Biology subjects

Groux, R.

Publications and source records attributed to Groux, R..

5 recordsLinked to original sources

bioRxiv2024

From insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic Arsenophonus strains

Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens Candidatus Arsenophonus phytopathogenicus (Ap) and Ca. Phlomobacter fragariae (Pf) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the "Triatominarum" clade whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode plant cell-wall degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse proteobacteria infecting the plant vasculature. In silico predictions and expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopathogenicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes first acquired from other proteobacteria including phytopathogens. ImportanceWe investigate the genetic mechanisms of a transition in bacterial lifestyle. We focus on two phloem pathogens belonging to the genus Arsenophonus: Ca. Arsenophonus phytopathogenicus and Ca. Phlomobacter fragariae. Both bacteria cause economically significant pathologies, and they have likely emerged among facultative insect endosymbionts. Our genomic analyses show that both strains are highly similar to other strains of the genus associated with sap-sucking hemipterans, indicative of a recent lifestyle shift. Importantly, although the phytopathogenic Arsenophonus strains belong to distant clades, they share a small set of orthologs unique in the genus pangenome. We provide evidence that several of these genes produce hydrolytic enzymes that are secreted and target plant substrates. The acquisition and exchange of these genes may thus have played a pivotal role in the lifestyle transition of the phytopathogenic Arsenophonus strains..

microbiology↗

bioRxiv2023

PAPET: a collection of performant algorithms to identify 5-methyl cytosine from PacBio SequelII data

BackgroundCytosine followed by guanine (CpG) rich genomic regions are known important regulatory sequences among vertebrates. Their cytosines can be subjected to a variety of chemical modifications, one of which being 5-methylcytosine (5mC), usually coined CpG methylation. CpG methylation has been demonstrated to have a deep impact on the nearby regulated genes. The advent of single molecule real time sequencing methods have proven to be powerful enablers in this field of research because of the possibility to detect DNA chemical modification directly from the raw sequencing data. In this perspective, several 5mC detection methods have been proposed. ResultsIn this work we present PAPET - PacBio Prediction of Epigenetic Toolkit - a computational method to detect 5mC directly from PacBio SequelII raw sequencing data. We characterized the 5mC signatures in the raw data and proposed a framework to model them. We also assessed the effect of the DNA sequence alone on the signal and propose a normalization method to leverage this effect. From this, we designed a probabilistic approach to predict the presence of cytosine methylation from the sequencing kinetics and benchmarked it. ConclusionsWe apply this framework to predict CpG methylation from SequelII data and demonstrate that the classifiers compare equally with PacBios prediction method counterparts in terms of AUC and achieve very high specificity and precision.

bioinformatics↗

bioRxiv2021

Sphingolipids are involved in Pieris brassicae egg-induced cell death in Arabidopsis thaliana

In Brassicaceae, hypersensitive-like (HR-like) cell death is a central component of direct defenses triggered against eggs of the large white butterfly Pieris brassicae. The signaling pathway leading to HR-like in Arabidopsis is mainly dependent on salicylic acid (SA) accumulation, but downstream components are unclear. Here, we found that treatment with P. brassicae egg extract (EE) trigger changes in expression of sphingolipid metabolism genes in Arabidopsis and Brassica nigra. Disruption of ceramide synthase activity led to a significant decrease of EE-induced HR-like whereas SA signaling and reactive oxygen species levels were unchanged, suggesting that ceramides are downstream activators of HR-like. Sphingolipid quantifications showed that ceramides with C16:0 side-chains accumulated in both species, and this response was independent on SA accumulation. Finally, we provide genetic evidence that the modification of fatty acyl chains of sphingolipids modulates HR-like. Altogether, these results show that sphingolipids play a key and specific role during insect egg-triggered HR-like.

plant biology↗

bioRxiv2020

Natural variation in insect egg-induced cell death uncovers a role for L-type LECTIN RECEPTOR KINASE-I.1 in Arabidopsis

In Arabidopsis thaliana, a hypersensitive-like response (HR-like) is triggered underneath the eggs of the large white butterfly Pieris brassicae, and this response is dependent on salicylic acid (SA) accumulation and signaling. Previous reports indicate that the clade I L-type lectin receptor kinase LecRK-I.8 is involved in early steps of egg recognition. A genome-wide association study (GWAS) was used to better characterize the genetic structure of HR-like and discover loci that contribute to this response. We report here the identification of LecRK-I.1, a close homolog of LecRK-I.8, and show that two main haplotypes that explain part of the variation in HR-like segregate amongst natural Arabidopsis accessions. In addition, signatures of balancing selection at this locus suggest that it may be ecologically important. Disruption of LecRK-I.1 resulted in decreased HR-like and SA signaling, indicating that this protein is important for the observed responses. Furthermore, we provide evidence that LecRK-I.1 functions in the same signaling pathway as LecRK-I.8. Altogether, our results show that the response to eggs of P. brassicae is controlled by LecRKs that operate at various steps of the signaling pathway.

plant biology↗

bioRxiv2017

A systematic screen for morphological abnormalities during fission yeast sexual reproduction identifies a mechanism of actin aster formation for cell fusion

In non-motile fungi, sexual reproduction relies on stron morphogenetic changes in response to pheromone signaling. We report here on asystematic screen for morphological abnormalities o the mating process in fission yeast Schizosaccharomyces pombe. We derived a homothallic (self-fertile) collection of viable deletions which, upon visual screening, revealed a plethora of phenotype affecting all stages of the mating process, including cell polarizati cell fusion and sporulation. Cell fusion relies onthe formation of the fusion focus, an aster-like F-actin structure that is marked by stron local accumulation of the myosin V Myo52, which concentrates secretion at the fusion site. A secondaryscreen for fusion-defective mutants identified the myosin V Myo51-associated coiled-coil proteins Rng8 and Rng9 as critical forthe coalescence of the fusion focus Indeed, rng8{triangleup} and rng9{triangleup} mutant cells exhibitmultiple stable dots a the cell-cell contact site, instead of the single cusfo observed in wildtype. Rng8 and Rng9 accumulate on the fusion focus, depende on Myo51 and tropomyosin Cdc8A. tropomyosin mutant allele, whic compromises Rng8/9 localization but not actin binding, similarly lea to multiple stable dots instead of a single focus.By contrast, myo51 deletion does not strongly affect fusion focus coalescenceWe. propose that focusing of the actinfilaments in the fusionaster primarily relies on Rng8/9-dependent cross-linking of tropomyosin-actin filaments.

cell biology↗