulator of transposition while ensuring the expression of tnpA, thus providing insights into the complex mechanisms underlying IS91-mediated gene dissemination and its potential role in antibiotic resistance propagation.

molecular biology↗

bioRxiv2024

Mobile Integrons Encode Phage Defence Systems

Integrons are bacterial genetic elements that capture, stockpile and modulate the expression of genes encoded in integron cassettes. Mobile Integrons (MI) are borne on plasmids, acting as a vehicle for hundreds of antimicrobial resistance genes among key pathogens. These elements also carry gene cassettes of unknown function (gcus) whose role and adaptive value remains unexplored. Here we show that gcus encode phage resistance systems, many of which are novel. Bacteriophage resistance integron cassettes (BRiCs) can be combined and mixed with resistance cassettes to produce multiphage or drug/phage-resistance. The fitness costs of BRiCs are variable, dependent on the genetic context, and can be modulated by changing the order of cassettes in the array. Hence, MIs act as highly mobile, low-cost defense islands. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/601719v4_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@965766org.highwire.dtl.DTLVardef@442763org.highwire.dtl.DTLVardef@7600d4org.highwire.dtl.DTLVardef@13068ca_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSummary FigureC_FLOATNO Novel phage defense systems identified in Mobile Integrons. We confronted genes of unknown function from mobile integrons against a panel of phage. We characterized 13 Bacteriophage Resistance integron Cassettes (BRiCs) and confirmed their function in Klebsiella pneumoniae and Pseudomonas aeruginosa. Combined with other cassettes, BRiCs produce multi-phage/antibiotic resistance. Additionally, their cost can be reduced in an array. C_FIG

microbiology↗

bioRxiv2023

Hospital and urban wastewaters shape the structure and active resistome of environmental biofilms

BackgroundDemonstration of the transfer, dynamics, and regulation of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in a complex environmental matrix is yet experimentally challenging, with many essential open questions such as how and where transfer and dissemination of ARGs happens in nature. The extent and conditions of MGEs transfer that carry ARGs is still largely unexplored in natural environments and microbial communities. Biofilms are structures that include high density multi-species bacterial communities embedded in self-produced extracellular polymeric substances (EPS) constituting a matrix that facilitates gene transfer and where bacteria exhibit high tolerance to stress and to antibiotics. In this study we implemented a sampling and analysis approach that allows phenotypic and genomic analyses of in situ and reconstituted in vitro hospital and urban wastewater (WW) biofilms. To assess the potential of hospital and urban WW biofilms to efficiently disseminate ARGs in the WW system, we explored the EPS within the biofilm matrix and assessed the expression of the resistome (ARGs) and mobilome (MGEs) by metatranscriptomics. ResultsWe first showed that a) the composition of EPS differs depending on their growth environment (in situ and in vitro) and their sampling origin (hospital vs urban WW) and that b) a low amount of ciprofloxacin impacted the composition of the EPS. Next, the metatranscriptomic approach showed that a) expression of ARGs and MGEs increase upon adding a low amount of ciprofloxacin for biofilms from hospital WW but not for those from urban WW and b) that expression of specific plasmids that carry individual or multiple ARGs varies depending on the WW origins of the biofilms. When the same plasmids were expressed in both, urban and hospital WW biofilms, they carried and expressed different ARGs. ConclusionWe show that hospital and urban wastewaters shape the structure and active resistome of environmental biofilms, and we confirmed that hospital WW is an important hot spot for the dissemination and selection of AMR. The different responses to antibiotic pressure in hospital vs urban biofilms, coupled with differences in biofilm structure helps delineate distinct characteristics of hospital and urban WW biofilms highlighting the relationships between the resistome and its expression in environmental biofilms and their surrounding ecosystems.

microbiology↗

bioRxiv2021

A qnr-plasmid allows aminoglycosides to induce SOS in Escherichia coli

The plasmid-mediated quinolone resistance (PMQR) genes have been shown to promote high-level bacterial resistance to fluoroquinolone antibiotics, potentially leading to clinical treatment failures. In Escherichia coli, sub-inhibitory concentrations (sub-MIC) of the widely used fluoroquinolones are known to induce the SOS response. Interestingly, the expression of several PMQR qnr genes is controlled by the SOS master regulator. During the characterization of a small qnrD-plasmid carried in E. coli, we observed that the aminoglycosides become able to induce the SOS response in this species, thus leading to the transcription of qnrD. We found that induction of the SOS response is due to nitric oxide (NO) accumulation in presence of sub-MIC of aminoglycosides. We demonstrated that the NO accumulation is driven by two plasmid genes, ORF3 and ORF4, whose products act at two levels. ORF3 encode a FAD-binding oxidoreductase which helps NO synthesis, while ORF4 code for an FNR-type transcription factor, related to an O2-responsive regulator of hmp expression, able to repress the Hmp-mediated NO detoxification pathway of E. coli. Thus, this discovery, that other major classes of antibiotics may induce the SOS response could have worthwhile implications for antibiotic stewardship efforts in preventing the emergence of resistance.

microbiology↗