Biology subjects

Brochier-Armanet, C.

Publications and source records attributed to Brochier-Armanet, C..

5 recordsLinked to original sources

bioRxiv2023

Description of a new genus of the Pectobacteriaceae family isolated from lake water in France; Prodigiosinella aquatilis gen. nov. sp. nov. includes two subspecies Prodigiosinella aquatilis subsp. aquatilis ssp. nov. and Prodigiosinella aquatilis subsp. natabilis ssp. nov.

The Pectobacteriaceae family comprises plant pathogens able to provoke diverse diseases, including plant maceration due to the production of pectinases disrupting the plant cell wall. To better understand their natural diversity, a survey of pectinolytic bacteria was performed in lakes of the French region La Camargue near the Mediterranean Sea. Sixteen atypical pectinolytic isolates were obtained from brackish water of three lakes. The genome of six isolates was sequenced; their size is around 4.8 to 5.0 Mb, including a plasmid of 59 to 61 kb; their G+C values range from 49.1 to 49.3 mol%. Phylogenetic analyses indicated that the novel strains formed a new clade of Pectobacteriaceae, separate from previously described genera of this family. These analyses suggested also that Acerihabitans does not belong to Pectobacteriaceae and should be reclassified in the Bruguierivoracaceae family, while Symbiopectobacterium could be a true Pectobacteriaceae member. Based on phenotypic, genomic and phylogenetic characteristics, we propose the creation of a new genus with the name Prodigiosinella gen. nov. Both the phenotypic and phylogenetic analyses separated the strains into two distinct subgroups. However, the DNA-DNA relatedness values revealed a close relationship between the two groups, supporting their appurtenance to the same species. Thus, it is proposed to classify them as two subspecies of Prodigiosinella aquatilis sp. nov., for which we propose the name Prodigiosinella aquatilis subsp. aquatilis ssp. nov. (LS101T = CFBP 8826T = LMG 32072T) and Prodigiosinella aquatilis subsp. natabilis ssp. nov. (CE70T = CFBP 9054T = LMG 32867T).

microbiology↗

bioRxiv2021

Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes.

O_LIWe recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants. Based on our estimate of its age, we predicted that it should be shared by its sister genus Humulus, which is known to also possess XY sex chromosomes. C_LIO_LIHere, we used transcriptome sequencing of a F1 family of Humulus lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETector. C_LIO_LIWe identified 265 sex-linked genes in H. lupulus, located on the chromosome that is also the C. sativa sex chromosome pair. Using phylogenies of sex-linked genes, we show that a region of these chromosomes had already stopped recombining in the common ancestor of the two species. Furthermore, as in C. sativa, Y gene expression was reduced in correlation to the position on the X chromosome, and strongly Y degenerated genes showed dosage compensation. C_LIO_LIHere we report, for the first time in the Angiosperms, a sex chromosome system that is shared by two different genera. Recombination suppression started at least 21-25 My ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes, leading to a strongly degenerated Y. C_LI

evolutionary biology↗

bioRxiv2019

The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Originality-Significance statementAlthough the reach of large-scale comparative studies has spread exponentially over the years, the phytopathogenic Dickeya group remains overlooked. In this work, we sequence the complete genome of Dickeya aquatica type strain, a species isolated from water that was first assumed to be non-phytopathogenic. We show that the proteome of D. aquatica contains a wide number of proteins involved in Dickeya virulence, including plant cell wall degrading enzymes, suggesting that this species could be in fact pathogenic. Using experimental approaches, we confirm this prediction and uncover the particular affinity of D. aquatica for acidic fruits. In-depth phylogenomic analyses reveal that Dickeya species display a great degree of genetic plasticity in the pathogenicity determinants, explaining how this bacterial group was able to colonize a wide variety of plants growing in different climates. These observations greatly advance our understanding of how bacteria adapt to new ecological niches.\n\nSummaryDickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep-branching species among Dickeya genus, its precise phylogenetic position remained elusive.\n\nHere, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquaticaT for acidic fruits such as tomato and cucumber, and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothetize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflects adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.

genomics↗

bioRxiv2018

Identification of a novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA

Polyamines are small amino-acid derived polycations capable of binding negatively charged macromolecules. Bacterial polyamines are structurally and functionally diverse, and are mainly produced biosynthetically by PLP-dependent amino acid decarboxylases referred to as LAOdcs (Lysine-Arginine-Ornithine decarboxylases). In a phylogenetically limited group of bacteria, LAOdcs are also induced in response to acid stress. Here, we performed an exhaustive phylogenetic analysis of the AAT-fold LAOdcs which showcased the ancestral nature of their short forms in Cyanobacteria and Firmicutes, and emergence of distinct subfamilies of long LAOdcs in Proteobacteria. We identified a novel subfamily of lysine decarboxylases, LdcA, ancestral in Betaproteobacteria and Pseudomortadaceae {Gammaproteobacteria). We analyzed the expression of LdcA from Pseudomonas aeruginosa, and uncovered its role, intimately linked to cadaverine production, in promoting growth and reducing persistence of this multidrug resistant human pathogen during carbenicillin treatment. Finally, we documented a certain redundancy in the function of the three main polyamines - cadaverine, putrescine and spermidine - in P. aeruginosa by demonstrating the link between their intracellular level, as well as the capacity of putrescine and spermidine to complement the growth phenotype of the IdcA mutant.

microbiology↗

bioRxiv2017

Osteo-Oto-Hepato-Enteric Syndrome (O2HE) is caused by loss of function mutations in UNC45A

Despite the rapid discovery of genes for rare genetic disorders, we continue to encounter individuals presenting with hitherto unknown syndromic manifestations. Here, we have studied four affected people in three families presenting with cholestasis, congenital diarrhea, impaired hearing and bone fragility, a clinical entity we have termed O2HE (Osteo-Oto-Hepato-enteric) syndrome. Whole exome sequencing of all affected individuals and their parents identified biallelic mutations in Unc-45 Myosin Chaperone A (UNC45A), as a likely driver for this disorder. Subsequent in vitro and in vivo functional studies of the candidate gene indicated a loss of function paradigm, wherein mutations attenuated or abolished protein activity with concomitant defects in gut development and function.

genetics↗