ORCID Profile
0000-0002-7633-8476
Current Organisation
INRA Centre Angers-Nantes
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Publisher: Microbiology Society
Date: 06-2011
Abstract: Bacteria encode multiple protein secretion systems that are crucial for interaction with the environment and with hosts. In recent years, attention has focused on type VI secretion systems (T6SSs), which are specialized transporters widely encoded in Proteobacteria. The myriad of processes associated with these secretion systems could be explained by subclasses of T6SS, each involved in specialized functions. To assess ersity and predict function associated with different T6SSs, comparative genomic analysis of 34 Pseudomonas genomes was performed. This identified 70 T6SSs, with at least one locus in every strain, except for Pseudomonas stutzeri A1501. By comparing 11 core genes of the T6SS, it was possible to identify five main Pseudomonas phylogenetic clusters, with strains typically carrying T6SSs from more than one clade. In addition, most strains encode additional vgrG and hcp genes, which encode extracellular structural components of the secretion apparatus. Using a combination of phylogenetic and meta-analysis of transcriptome datasets it was possible to associate specific subsets of VgrG and Hcp proteins with each Pseudomonas T6SS clade. Moreover, a closer examination of the genomic context of vgrG genes in multiple strains highlights a number of additional genes associated with these regions. It is proposed that these genes may play a role in secretion or alternatively could be new T6S effectors.
Publisher: Springer Science and Business Media LLC
Date: 26-07-2011
Publisher: Wiley
Date: 08-10-2012
DOI: 10.1111/J.1758-2229.2012.00394.X
Abstract: Bacteria can manipulate their surrounding environment through the secretion of proteins into other living organisms and into the extracellular milieu. In Gram stain negative bacteria this process is mediated by different types of secretion systems from type I through type VI secretion system (T1SS-T6SS). In this study the prevalence of these secretion systems in 312 publicly available microbiomes derived from a wide range of ecosystems was investigated by a gene-centric approach. Our analysis demonstrates that some secretion systems are over-represented in some specific s les. In addition, some T3SS and T6SS phylogenetic clusters were specifically enriched in particular ecological niches, which could indicate specific bacterial adaptation to these environments.
Publisher: Elsevier BV
Date: 03-2013
DOI: 10.1016/J.YMPEV.2012.12.014
Abstract: Signal perception and transduction through tightly coordinated circuits is integral to the survival and persistence of microbes in erse ecological niches. The capacity to adapt to changes in the environment is central to their ability to thrive under adverse circumstances. Signal dependent transcriptional regulators are a key mechanism through which microbes assimilate environmental cues and mediate the appropriate adaptive response. By far the largest class of transcriptional regulator is the LysR-class, which is universally distributed among bacteria, archaea, and even eukaryotic organisms. The number of LysR-Type Transcriptional Regulators (LTTRs) varies among species with one of the largest repertoires encoded in the genome of the nosocomial pathogen Pseudomonas aeruginosa. To understand the evolutionary basis for this, we undertook to analyse the relationship between the LTTRs, both at the species and genus level. Phylogenetic analysis of the complete Pseudomonas LTTR dataset revealed significant cluster patterns based on full length and domain analysis. Interestingly, evidence of acquisition through horizontal gene transfer was rare, with ergent evolution apparently favoured. Furthermore, genes that appear to have been acquired, as well as those with a non-classical topological arrangement were clustered in distinct groups in the phylogenetic trees, indicating some ancestral association. The conservation within clusters identified in this study will provide a useful platform for future molecular analyses.
Publisher: American Society for Microbiology
Date: 11-02-2012
DOI: 10.1128/JB.06601-11
Publisher: Springer Science and Business Media LLC
Date: 25-11-2010
Abstract: Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Catabolite repression control regulates a broad spectrum of genes in Pseudomonas . Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate nutritional status cues with the regulation of traits that are of ecological, industrial and clinical importance.
Publisher: Frontiers Media SA
Date: 2014
Publisher: Springer Science and Business Media LLC
Date: 25-01-2013
Abstract: Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens , as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. The F113 genome sequence and annotation has been recently reported. Comparative analysis of 50 genome sequences of strains belonging to the P. fluorescens group has revealed the existence of five distinct subgroups. F113 belongs to subgroup I, which is mostly composed of strains classified as P. brassicacearum . The core genome of these five strains is highly conserved and represents approximately 76% of the protein-coding genes in any given genome. Despite this strong conservation, F113 also contains a large number of unique protein-coding genes that encode traits potentially involved in the rhizocompetence of this strain. These features include protein coding genes required for denitrification, diterpenoids catabolism, motility and chemotaxis, protein secretion and production of antimicrobial compounds and insect toxins. The genome of P. fluorescens F113 is composed of numerous protein-coding genes, not usually found together in previously sequenced genomes, which are potentially decisive during the colonisation of the rhizosphere and/or interaction with other soil organisms. This includes genes encoding proteins involved in the production of a second flagellar apparatus, the use of abietic acid as a growth substrate, the complete denitrification pathway, the possible production of a macrolide antibiotic and the assembly of multiple protein secretion systems.
Publisher: Korean Society for Microbiology and Biotechnology
Date: 28-01-2014
Abstract: Environmental microorganisms are emerging as an important source of new enzymes for wide-scale industrial application. In this study, novel phytase genes were identified from a soil microbial community. For this, a function-based screening approach was utilized for the identification of phytase activity in a metagenomic library derived from an agricultural soil. Two novel phytases were identified. Interestingly, one of these phytases is an unusual histidine acid phosphatase family phytase, as the conserved motif of the active site of PhyX possesses an additional amino acid residue. The second phytase belongs to a new type, which is encoded by multiple open reading frames (ORFs) and is different to all phytases known to date, which are encoded by a single ORF.
Publisher: Wiley
Date: 25-02-2013
Abstract: Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar beet rhizosphere. The recent annotation of the F113 genome sequence has revealed that this strain encodes a wide array of secretion systems, including two complete type three secretion systems (T3SSs) belonging to the Hrp1 and SPI-1 families. While Hrp1 T3SSs are frequently encoded in other P. fluorescens strains, the presence of a SPI-1 T3SS in a plant-beneficial bacterial strain was unexpected. In this work, the genetic organization and expression of these two T3SS loci have been analysed by a combination of transcriptional reporter fusions and transcriptome analyses. Overexpression of two transcriptional activators has shown a number of genes encoding putative T3 effectors. In addition, the influence of these two T3SSs during the interaction of P. fluorescens F113 with some bacterial predators was also assessed. Our data revealed that the transcriptional activator hilA is induced by amoeba and that the SPI-1 T3SS could potentially be involved in resistance to amoeboid grazing.
Publisher: MDPI AG
Date: 03-06-2013
DOI: 10.3390/MD11061878
No related grants have been discovered for Matthieu Barret.