Biology subjects

Lecointe, F.

Publications and source records attributed to Lecointe, F..

4 recordsLinked to original sources

bioRxiv2025

A Pair of DNA Glucosyltransferases Elevate Counter-defense in Bacteriophage T4

Bacteriophages encode diverse pathways to modify their nucleobases. These modifications help phages to evade the host defense systems such as restriction-modification (RM), and type II and type V CRISPR-Cas systems. On the other hand, modifications can also serve as a target for other host defense systems, illustrating the complexity of the defense and counter-defense landscape. Bacteriophage T4 encodes two glucosyltransferases (GTs), -GT and {beta}-GT, that post-replicatively add a glucose moiety to the hydroxymethylated deoxycytosines (5-hmC) on phage DNA in the - and {beta}-conformation, respectively. Among all known phages, only six closely related phages encode both -GT and {beta}-GT. Here, through biochemical and genetic analysis, we show that {beta}-GT has higher catalytic activity, whereas -GT is more strongly expressed. During the T4 infection, these factors determine the contributions of both GTs, with -GT and {beta}-GT contributing respectively to glucosylation of 66% and 33% of all 5-hmC. Encoding a single GTs is sufficient for T4 to overcome the E. coli type I and type IV RM systems, unless the glucosylation capacity decreases below the 80% threshold. However, when encountering a host encoding DNA glycosylase Brig1 in addition to type I and type IV RM systems, a second GT is necessary to enable Brig1 escapers to resist RM systems. These results demonstrate that encoding multiple GTs with redundant functionalities provides an evolutionary advantage when simultaneously confronted with multiple antiphage defense systems.

microbiology↗

bioRxiv2025

Atypical Replication Error Pattern and Limited Repair Efficiency Contribute to Elevated Mutation Rate in Phage lambda

Understanding the rate and nature of spontaneous mutations is crucial for understanding and modulating the pace and trajectory of evolution. Yet, both remain poorly characterized in double-stranded DNA (dsDNA) phages, despite their relevance for phage-based therapies. Here, we address this gap for the dsDNA phage lambda, using four complementary approaches: mutation accumulation assay combined with whole-genome sequencing, mutation visualization assay, duplex sequencing and fluctuation assay. We find that the mutation rate of wild-type phage lambda is 4.9 {+/-} 1.8 x10-9 per base per replication, approximately 15 times lower than previously estimated and about 20 times higher than that of its host, Escherichia coli (E. coli). Inactivation of Mismatch Repair (MMR), a major conserved cellular system for mutation avoidance, increases the lambda mutation rate by only 2-to 10-fold, in contrast to the approximately 150-fold increase in E. coli, however lambda does not exhibit the characteristic mutational bias associated with MMR deficiency. Interestingly replication of the lambda genome generates an error spectrum distinct from that of E. coli, characterized by a marked increase in transversions, poorly repaired by MMR. Together, these results reveal that lambda exhibits a replication error profile that is less amenable to repair, likely contributing to its elevated mutation rate.

microbiology↗

bioRxiv2023

Phage-mediated dispersal of multicellular bacteria

Streptomyces are renowned for their prolific production of specialized metabolites with applications in medicine and agriculture. These multicellular bacteria present a sophisticated developmental cycle, and play a key role in soil ecology. Little is known about Streptomyces-phage interactions and the impact of phages on Streptomyces physiology. In this study, we investigated the conditions governing the expression and production of Samy, a prophage found in Streptomyces ambofaciens ATCC 23877. This siphoprophage is produced simultaneously with the activation of other mobile genetic elements. We show that Samy production increases bacterial dispersal under in vitro stress conditions. Altogether, we unveiled a new property of a bacteriophage infection that it is closely linked to the multicellular community life of Streptomyces bacteria. Graphical summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/549817v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@126b3fcorg.highwire.dtl.DTLVardef@1f26808org.highwire.dtl.DTLVardef@18bfdcforg.highwire.dtl.DTLVardef@1c44be3_HPS_FORMAT_FIGEXP M_FIG C_FIG IMPORTANCEStreptomyces are multicellular bacteria producing valuable metabolites, including antibiotics, with applications in medicine and agriculture. In this study, we characterized a novel temperate phage, named Samy, and its impact on bacteria physiology. Remarkably, the presence and production of Samy increases bacterial dispersal under in vitro stress conditions. This constitutes an emerging property associated with bacteriophage infection that might enhance the spread of the species. Our study reveals a new aspect of bacteriophage infection in the context of multicellular aggregate dynamics.

microbiology↗

bioRxiv2022

Prophage taming by the adherent-invasive Escherichia coli LF82 upon macrophage infection

Adherent-invasive Escherichia coli (AIEC) strains are frequently recovered from stools of patients with dysbiotic microbiota. They have remarkable properties of adherence to the intestinal epithelium, and survive better than other E. coli in macrophages. The best studied of these AIEC is probably strain LF82, which was isolated from a Crohns disease patient. This strain contains five complete prophages, which have not been studied until now. We undertook their analysis, both in vitro and inside macrophages, and show that all of them form virions. The Gally prophage is by far the most active, generating spontaneously over 108 viral particles per mL of culture supernatants in vitro, more than 100-fold higher than the other phages. Gally is over-induced after a genotoxic stress generated by ciprofloxacin and trimethoprim. However, upon macrophage infection, Gally virion production is decreased by more than 20-fold, and the transcription profile of the prophage indicates that part of the structural module is specifically repressed while the replication module is overexpressed compared to unstressed culture conditions. We conclude that strain LF82 has evolved an efficient way to "tame" its most active prophage upon macrophage infection, which may participate to its good survival in macrophages. The results are discussed in light of the active lysogeny process. AUTHOR SUMMARYProphages are bacterial viruses stably integrated into their host, to which they can provide new functions, thus increasing their fitness in the environment. Thereby, they can participate to the virulence of bacterial pathogens. However, prophages are double-edged swords that can be awakened in response to genotoxic stresses, resulting in the death of their bacterial host. This raises the question of the effect of this type of stress in the natural environments where their bacterial hosts exert their virulence. In this study, we characterized the five active prophages present in Escherichia coli LF82, a strain belonging to the intestinal microbiota and suspected to be involved in Crohns disease via its ability to invade macrophages, a highly genotoxic environment. We show that LF82 inhibits the awakening of its prophages in macrophages, allowing it to survive there. Moreover, deletion of its most active prophage does not affect the viability of LF82 in this environment. These results show that LF82 has tamed its prophages in macrophages and also suggest that if they convey fitness advantages, they probably do so in environments differing from macrophages, and which remain to be discovered.

microbiology↗