Biology subjects

Littner, E.

Publications and source records attributed to Littner, E..

5 recordsLinked to original sources

bioRxiv2025

Unraveling the prevalence and multifaceted roles of accessory peptide deformylases in bacterial adaptation and resistance

Peptide deformylases (PDFs) are enzymes that are essential for bacterial viability and attractive targets for antibiotic development. Yet, despite their conserved function, many bacteria encode multiple PDFs, a genomic feature whose prevalence and implications remain largely unexplored. Here, we reveal that nearly half of all bacterial genomes carry more than one PDF gene, frequently embedded within mobile genetic elements such as plasmids and integrons. In Vibrio cholerae, the accessory PDF (Def2VCH) confers reduced susceptibility to actinonin (ACT), the most studied PDF inhibitor, while still supporting bacterial growth in absence of the canonical PDF copies (Def1VCH). Crystallographic analysis shows that this reduced susceptibility stems from an arginine-to-tyrosine substitution that probably reduces ACT binding. Strikingly, this resistance signature is shared by integron-encoded PDFs, and transfer of an integron-encoded PDF cassette from Pseudoxanthomonas into a susceptible V. cholerae is sufficient to abolish ACT susceptibility. These findings expose a cryptic reservoir of resistance within the bacterial mobilome and highlight a challenge to the therapeutic potential of PDF-targeting antibiotics: resistance may not only emerge, but is already encoded, mobile, and ready to spread.

microbiology↗

bioRxiv2024

Sedentary chromosomal integrons as biobanks of bacterial anti-phage defence systems

Integrons are genetic systems that accelerate bacterial adaptation by acquiring and shuffling gene cassettes. Mobile integrons spread antibiotic resistance genes among bacteria, while the sedentary chromosomal integrons contain up to hundreds of cassettes of unknown function. Here, we show that many of these cassettes encode anti-phage defence systems. We found numerous streamlined variants of known systems, which have presumably evolved to fit the small size constraints of integron cassettes recombination and genesis. Intrigued by the rarity of known systems in the sedentary chromosomal integron of the Vibrio cholerae 7th cholera pandemic strain, we tested the presence of anti-phage functions in all its cassettes of unknown function. We found that at least 16 of the strain cassettes have an anti-phage activity in V. cholerae or E. coli. This represents 18% of the tested cassettes and almost 10% of all the integron cassettes, providing at long last a key adaptive role for a significant fraction of the sedentary integrons. Most of the newly discovered systems have little or no similarity to previously known ones and our experiments show that several mediate defence through cell lysis or growth arrest. One of these systems encodes a 64 amino acids protein, which represents the smallest known protein providing autonomous phage resistance. Given the thousands of uncharacterized integron cassette families, integrons could represent an untapped treasure trove of streamlined anti-phage systems.

genetics↗

bioRxiv2023

Belt and braces: two escape ways to maintain the cassette reservoir of large chromosomal integrons

Integrons are adaptive devices that capture, stockpile, shuffle and express gene cassettes thereby sampling combinatorial phenotypic diversity. Some integrons called sedentary chromosomal integrons (SCIs) can be massive structures containing hundreds of cassettes. Since most of these cassettes are non-expressed, it is not clear how they remain stable over long evolutionary timescales. Recently, it was found that the experimental inversion of the SCI of Vibrio cholerae led to a dramatic increase of the cassette excision rate associated to a fitness defect. Here, we question the evolutionary sustainability of this apparently counter selected genetic context through experimental evolution. We find that the integrase is rapidly inactivated and that the inverted SCI can recover its original orientation by homologous recombination between two insertion sequences (ISs) present in the array. These two outcomes of SCI inversion restore the normal growth and prevent the loss of cassettes, enabling SCIs to retain their roles as reservoirs of functions. These results illustrate an interesting interplay between gene orientation, genome rearrangement, bacterial fitness and demonstrate how integrons can benefit from their embedded ISs.

genetics↗

bioRxiv2022

Genetic drivers of chromosomal integron stability

Integrons are adaptive bacterial devices that rearrange promoter less gene cassettes into variable ordered arrays under stress conditions, to sample combinatorial phenotypic diversity. Chromosomal integrons often carry hundreds of silent gene cassettes, with integrase-mediated recombination leading to rampant DNA excision and integration, posing a potential threat to genome integrity. How this activity is regulated and controlled, particularly through selective pressures, to maintain such large cassette arrays is unknown. Here we show a key role of promoter-containing toxin-antitoxin (TA) cassettes as abortive systems that kill the cell when the overall cassette excision rate is too high. These results highlight the importance of TA cassettes regulating the cassette recombination dynamics and provide insight into the evolution and success of integrons in bacterial genomes. TeaserThe accumulation of cassette functions in integrons is ensured by toxin-antitoxin systems which kill the cell when the cassette excision rate is too high.

genetics↗

bioRxiv2022

IntegronFinder 2.0: identification and analysis of integrons across Bacteria, with a focus on antibiotic resistance in Klebsiella

Integrons are mobile genetic elements that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4 thousand Klebsiella pneumoniae genomes for the presence of integrons and antibiotic resistance genes within them. Our data shows that K. pneumoniae has a large diversity of integrons and the largest mobile integron in our database of plasmids. The pangenome of these integrons contains a total of 165 different gene families with most of the largest families being related with resistance to numerous types of antibiotics. IntegronFinder is a free and open-source software available at https://github.com/gem-pasteur/Integron_Finder.

bioinformatics↗