Transposable Prophages in Leptospira: An Ancient, Now Diverse, Group Predominant in Causative Agents of Weil’s Disease

Ndela, Éric Olo; Enault, François; Toussaint, Ariane

doi:10.3390/ijms222413434

Cited by 4 publications

(3 citation statements)

References 51 publications

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“…Of note, insertion sequence (IS) transposase-like CDSs were found at or near the boundaries of the rfb cluster ( Fig S4 and Table S5, fourth and fifth sheets). Genomic rearrangements involving inversions have been reported in other Leptospira species ( Nascimento et al, 2004 ; Olo Ndela et al, 2021 ), some of which are indeed IS-mediated ( Nascimento et al, 2004 ).…”

Section: Resultsmentioning

confidence: 99%

Horizontal transfer of therfbcluster inLeptospirais a genetic determinant of serovar identity

et al. 2022

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Leptospirabacteria comprise numerous species, several of which cause serious disease to a broad range of hosts including humans. These spirochetes exhibit large intraspecific variation, resulting in complex tabulations of serogroups/serovars that crisscross the species classification. Serovar identity, linked to biological/clinical phenotypes, depends on the structure of surface-exposed LPS. Many LPS biosynthesis–encoding genes reside within the chromosomicrfbgene cluster. However, the genetic basis of intraspecies variability is not fully understood, constraining diagnostics/typing methods to cumbersome serologic procedures. We now show that the gene content of therfbcluster strongly correlates withLeptospiraserovar designation. Whole-genome sequencing of pathogenicL. noguchii, including strains of different serogroups, reveals that therfbcluster undergoes extensive horizontal gene transfer. Therfbclusters from severalLeptospiraspecies disclose a univocal correspondence between gene composition and serovar identity. This work paves the way to genetic typing ofLeptospiraserovars, and to pinpointing specific genes within the distinctrfbclusters, encoding host-specific virulence traits. Further research shall unveil the molecular mechanism ofrfbtransfer amongLeptospirastrains and species.

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Section: Resultsmentioning

confidence: 99%

Horizontal transfer of therfbcluster inLeptospirais a genetic determinant of serovar identity

et al. 2022

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“…The final dataset consisted of 172 viral sequences, in total. All the proteins encoded in these sequences were categorized into OGs by a two‐step procedure as described in Olo Ndela et al (2021) and in the Supplementary Information (Section 1.2.2).…”

Section: Methodsmentioning

confidence: 99%

Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics

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Enault

Midoux

et al. 2022

Environmental Microbiology

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Diversity of viruses infecting non‐extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head‐tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near‐complete genomes of spindle‐shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head‐tailed virus‐like particles and the presence of spindle‐shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens.

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“…To identify all protein coding genes in these small genomes, including overlapping and overprinted ones, all ORFs of at least eighteen residues were identified in these forty-nine microvirus genomes using getorf from the EMBOSS suite ( Rice, Longden, and Bleasby 2000 ). The 4,719 identified ORFs were organized into orthologous groups (OGs) in a two-step procedure as in Olo Ndela, Enault, and Toussaint (2021) : (1) all proteins were compared to each other using MMseqs2 ( Steinegger and Söding 2017 ) (bit-score ≥50 and reciprocal coverage >70%) and clustered using MCL v14-137 ( Enright, Van Dongen, and Ouzounis 2002 ) (inflation 2.0); and (2) for each protein cluster, a multiple alignment was built using Clustal Omega ( Sievers et al. 2011 ) and transformed into an HMM profile and all profiles were compared to each other using HHsearch of the HH-suite toolkit ( Steinegger et al 2019 ) (version 2.0.16, cut-offs: probability ≥90% and coverage ≥50%).…”

Section: Methodsmentioning

confidence: 99%

Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages

et al. 2022

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Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, the Amoyvirinae, has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics datasets from various aquatic ecosystems, of 16 complete microvirus genomes significantly smaller (from 2.991 to 3.692 kb) than known ones. Phylogenetic analysis reveals that these 16 genomes represent two related, yet distinct and diverse, novel groups of microviruses, amoyviruses being their closest known relatives. We propose that these small microviruses be members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae. As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction softwares, we developed a new methodology to identify all genes based on protein conservation, amino-acid composition, and selection pressure estimations. Surprisingly, only 4 to 5 genes could be identified per genome, with a number of overprinted genes lower than in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small numbers of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and is further evidence that these viruses have explored a wide range of possibilities during their long evolution.

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Transposable Prophages in Leptospira: An Ancient, Now Diverse, Group Predominant in Causative Agents of Weil’s Disease

Cited by 4 publications

References 51 publications

Horizontal transfer of therfbcluster inLeptospirais a genetic determinant of serovar identity

Horizontal transfer of therfbcluster inLeptospirais a genetic determinant of serovar identity

Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics

Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages

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