Biology subjects

Ares-Arroyo, M.

Publications and source records attributed to Ares-Arroyo, M..

5 recordsLinked to original sources

bioRxiv2026

Genomic Islands as minimal hitchers of conjugative elements

Bacterial chromosomes contain Genomic Islands carrying genes involved in virulence, mutualism, and resistance to antibiotics that are transferred horizontally. Some of them conjugate autonomously (Integrative Conjugative Elements, ICEs), while others use relaxases to hitch on the formers conjugation machinery (Integrative Mobilizable Elements, IMEs). Yet, the mobility mechanism of most Genomic Islands remains elusive. Here, we explore the hypothesis that many carry origins of transfer (oriTs) by conjugation. Since very few known oriTs were found in ICEs and IMEs, we identified 52 novel families of oriTs that cover most integrative elements in 6 major nosocomial species. Most of these oriTs are specific to integrative elements, suggesting a clear split in the targets of hitchers of conjugative elements between plasmids and integrative elements. Among 7,363 Genomic Islands, we discovered more than 1,500 IMEs carrying an oriT and lacking relaxases and MPF systems. These elements, coined iOriTs, form diverse large ancient families that can be found in different species. These hitchers are genetically unrelated to the putative helpers, beyond the similarity at the oriT sequence, and often outnumber them. They include well-known pathogenicity islands, for which the mechanisms of mobility remained unknown. Unlike plasmids, iOriTs have few antibiotic resistance genes, but high density of virulence factors. Like plasmids, the vicinity of oriTs concentrates defense and counter-defense systems potentially favoring Genomic Islands dissemination. Hence, iOriTs are frequent integrative mobile genetic elements that evolved to transfer horizontally by hitching on other elements while contributing to bacterial genetic adaptation.

microbiology↗

bioRxiv2024

Identification of novel origins of transfer across bacterial plasmids

Conjugative plasmids are important drivers of bacterial evolution, but most plasmids lack genes for conjugation. It is currently not known if the latter can transfer because origins of transfer by conjugation (oriT), which would allow their mobilization by conjugative plasmids, are poorly known. Here, we identify and characterize occurrences of known oriT families across thousands of plasmids confirming that most conjugative and mobilizable plasmids still lack identifiable families of oriTs. They reveal clear patterns in terms of intergenic position, distance to the relaxases, and MOB-type association. This allowed to develop a computational method to discover novel oriTs. As a proof of concept, we identify 21 novel oriTs from the nosocomial pathogens Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii, some of them responsible for the mobility of critical antimicrobial resistance genes. These 21 oriT families share key characteristics of the others and fill most of the missing diversity of oriTs in relaxase-encoding plasmids both in terms of frequency and phylogeny. We confirmed experimentally the function of six of them. The ability to identify novel oriTs paves the way to explore conjugation across bacterial plasmids, notably among the majority lacking conjugation-related genes.

microbiology↗

bioRxiv2023

Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans

Type IV-A CRISPR-Cas systems are primarily encoded on plasmids and form multi-subunit ribonucleoprotein complexes with unknown biological functions. In contrast to other CRISPR-Cas types, they lack the archetypical CRISPR acquisition module and encode a DinG helicase instead of a nuclease component. Type IV-A3 systems are carried by large conjugative plasmids that often harbor multiple antibiotic-resistance genes. Although their CRISPR array contents suggest a role in inter-plasmid conflicts, this function and the underlying mechanisms have remained unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 CRISPR-Cas system co-opts the type I-E adaptation machinery from its clinical Klebsiella pneumoniae host to update its CRISPR array. Furthermore, we demonstrate that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By targeting plasmid core functions, type IV-A3 can prevent the uptake of incoming plasmids, limit their horizontal transfer, and destabilize co-residing plasmids, altogether supporting type IV-A3s involvement in plasmid competition. Collectively, our findings shed light on the molecular mechanisms and ecological function of type IV-A3 systems and have broad implications for understanding and countering the spread of antibiotic resistance in clinically relevant strains.

microbiology↗

bioRxiv2022

Towards solving the conundrum of plasmid mobility: networks of functional dependencies shape plasmid transfer

Plasmids are key drivers of bacterial evolution by transferring genes between cells via conjugation. Yet, half of the plasmids lack all protein coding genes for this process. We searched to solve this conundrum by identifying conjugative origins of transfer over thousands of plasmids and chromosomes of Escherichia coli and Staphylococcus aureus. We found that plasmids carrying these sequences are very abundant and have the highest densities of antimicrobial resistance genes. They are hyper-parasites that directly hijack conjugative or mobilizable elements, but not both. These functional dependencies explain the co-occurrence of each type of plasmid in cells and illuminate the evolutionary relationships between the elements. We characterized systematically the genetic traits of plasmids in relation to conjugation and alternative mechanisms of transfer, and can now propose a confident putative mechanism of transfer for ca. 90% of them. The few exceptions could be passively mobilized by other processes. We conclude there is no conundrum concerning plasmid mobility.

genomics↗

bioRxiv2017

Compensatory evolution facilitates the acquisition of multiple plasmids in bacteria

The coexistence of multicopy plasmids is a common phenomenon. However, the evolutionary forces promoting these genotypes are poorly understood. In this study, we have analyzed multiple ColE1 plasmids (pB1000, pB1005 and pB1006) coexisting within Haemophilus influenzae RdKW20 in all possible combinations. When transformed into the naive host, each plasmid type presented a particular copy number and produced a specific resistance profile and biological cost, whether alone or coexisting with the other plasmids. Therefore, there was no fitness advantage associated with plasmid coexistence that could explain these common plasmid associations in nature. Using experimental evolution, we showed how H. influenzae Rd was able to completely compensate the fitness cost produced by any of these plasmids. Crucially, once the bacterium has compensated for a first plasmid, the acquisition of new multicopy plasmid(s) did not produced any extra biological cost. We argue therefore that compensatory adaptation pave the way for the acquisition of multiple coexisting ColE1 plasmids.\n\nImportanceAntibiotic resistance is a major concern for human and animal health. Plasmids play a major role in the acquisition and dissemination of antimicrobial resistance genes. In this report we investigate, for the first time, how plasmids are capable to cohabit stably in populations. This coexistence of plasmids is driven by compensatory evolution alleviating the cost of a first plasmid, which potentiates the acquisition of further plasmids at no extra cost. This phenomenon explains the high prevalence of plasmids coexistance in wild type bacteria, which generates multiresistant clones and contributes to the maintenance and spread of antibiotic resistance genes within bacterial populations.

microbiology↗