Biology subjects

Leconte, J.

Publications and source records attributed to Leconte, J..

7 recordsLinked to original sources

bioRxiv2025

Capsular specificity in temperate phages of Klebsiella pneumoniae is driven by diverse receptor-binding enzymes

In bacteriophages infecting Klebsiella pneumoniae, capsule specificity is a major determinant of host range due to the presence of capsule-specific depolymerases. Yet for temperate phages, the genetic and functional basis of this specificity remains less well understood. Depolymerases appear unexpectedly rare in prophage genomes, raising unresolved questions about which prophage genes mediate capsule tropism, whether this apparent scarcity reflects biological or ecological differences versus annotation limits, and whether prophage-encoded receptor-binding proteins (RBPs) are functionally active. To address these questions, we analysed 3,900 Klebsiella genomes from diverse ecological niches to identify prophage-encoded proteins mediating capsule tropism. We conducted a genome-wide association study (GWAS) correlating prophage protein clusters (from 8,105 prophages) with confidently assigned bacterial K-loci. GWAS identified high-confidence predictors for 16 out of 35 most diverse K-loci, of which 14 were receptor-binding proteins (RBPs) belonging to classical depolymerases (n = 6), SGNH hydrolases which deacetylate polysaccharides (n = 6), and structurally novel RBPs (n = 2). Overall, we predicted K-locus specificity for 26 putative depolymerases, of which 12 were deemed as strong predictions against 10 K-loci. In parallel, we attempted recombinant production of 50 putative depolymerases selected from 469 candidate proteins identified in prophages from a representative subset of 99 bacterial isolates, together with an additional 10 depolymerases selected based on GWAS predictions. All recombinant proteins were tested against a Klebsiella reference panel of 119 K-types. Of the 50 manually chosen putative depolymerases, 34 failed to yield detectable recombinant expression, a pattern unlikely to be explained by degraded or defective prophages. Of the 14 active enzymes, 5 targeted a K-locus different from that of their bacterial host, and enzyme specificity could not always be reliably inferred from sequence similarity or structural homology. Comparison of GWAS predictions with experimental validation results revealed that 10 of the 12 strongest GWAS predictors were confirmed experimentally, while 2 produced soluble protein but showed no detectable activity against the tested K-types. Together, these results highlight the intrinsic difficulty of predicting activity and capsule specificity of prophage-encoded RBPs from genomic information alone. Finally, analysis of 4,598 high-completeness prophages revealed that SGNH-domain hydrolases are among the most prevalent enzymatic domains in prophage RBPs. Two SGNH-domain RBPs identified by GWAS were experimentally confirmed as active esterases, supporting capsule deacetylation as a widespread alternative to polysaccharide depolymerisation in temperate phages. Our findings reveal that Klebsiella prophages encode structurally diverse RBPs, suggesting temperate phages may rely not only on depolymerisation but also on capsule modification--such as deacetylation--for infection. This also implies that capsule diversity in K. pneumoniae may be substantially underestimated, with implications for phage specificity, competition and vaccine design.

microbiology↗

bioRxiv2024

Rapid and Accurate Estimation of Genetic Relatedness Between Millions of Viral Genome Pairs Using MANIAC

Average Nucleotide Identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimised for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference datasets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, here we introduce MANIAC, an efficient computational pipeline optimised for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%. Using a rigorous simulation framework, we demonstrate MANIACs accuracy and scalability compared to existing approaches, even to datasets of hundreds-of-thousands of viral genomes. Applying MANIAC to a curated dataset of complete bacterial dsDNA viruses revealed a multimodal ANI distribution, with a distinct gap around 80%, akin to the bacterial ANI gap ([~]90%) but shifted, likely due to viral-specific evolutionary processes such as recombination dynamics and mosaicism. We then evaluated ANI and AF as predictors of genus-level taxonomy using a logistic regression model. We found that this model has strong predictive power (PR-AUC=0.981), but that it works much better for virulent (PR-AUC=0.997) than temperate (PR-AUC=0.847) bacterial viruses. This highlights the complexity of taxonomic classification in temperate phages, known for their extensive mosaicism, and cautions against over-reliance on ANI in such cases. MANIAC can be accessed under https://github.com/bioinf-mcb/MANIAC. ImportanceWe introduce a novel computational pipeline called MANIAC, designed to accurately assess Average Nucleotide Identity (ANI) and alignment fraction (AF) between diverse viral genomes, scalable to datasets of over 100k genomes. Through the use of computer simulations and real data analyses, we show that MANIAC could ac- curately estimate genetic relatedness between pairs of viral genomes around 60-70% ANI. We applied MANIAC to investigate the question of ANI discontinuity in bacterial dsDNA viruses, finding evidence for an ANI gap, akin to the one seen in bacteria but around ANI of 80%. We then assessed the ability of ANI and AF to predict taxonomic genus boundaries, finding its strong predictive power in virulent, but not in temperate phages. Our results suggest that bacterial dsDNA viruses may exhibit an ANI threshold (on average around 80%) above which recombination helps maintain population cohesiveness, as previously argued in bacteria.

bioinformatics↗

bioRxiv2022

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

The ever-increasing number of available microbial genomes and metagenomes provide new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, notably for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we first showed that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We then managed to identify clusters of adjacent genes that display specific distribution patterns in the field (CAGs) and are thus potentially involved in the adaptation to particular environmental niches. Several CAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine or phosphonates, which might be either directly used by cells, for e.g. the biosynthesis of proteins or DNA, or degraded into inorganic nitrogen and/or phosphorus forms. We also highlight the frequent presence of CAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas, which are absent in low-iron regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in these areas. In contrast, Prochlorococcus populations thriving in iron-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) into Fe(II). Together, this study provides insights into how these key members of the phytoplankton community might behave in response to ongoing global change. Significance StatementPicocyanobacteria face various environmental conditions in the ocean and numerous studies have shown that genetically distinct ecotypes colonize different niches. Yet the functional basis of their adaptation remains poorly known, essentially due to the large number of genes of yet unknown function, many of which have little or no beneficial effect on fitness. Here, by combining comparative genomics and metagenomics approaches, we have identified not only single genes but also entire gene clusters, potentially involved in niche adaptation. Although being sometimes present in only one or a few sequenced strains, they occur in a large part of the population in specific ecological niches and thus constitute precious targets for elucidating the biochemical function of yet unknown niche-related genes.

microbiology↗

bioRxiv2022

Global phylogeography of marine Synechococcus in coastal areas reveals strikingly different communities than in the open ocean

Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome dataset of the Ocean Sampling Day (June 21st 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study tackles the main differences between open-ocean and coastal communities worldwide.

microbiology↗

bioRxiv2021

Equatorial to Polar genomic variability of the microalgae Bathycoccus prasinos

Phytoplankton plays a fundamental role in the ecology of ocean systems and is the key player in the global carbon cycle. At a time of global warming, understanding the mechanisms of its adaptation to temperature is therefore of paramount importance. Cosmopolitan planktonic species abundant in different marine environments provide both a unique opportunity and an efficient methodological tool to study the genomic bases of their adaptation. This is the case for the eukaryotic picoalga Bathycoccus prasinos, whose genomic variability we chose to study in temperate and polar oceanic waters. Using multiple metagenomic datasets, we found that ~5% of B. prasinos genomic positions are variable, with an overwhelming majority of biallelic motifs. Cold and temperate waters are clearly associated with changes in variant frequencies, whereas in transitional waters we found more balanced polymorphism at most of these positions. Mesophilic and psychrophilic gene variants are distinguished by only a few amino acid changes located at positions critical for physical and functional protein properties. These results provide new information on the genomic diversity of a cosmopolitan eukaryotic planktonic specie and reveal "minimal mutational strategies" which finely tune the properties of specific proteins at different temperatures.

genomics↗

bioRxiv2020

Restructuring of genomic provinces of surface ocean plankton under climate change

The impact of climate change on diversity, functioning and biogeography of marine plankton remains a major unresolved issue. Here, niche theory is applied to plankton metagenomes of 6 size fractions, from viruses to meso-zooplankton, sampled during the Tara Oceans expedition. Niches are used to derive plankton size-dependent structuring of the oceans south of 60{degrees}N in climato-genomic provinces characterized by signature genomes. By 2090, assuming the RCP8.5 high warming scenario, provinces would be reorganized over half of the considered ocean area and quasi-systematically displaced poleward. Particularly, tropical provinces would expand at the expense of temperate ones. Sea surface temperature is identified as the main driver of changes (50%) followed by phosphate (11%) and salinity (10%). Compositional shifts among key planktonic groups suggest impacts on the nitrogen and carbon cycles. Provinces are linked to estimates of carbon export fluxes which are projected to decrease on average by 4% in response to biogeographical restructuring.

ecology↗

bioRxiv2019

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical and physical context of the ocean (the seascape) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.

ecology↗