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[hal-01190026] High genetic diversity among strains of the unindustrialized lactic acid bacterium carnobacterium maltaromaticum in dairy products as revealed by multilocus sequence typing
Dairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter. Carnobacterium maltaromaticum is a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makes C. maltaromaticum an interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genes dapE, ddlA, glpQ, ilvE, pyc, pyrE, and leuS was applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products.
ano.nymous@ccsd.cnrs.fr.invalid (Abdur Rahman) 01 Sep 2015
https://hal.science/hal-01190026v1
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[hal-02498291] Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective
Lactic acid bacteria (LAB) are representative members of multiple ecosystems on earth, displaying dynamic interactions within animal and plant kingdoms in respect with other microbes. This highly heterogeneous phylogenetic group has coevolved with plants, invertebrates, and vertebrates, establishing either mutualism, symbiosis, commensalism, or even parasitism-like behavior with their hosts. Depending on their location and environment conditions, LAB can be dominant or sometimes in minority within ecosystems. Whatever their origins and relative abundance in specific anatomic sites, LAB exhibit multifaceted ecological and functional properties. While some resident LAB permanently inhabit distinct animal mucosal cavities, others are provided by food and may transiently occupy the gastrointestinal tract. It is admitted that the overall gut microbiome has a deep impact on health and diseases. Here, we examined the presence and the physiological role of LAB in the healthy human and several animal microbiome. Moreover, we also highlighted some dysbiotic states and related consequences for health, considering both the resident and the so-called "transionts" microorganisms. Whether LAB-related health effects act collectively or follow a strain-specificity dogma is also addressed. Besides the highly suggested contribution of LAB to interplay with immune, metabolic, and even brain-axis regulation, the possible involvement of LAB in xenobiotic detoxification processes and metal equilibrium is also tackled. Recent technological developments such as functional metagenomics, metabolomics, high-content screening and design in vitro and in vivo experimental models now open new horizons for LAB as markers applied for disease diagnosis, susceptibility, and follow-up. Moreover, identification of general and more specific molecular mechanisms based on antioxidant, antimicrobial, anti-inflammatory, and detoxifying properties of LAB currently extends their selection and promising use, either as probiotics, in traditional and functional foods, for dedicated treatments and mostly for maintenance of normobiosis and homeostasis.
ano.nymous@ccsd.cnrs.fr.invalid (Fanny George) 05 Mar 2020
https://hal.univ-lorraine.fr/hal-02498291v1
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[hal-01204353] The genome of the white-rot fungus [i]Pycnoporus cinnabarinus[/i]: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown
Saprophytic filamentous fungi are ubiquitous micro-organisms that play an essential role in photosynthetic carbon recycling. The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall decomposition and is used for a number of applications in green and white biotechnology.[br/] The 33.6 megabase genome of P. cinnabarinus was sequenced and assembled, and the 10,442 predicted genes were functionally annotated using a phylogenomic procedure. In-depth analyses were carried out for the numerous enzyme families involved in lignocellulosic biomass breakdown, for protein secretion and glycosylation pathways, and for mating type. The P. cinnabarinus genome sequence revealed a consistent repertoire of genes shared with wood-decaying basidiomycetes. P. cinnabarinus is thus fully equipped with the classical families involved in cellulose and hemicellulose degradation, whereas its pectinolytic repertoire appears relatively limited. In addition, P. cinnabarinus possesses a complete versatile enzymatic arsenal for lignin breakdown. We identified several genes encoding members of the three ligninolytic peroxidase types, namely lignin peroxidase, manganese peroxidase and versatile peroxidase. Comparative genome analyses were performed in fungi displaying different nutritional strategies (white-rot and brown-rot modes of decay). P. cinnabarinus presents a typical distribution of all the specific families found in the white-rot life style. Growth profiling of P. cinnabarinus was performed on 35 carbon sources including simple and complex substrates to study substrate utilization and preferences. P. cinnabarinus grew faster on crude plant substrates than on pure, mono- or polysaccharide substrates. Finally, proteomic analyses were conducted from liquid and solid-state fermentation to analyze the composition of the secretomes corresponding to growth on different substrates. The distribution of lignocellulolytic enzymes in the secretomes was strongly dependent on growth conditions, especially for lytic polysaccharide mono-oxygenases.[br/] With its available genome sequence, P. cinnabarinus is now an outstanding model system for the study of the enzyme machinery involved in the degradation or transformation of lignocellulosic biomass.
ano.nymous@ccsd.cnrs.fr.invalid (Anthony Levasseur) 29 Nov 2016
https://hal.science/hal-01204353v1
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[hal-01019483] Malate-mediated carbon catabolite repression in bacillus subtilis involves the HPrK/CcpA pathway
Most organisms can choose their preferred carbon source from a mixture of nutrients. This process is called carbon catabolite repression. The Gram-positive bacterium Bacillus subtilis uses glucose as the preferred source of carbon and energy. Glucose-mediated catabolite repression is caused by binding of the CcpA transcription factor to the promoter regions of catabolic operons. CcpA binds DNA upon interaction with its cofactors HPr(Ser-P) and Crh(Ser-P). The formation of the cofactors is catalyzed by the metabolite-activated HPr kinase/ phosphorylase. Recently, it has been shown that malate is a second preferred carbon source for B. subtilis that also causes catabolite repression. In this work, we addressed the mechanism by which malate causes catabolite repression. Genetic analyses revealed that malate-dependent catabolite repression requires CcpA and its cofactors. Moreover, we demonstrate that HPr(Ser-P) is present in malate-grown cells and that CcpA and HPr interact in vivo in the presence of glucose or malate but not in the absence of a repressing carbon source. The formation of the cofactor HPr(Ser-P) could be attributed to the concentrations of ATP and fructose 1,6-bisphosphate in cells growing with malate. Both metabolites are available at concentrations that are sufficient to stimulate HPr kinase activity. The adaptation of cells to environmental changes requires dynamic metabolic and regulatory adjustments. The repression strength of target promoters was similar to that observed in steady-state growth conditions, although it took somewhat longer to reach the second steady-state of expression when cells were shifted to malate.
ano.nymous@ccsd.cnrs.fr.invalid (Frederik M. Meyer) 29 May 2020
https://hal.science/hal-01019483v1
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[hal-01000245] Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis
Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature.We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.
ano.nymous@ccsd.cnrs.fr.invalid (Pierre P. Nicolas) 04 Jun 2014
https://hal.science/hal-01000245v1
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[hal-04197408] Comprehensive Probiogenomics Analysis of the Commensal Escherichia Coli CEC15 as a Potential Probiotic Strain
ckground: Probiotics have gained attention for their potential maintaining gut and immune homeostasis. They have been found to confer protection against pathogen colonization, possess immunomodulatory effects, enhance gut barrier functionality, and mitigate inflammation. However, a thorough understanding of the unique mechanisms of effects triggered by individual strains is necessary to optimize their therapeutic efficacy. Probiogenomics, involving high-throughput techniques, can help identify uncharacterized strains and aid in the rational selection of new probiotics. This study evaluates the potential of the Escherichia coli CEC15 strain as a probiotic through in silico, in vitro, and in vivo analyses, comparing it to the reference E. coli Nissle 1917. Genomic analysis was conducted to identify traits with potential beneficial activity and to assess the safety of each strain (genomic islands, bacteriocin production, antibiotic resistance, production of proteins involved in host homeostasis, and proteins with adhesive properties). In vitro studies assessed survival in gastrointestinal simulated conditions and adhesion to cultured human intestinal cells. Safety was evaluated in BALB/c mice, monitoring the impact of E. coliconsumption on clinical signs, intestinal architecture, intestinal permeability, and fecal microbiota. Additionally, the protective effects of both strains were assessed in a murine model of 5-FU-induced mucositis. Results:CEC15 mitigates inflammation, reinforces intestinal barrier and modulates intestinal microbiota. In silico analysis revealed fewer pathogenicity-related traits in CEC15, when compared to Nissle 1917, with fewer toxin-associated genes and no gene suggesting the production of colibactin (a genotoxic agent). The majority of predicted antibiotic-resistance genes were neither associated with actual resistance, nor with transposable elements. The genome of CEC15 strain encodes proteins related to stress tolerance and to adhesion, in line with its better survival during digestion and higher adhesion to intestinal cells, when compared to Nissle 1917. Moreover, CEC15 exhibited beneficial effects on mice and its intestinal microbiota, both in healthy animals and against 5FU-induced intestinal mucositis. Conclusions: These findings suggest that the CEC15 strain holds promise as a probiotic, capable of modulating the intestinal microbiota, providing immunomodulatory and anti-inflammatory effects, and reinforcing the intestinal barrier. These findings may have implications for the treatment of gastrointestinal disorders, particularly inflammatory bowel disease.
ano.nymous@ccsd.cnrs.fr.invalid (Fernando Tales) 06 Sep 2023
https://hal.inrae.fr/hal-04197408v1
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[hal-01001442] Prevention of cross-talk in conserved regulatory systems: identification of specificity determinants in RNA-binding anti-termination proteins of the BglG family
Each family of signal transduction systems requires specificity determinants that link individual signals to the correct regulatory output. In Bacillus subtilis, a family of four anti-terminator proteins controls the expression of genes for the utilisation of alternative sugars. These regulatory systems contain the anti-terminator proteins and a RNA structure, the RNA anti-terminator (RAT) that is bound by the anti-terminator proteins. We have studied three of these proteins (SacT, SacY, and LicT) to understand how they can transmit a specific signal in spite of their strong structural homology. A screen for random mutations that render SacT capable to bind a RNA structure recognized by LicT only revealed a substitution (P26S) at one of the few non-conserved residues that are in contact with the RNA. We have randomly modified this position in SacT together with another non-conserved RNA-contacting residue (Q31). Surprisingly, the mutant proteins could bind all RAT structures that are present in B. subtilis. In a complementary approach, reciprocal amino acid exchanges have been introduced in LicT and SacY at non-conserved positions of the RNA-binding site. This analysis revealed the key role of an arginine side-chain for both the high affinity and specificity of LicT for its cognate RAT. Introduction of this Arg at the equivalent position of SacY (A26) increased the RNA binding in vitro but also resulted in a relaxed specificity. Altogether our results suggest that this family of anti-termination proteins has evolved to reach a compromise between RNA binding efficacy and specific interaction with individual target sequences.
ano.nymous@ccsd.cnrs.fr.invalid (Sebastian S. Huebner) 29 May 2020
https://hal.science/hal-01001442v1
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[hal-04308495] Comprehensive probiogenomics analysis of the commensal Escherichia coli CEC15 as a potential probiotic strain
Background Probiotics have gained attention for their potential maintaining gut and immune homeostasis. They have been found to confer protection against pathogen colonization, possess immunomodulatory effects, enhance gut barrier functionality, and mitigate inflammation. However, a thorough understanding of the unique mechanisms of effects triggered by individual strains is necessary to optimize their therapeutic efficacy. Probiogenomics, involving high-throughput techniques, can help identify uncharacterized strains and aid in the rational selection of new probiotics. This study evaluates the potential of the Escherichia coli CEC15 strain as a probiotic through in silico, in vitro, and in vivo analyses, comparing it to the well-known probiotic reference E. coli Nissle 1917. Genomic analysis was conducted to identify traits with potential beneficial activity and to assess the safety of each strain (genomic islands, bacteriocin production, antibiotic resistance, production of proteins involved in host homeostasis, and proteins with adhesive properties). In vitro studies assessed survival in gastrointestinal simulated conditions and adhesion to cultured human intestinal cells. Safety was evaluated in BALB/c mice, monitoring the impact of E. coli consumption on clinical signs, intestinal architecture, intestinal permeability, and fecal microbiota. Additionally, the protective effects of both strains were assessed in a murine model of 5-FU-induced mucositis. Results CEC15 mitigates inflammation, reinforces intestinal barrier, and modulates intestinal microbiota. In silico analysis revealed fewer pathogenicity-related traits in CEC15, when compared to Nissle 1917, with fewer toxin-associated genes and no gene suggesting the production of colibactin (a genotoxic agent). Most predicted antibiotic-resistance genes were neither associated with actual resistance, nor with transposable elements. The genome of CEC15 strain encodes proteins related to stress tolerance and to adhesion, in line with its better survival during digestion and higher adhesion to intestinal cells, when compared to Nissle 1917. Moreover, CEC15 exhibited beneficial effects on mice and their intestinal microbiota, both in healthy animals and against 5FU-induced intestinal mucositis.
ano.nymous@ccsd.cnrs.fr.invalid (Tales Fernando da Silva) 27 Nov 2023
https://hal.inrae.fr/hal-04308495v1
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[anses-04171498] Avis de l'Anses relatif à la définition des souches pathogènes d’Escherichia coli productrices de shigatoxines
Les Escherichia coli entérohémorragiques (EHEC) sont des souches pathogènes d’E. coli responsables de diarrhée ou de colite hémorragique pouvant s’aggraver en syndrome hémolytique et urémique (SHU), surtout chez le jeune enfant, le sujet âgé et/ou immunodéprimé. L’avis de l’Anses du 18 mai 2017 indique que toute souche d’E. coli isolée chez l’Homme ou dans les aliments devrait être considérée comme une EHEC si elle possède les gènes de virulence stx1 et/ou stx2 et eae ou d’autre(s) gène(s) codant un système d’adhésion au tube digestif de l’Homme (Anses 2017). Certains sérotypes d’EHEC sont plus fréquemment associés à une maladie grave (SHU). L’Agence avait établi dans cet avis une classification des souches en fonction de leur risque pour la santé publique en France, selon les critères définis par le panel BIOHAZ de l’EFSA en 2013 (sérotypes et facteurs de virulence) et en se fondant sur les données épidémiologiques françaises et européennes. En 2018, un groupe d’experts FAO/OMS a proposé un ensemble de critères pour catégoriser les souches d’E. coli productrices de shigatoxines (STEC) en fonction du risque de forme clinique sévère (FAO/WHO 2018). Cinq niveaux de risque sont définis sur la base des profils de gènes de virulence. Le groupe conclut que le sérotype ne devrait pas être considéré comme un critère pour prédire la virulence des souches. En janvier 2020, l'EFSA a publié l’avis du panel BIOHAZ concernant l’évaluation de la pathogénicité des STEC sur la base des données de santé publique disponibles en Europe (EFSA BIOHAZ Panel 2020). Cet avis conclut que toutes les souches de STEC sont pathogènes avec la capacité de causer a minima une diarrhée, et que tous les sous-types de STEC peuvent être associés à des maladies sévères chez l’Homme. Le panel BIOHAZ de l’EFSA considère que la classification de la pathogénicité des STEC en fonction des sérotypes et de la présence de facteurs de virulence proposée dans son précédent avis de 2013 n’est plus valide. L’Anses est saisie pour actualiser voire compléter la définition des souches pathogènes proposée dans l'avis de mai 2017 au vu de l'avis du panel BIOHAZ de l'EFSA (2020), du rapport FAO/OMS (2018) et des autres données et publications récentes qui pourraient alimenter la réflexion. Les questions posées dans la saisine sont les suivantes : - « Sur la base des données de santé publique disponibles, quels sont les déterminants de la virulence des souches de STEC ? - Dans quelle mesure la prise en compte des sous-types du gène stx ou de tout autre facteur génétique permettrait-elle de rendre plus discriminante la typologie des souches de STEC proposée dans votre avis de mai 2017 au regard de leur niveau de pathogénicité ? »
ano.nymous@ccsd.cnrs.fr.invalid (Frédéric Auvray) 26 Jul 2023
https://anses.hal.science/anses-04171498v1
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[anses-04854468] Avis de l’Anses relatif à l’évaluation du risque de transmission du complexe Mycobacterium tuberculosis à l'humain via la consommation de produits laitiers crus issus d’un élevage caprin infecté
La tuberculose bovine à déclaration obligatoire est provoquée par les bactéries du complexe Mycobacterium tuberculosis : M. bovis, M. caprae et M. tuberculosis. Cependant, en France, le seul agent pathogène impliqué dans des cas autochtones de tuberculose animale est M. bovis. La tuberculose à M. bovis constitue un problème sanitaire majeur de l’élevage notamment bovin et porcin en Corse. Les foyers bovins en Corse représentent 20 % des foyers bovins de tuberculose de France hexagonale. La tuberculose à M. bovis y est également présente au sein de la faune sauvage, notamment chez les sangliers et chez les bovins féraux, constituant ainsi un système multi-hôtes complexe où l’environnement et la faune sauvage pourraient constituer une source de recontamination des troupeaux. C’est dans ce contexte qu’un foyer de tuberculose à M. bovis a été détecté dans un atelier caprin en lien épidémiologique avec un foyer bovin, dans le Cap-Corse, en avril 2023, constituant le premier foyer dans un cheptel caprin en Corse depuis 2009. L’élevage caprin en race Corse est un système d’élevage pastoral, où le lait sert quasi-exclusivement à la fabrication de fromage au lait cru, très majoritairement fabriqué à la ferme.
ano.nymous@ccsd.cnrs.fr.invalid (Georges Daube) 23 Jan 2025
https://anses.hal.science/anses-04854468v1
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[anses-04350896] Avis de l'Anses relatif à la présence de parasites Toxocara spp. dans les viandes de sanglier sauvage
Des analyses sur les carcasses de sangliers sauvages inspectées dans les établissements français de traitement de gibiers sauvages ont révélé depuis deux ans la présence régulière de larves de Toxocara spp. Ce constat a conduit les services vétérinaires d'inspection à saisir ces carcasses, conformément à l'article 45 du règlement d'exécution (UE) n°2019/627 de la Commission du 15 mars 2019 qui prévoit que les viandes présentant une infestation parasitaire sont déclarées impropres à la consommation humaine. La problématique pour le gestionnaire est double. Le premier enjeu est lié au risque de toxocarose pour les consommateurs de viandes de sanglier et des recommandations relatives à la conservation et la cuisson des viandes à adresser aux chasseurs. Le second enjeu est relatif à la gestion des lots de sangliers détectés positifs. Les demandes instruites dans le cadre de cette expertise sont les suivantes : Demande 1 : Établir un profil de risque pour Toxocara spp. dans les viandes de sanglier sauvage. Demande 2 : Évaluer l’efficacité de traitements assainissants de la carcasse sur la viabilité du parasite Toxocara spp., plus particulièrement la congélation et la cuisson, dans le cas où ces traitements sont réalisés, soit par les établissements du secteur alimentaire, soit directement par les consommateurs.
ano.nymous@ccsd.cnrs.fr.invalid (Philippe Fravalo) 12 Mar 2024
https://anses.hal.science/anses-04350896v1
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[hal-04172926] Recent Advances in Electrochemical Biosensors for Food Control
The rapid and sensitive detection of food contaminants is becoming increasingly important for timely prevention and treatment of foodborne disease. In this review, we discuss recent developments of electrochemical biosensors as facile, rapid, sensitive, and user-friendly analytical devices and their applications in food safety analysis, owing to the analytical characteristics of electrochemical detection and to advances in the design and production of bioreceptors (antibodies, DNA, aptamers, peptides, molecular imprinted polymers, enzymes, bacteriophages, etc.). They can offer a low limit of detection required for food contaminants such as allergens, pesticides, antibiotic traces, toxins, bacteria, etc. We provide an overview of a broad range of electrochemical biosensing designs and consider future opportunities for this technology in food control.
ano.nymous@ccsd.cnrs.fr.invalid (Francesco Rizzotto) 25 Oct 2023
https://hal.science/hal-04172926v1
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[hal-04792054] Prophages divert Staphylococcus aureus defenses against host lipids
Phages are ubiquitous in bacteria, including clinical Staphylococcus aureus, where Sfi 21/Sa3 phages often integrate into the hlb gene, which encodes Hlb sphingomyelinase. This integration acts as a rapid regulatory switch for Hlb production. Our findings suggest that Sfi 21/Sa3 prophages and Hlb activity influence S. aureus fitness by modulating the incorporation of the toxic linoleic acid (C18:2) from serum into the bacterial membrane. This process relies on C18:2 derived from 1,3-diglyceride, facilitated by the FakB1 kinase subunit. Palmitic acid (C16), primarily released from serum through Hlb activity, competes with C18:2 for FakB1. This mechanism contributes to adaptation to AFN-1252, an antibiotic inhibiting the fatty acid synthesis pathway (anti-FASII). Since S. aureus relies on exogenous fatty acids for growth, AFN-1252 treatment leads to increased proportion of C18:2 in the membrane. Furthermore, Hlb inhibition, whether by prophage insertion, gene inactivation, or enzyme inhibition, delays S. aureus adaptation, resulting in a higher proportion of C18:2 in the membrane. This study sheds light on the role of lipid environments in infections and may contribute to the accurate prediction of infection risks and therapeutic efficacy. Moreover, since both anti-FASII agent and Hlb inhibitor enhance C18:2 incorporation, they represent potential candidates for combined strategies against S. aureus.
ano.nymous@ccsd.cnrs.fr.invalid (Biyang Zhou) 20 Nov 2024
https://hal.inrae.fr/hal-04792054v2
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[hal-04918234] Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs
Background: Persons living with HIV (PWH) harbor an altered gut microbiome (higher abundance of Prevotella and lower abundance of Bacillota and Ruminococcus lineages) compared to non-infected individuals. Some of these alterations are linked to sexual preference and others to the HIV infection. The relationship between these lineages and metabolic alterations, often present in aging PWH, has been poorly investigated. Methods: In this study, we compared fecal metagenomes of 25 antiretroviral-treatment (ART)-controlled PWH to three independent control groups of 25 non-infected matched individuals by means of univariate analyses and machine learning methods. Moreover, we used two external datasets to validate predictive models of PWH classification. Next, we searched for associations between clinical and biological metabolic parameters with taxonomic and functional microbiome profiles. Finally, we compare the gut microbiome in 7 PWH after a 17-week ART switch to raltegravir/maraviroc. Results: Three major enterotypes (Prevotella, Bacteroides and Ruminococcaceae) were present in all groups. The first Prevotella enterotype was enriched in PWH, with several of characteristic lineages associated with poor metabolic profiles (low HDL and adiponectin, high insulin resistance (HOMA-IR)). Conversely butyrate-producing lineages were markedly depleted in PWH independently of sexual preference and were associated with a better metabolic profile (higher HDL and adiponectin and lower HOMA-IR). Accordingly with the worst metabolic status of PWH, butyrate production and amino-acid degradation modules were associated with high HDL and adiponectin and low HOMA-IR. Random Forest models trained to classify PWH vs. control on taxonomic abundances displayed high generalization performance on two external holdout datasets (ROC AUC of 80-82%). Finally, no significant alterations in microbiome composition were observed after switching to raltegravir/maraviroc. Conclusion: High resolution metagenomic analyses revealed major differences in the gut microbiome of ART-controlled PWH when compared with three independent matched cohorts of controls. The observed marked insulin resistance could result both from enrichment in Prevotella lineages, and from the depletion in species producing butyrate and involved into amino-acid degradation, which depletion is linked with the HIV infection.
ano.nymous@ccsd.cnrs.fr.invalid (Eugeni Belda) 29 Jan 2025
https://hal.sorbonne-universite.fr/hal-04918234v1
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[hal-03753288] Modulation of skeletal muscle function by gut microbiota dysbiosis and reseeding
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Kevin Nay) 18 Aug 2022
https://hal.inrae.fr/hal-03753288v1
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[hal-03753297] Evidence of inter-organ dialogue: Specific gut microbiota signatures in specific-skeletal muscle phenotypes
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Maxence Jollet) 18 Aug 2022
https://hal.inrae.fr/hal-03753297v1
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[hal-03753298] Modulation of skeletal muscle function by gut Microbiota Dysbiosis and reseeding
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Kevin Nay) 18 Aug 2022
https://hal.inrae.fr/hal-03753298v1
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[hal-04879243] Responses to and detoxification of esculin in white-rot fungi
Bio-based molecules have become one of the main alternatives to traditional products for limiting the spread of harmful fungi. However, a better understanding of the mode of action of these molecules and the defense systems developed by fungi to resist them, is needed to assess the benefits/risks of using them as antifungal treatment. White-rot fungi are excellent models in this respect, as they have adapted to the hostile habitat that is wood. In fact, wood is a source of putative antifungal compounds known as extractives. In this study, we demonstrated that esculin and the aglycone form esculetin, which are coumarins found in plants and wood, reduce the growth of Phanerochaete chrysosporium, Pycnoporus cinnabarinus, Trametes versicolor and Fomitiporia mediterranea, with some differences depending on the specie. We have shown that various strategies are developed by the fungi to deal with esculin both at the extracellular level, through the involvement of laccases, peroxidases and glycoside hydrolases, and at the intracellular level, mainly by stimulating protein translation. Using comparative proteomic and metabolomic approaches, our results showed that despite the fact that the species analyzed are closely related (they all belong to the Agaricomycotina, and have the same trophic mode), their defense responses to esculin are different.
ano.nymous@ccsd.cnrs.fr.invalid (Raphael Bchini) 30 Jan 2025
https://hal.inrae.fr/hal-04879243v1
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[hal-02941029] Sulfiredoxin Protects Mice from Lipopolysaccharide-Induced Endotoxic Shock
Peroxiredoxins constitute a major family of cysteine-based peroxide-scavenging enzymes. They carry an intriguing redox switch by undergoing substrate-mediated inactivation via overoxidation of their catalytic cysteine to the sulfinic acid form that is reverted by reduction catalyzed by the sulfinic acid reductase sulfiredoxin (Srx). The biological significance of such inactivation is not understood, nor is the function of Srx1. To address this question, we generated a mouse line with a null deletion of the Srx1-encoding Srxn1 gene. We show here that Srxn1(-/-) mice are perfectly viable and do not suffer from any apparent defects under laboratory conditions, but have an abnormal response to lipopolysaccharide that manifests by increased mortality during endotoxic shock. Microarray-based mRNA profiles show that although the response of Srxn1(-/-) mice to lipopolysaccharide is typical, spanning all spectrum and all pathways of innate immunity, it is delayed by several hours and remains intense when the response of Srxn1(+/+) mice has already dissipated. These data indicate that Srx1 activity protects mice from the lethality of endotoxic shock, adding this enzyme to other host factors, as NRF2 and peroxiredoxin 2, which by regulating cellular reactive oxygen species levels act as important modifiers in the pathogenesis of sepsis.
ano.nymous@ccsd.cnrs.fr.invalid (Anne-Gaëlle Planson) 16 Sep 2020
https://hal.inrae.fr/hal-02941029v1
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[hal-01193995] Sus-Flora project: a genetic and genomic study of gut microbiota and immune system homeostasis in swine
absent
ano.nymous@ccsd.cnrs.fr.invalid (Claire Gaillard) 06 Jun 2020
https://hal.science/hal-01193995v1
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[hal-02739158] Lung neonatal responses to respiratory syncytial virus reveal deficiencies in dendritic cells and type I interferon in a mouse model of airway enhanced disease
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Aude Remot) 02 Jun 2020
https://hal.inrae.fr/hal-02739158v1
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[hal-02356215] Immunome differences between porcine ileal and jejunal Peyer’s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues
The epithelium of the intestinal mucosa and the gut-associated lymphoid tissues (GALT) constitute an essential physical and immunological barrier against pathogens. In order to study the specificities of the GALT transcriptome in pigs, we compared the transcriptome profiles of jejunal and ileal Peyer's patches (PPs), mesenteric lymph nodes (MLNs) and peripheral blood (PB) of four male piglets by RNA-Seq. We identified 1,103 differentially expressed (DE) genes between ileal PPs (IPPs) and jejunal PPs (JPPs), and six times more DE genes between PPs and MLNs. The master regulator genes FOXP3, GATA3, STAT4, TBX21 and RORC were less expressed in IPPs compared to JPPs, whereas the transcription factor BCL6 was found more expressed in IPPs. In comparison between IPPs and JPPs, our analyses revealed predominant differential expression related to the differentiation of T cells into Th1, Th2, Th17 and iTreg in JPPs. Our results were consistent with previous reports regarding a higher T/B cells ratio in JPPs compared to IPPs. We found antisense transcription for respectively 24%, 22% and 14% of the transcripts detected in MLNs, PPs and PB, and significant positive correlations between PB and GALT transcriptomes. Allele-specific expression analyses revealed both shared and tissue-specific cis-genetic control of gene expression.
ano.nymous@ccsd.cnrs.fr.invalid (T. Maroilley) 26 May 2020
https://hal.science/hal-02356215v1
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[hal-02740120] Lung neonatal responses to respiratory syncytial virus reveal deficiencies in dendritic cells and type I interferon in a mouse model of airway enhanced disease
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Aude Remot) 03 Jun 2020
https://hal.inrae.fr/hal-02740120v1
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[hal-01834453] Live intramacrophagic Staphylococcus aureus as a potential cause of antibiotic therapy failure observations in an in vivo mouse model of prosthetic vascular material infections
Objectives: To evaluate the significant role played by biofilms during prosthetic vascular material infections (PVMIs).Methods: We developed an in vivo mouse model of Staphylococcus aureus PVMI allowing its direct observation by confocal microscopy to describe: (i) the structure of biofilms developed on Dacron® vascular material; (ii) the localization and effect of antibiotics on these biostructures; and (iii) the interaction between bacteria and host tissues and cells during PVMI.Results: In this model we demonstrated that the biofilm structures are correlated to the activity of antibiotics. Furthermore, live S. aureus bacteria were visualized inside the macrophages present at the biofilm sites, which is significant as antibiotics do not penetrate these immune cells.Conclusions: This intracellular situation may explain the limited effect of antibiotics and also why PVMIs can relapse after antibiotic therapy.
ano.nymous@ccsd.cnrs.fr.invalid (Rym Boudjemaa) 06 Sep 2018
https://univ-rennes.hal.science/hal-01834453v2
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[hal-04004063] Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates
Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering and mortality and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of diseaseassociated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last 10 years from 16 French broiler farms. Comparative genomics, genome-wide association studies, and the measured susceptibility to serum, biofilm-forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate the origin of the isolates or the phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically, and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster into a few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole-genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first data set on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage that is probably also circulating elsewhere that should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum-related diseases.
ano.nymous@ccsd.cnrs.fr.invalid (Jeanne Laurentie) 23 Oct 2023
https://hal.inrae.fr/hal-04004063v1
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[hal-04281314] Comparative genome analysis of Enterococcus cecorum reveals intercontinental spread of a lineage of clinical poultry isolates
ABSTRACT Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering, mortality, and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last ten years in 16 French broiler farms. Comparative genomics, genome-wide association study, and measured susceptibility to serum, biofilm forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate origin of the isolates or phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster in few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen in poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first dataset on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage probably also circulating elsewhere and which should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum -related diseases.
ano.nymous@ccsd.cnrs.fr.invalid (Jeanne Laurentie) 12 Nov 2023
https://hal.science/hal-04281314v1
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[hal-04296461] Antimicrobial Resistance Analysis of French Isolates of Enterococcus cecorum
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Laurentie J.) 20 Nov 2023
https://hal.science/hal-04296461v1
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[hal-04314354] Investigating the Links between Transformation and Cell Division in Streptococcus pneumoniae
Streptococcus pneumoniae (the Pneumococcus), is a commensal gram-positive bacterium that can cause pneumonia, meningitis or septicemia under certain conditions. During a specific physiological state called 'competence', S. pneumoniae develops natural transformation and can incorporate exogenous DNA into its genome to promote genetic diversification and drive evolution. In the pneumococcus, competent cells exhibit a transient delay in the cell division process. It is thought that this delay allows the cells to complete the final stages of transformation without compromising the integrity of their genome (Berge et al. 2017). ComM, a membrane protein produced during competence and localized at the septum, is necessary and sufficient to inhibit cell division. However, its mechanism of action remains unknown. Here we investigated the underlying links between ComM and the cell division and peptidoglycan (PG) synthesis machineries of S. pneumoniae using a combination of high-resolution fluorescence microscopy and interactomics approaches.
ano.nymous@ccsd.cnrs.fr.invalid (Dimitri Juillot) 29 Nov 2023
https://hal.inrae.fr/hal-04314354v1
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[hal-01004510] ComE/ComE similar to P interplay dictates activation or extinction status of pneumococcal X-state (competence)
Since 1996, induction of competence for genetic transformation of Streptococcus pneumoniae is known to be controlled by the ComD/ComE two-component regulatory system. The mechanism of induction is generally described as involving ComD autophosphorylation, transphosphorylation of ComE and transcriptional activation by ComE similar to P of the early competence (com) genes, including comX which encodes the competence-specific sigma(X). However, none of these features has been experimentally established. Here we document the autokinase activity of ComD proteins in vitro, and provide an estimate of the stoichiometry of ComD and ComE in vivo. We report that a phosphorylmimetic mutant, ComE(D58E), constructed because of the failure to detect transphosphorylation of purified ComE in vitro, displays full spontaneous competence in Delta comD cells, an that in vitro ComE(D58E) exhibits significantly improved binding affinity for P-comCDE. We also provide evidence for a differential transcriptional activation and repression of P-comCDE and P-comX. Altogether, these data support the model of ComE similar to P-dependent activation of transcription. Finally, we establish that ComE antagonizes expression of the early com genes and propose that the rapid deceleration of transcription from P-comCDE observed even in cells lacking sigma(X) is due to the progressive accumulation of ComE, which outcompetes ComE similar to P.
ano.nymous@ccsd.cnrs.fr.invalid (Bernard B. Martin) 11 Jun 2014
https://hal.science/hal-01004510v1
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[hal-02754366] SSB : coordinateur des mécanismes de réparation des fourches de réplication ?
[...]
ano.nymous@ccsd.cnrs.fr.invalid (François Lecointe) 03 Jun 2020
https://hal.inrae.fr/hal-02754366v1
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[hal-02667913] The C-Terminal Domain of the Bacterial SSB Protein Acts as a DNA Maintenance Hub at Active Chromosome Replication Forks
We have investigated in vivo the role of the carboxy-terminal domain of the Bacillus subtilis Single-Stranded DNA Binding protein (SSB(Cter)) as a recruitment platform at active chromosomal forks for many proteins of the genome maintenance machineries. We probed this SSB(Cter) interactome using GFP fusions and by Tap-tag and biochemical analysis. It includes at least 12 proteins. The interactome was previously shown to include PriA, RecG, and RecQ and extended in this study by addition of DnaE, SbcC, RarA, RecJ, RecO, XseA, Ung, YpbB, and YrrC. Targeting of YpbB to active forks appears to depend on RecS, a RecQ paralogue, with which it forms a stable complex. Most of these SSB partners are conserved in bacteria, while others, such as the essential DNA polymerase DnaE, YrrC, and the YpbB/RecS complex, appear to be specific to B. subtilis. SSB(Cter) deletion has a moderate impact on B. subtilis cell growth. However, it markedly affects the efficiency of repair of damaged genomic DNA and arrested replication forks. ssb Delta Cter mutant cells appear deficient in RecA loading on ssDNA, explaining their inefficiency in triggering the SOS response upon exposure to genotoxic agents. Together, our findings show that the bacterial SSB(Cter) acts as a DNA maintenance hub at active chromosomal forks that secures their propagation along the genome.
ano.nymous@ccsd.cnrs.fr.invalid (Audrey Costes) 31 May 2020
https://hal.inrae.fr/hal-02667913v1
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[hal-04746870] DivIVA controls the dynamics of septum splitting and cell elongation in Streptococcus pneumoniae
Bacterial shape and division rely on the dynamics of cell wall assembly, which involves regulated synthesis and cleavage of the peptidoglycan. In ovococci, these processes are coordinated within an annular mid-cell region with nanometric dimen sions. More precisely, the cross-wall synthesized by the divisome is split to generate a lateral wall, whose expansion is insured by the insertion of the so-called peripheral peptidoglycan by the elongasome. Septum cleavage and peripheral peptidoglycan synthesis are, thus, crucial remodeling events for ovococcal cell division and elongation. The structural DivIVA protein has long been known as a major regulator of these processes, but its mode of action remains unknown. Here, we integrate click chemis try-based peptidoglycan labeling, direct stochastic optical reconstruction microscopy, and in silico modeling, as well as epifluorescence and stimulated emission depletion microscopy to investigate the role of DivIVA in Streptococcus pneumoniae cell morpho genesis. Our work reveals two distinct phases of peptidoglycan remodeling during the cell cycle that are differentially controlled by DivIVA. In particular, we show that DivIVA ensures homogeneous septum cleavage and peripheral peptidoglycan synthesis around the division site and their maintenance throughout the cell cycle. Our data additionally suggest that DivIVA impacts the contribution of the elongasome and class A penicillin-binding proteins to cell elongation. We also report the position of DivIVA on either side of the septum, consistent with its known affinity for negatively curved membranes. Finally, we take the opportunity provided by these new observations to propose hypotheses for the mechanism of action of this key morphogenetic protein.
ano.nymous@ccsd.cnrs.fr.invalid (Jennyfer Trouve) 21 Oct 2024
https://hal.science/hal-04746870v1
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[hal-04492600] Transient inhibition of cell division in competent pneumococcal cells results from deceleration of the septal peptidoglycan complex
Bacterial cells are known to produce inhibitors of cell division in response to stress responses and developmental programs. Knowledge of the underlying molecular mechanisms remains however largely limited. In this study, we investigated the mechanism of transient cell division inhibition observed during the development of competence for transformation in the human pathogen Streptococcus pneumoniae . In this species, ComM, a membrane protein specifically produced during competence, transiently inhibits cell division to preserve genomic integrity during transformation. We show that ComM reduces specifically the dynamics of the septal peptidoglycan synthetic complex FtsW:PBP2x. We also present evidence that ComM interacts with the peptidoglycan precursor synthetic enzyme MurA, and show that overproduction of MurA suppresses FtsW:PBP2x deceleration along the cell division delay in competent cells. Collectively, our data support a model in which ComM interferes with MurA activity to reduce septal peptidoglycan synthesis during competence in S. pneumoniae .
ano.nymous@ccsd.cnrs.fr.invalid (Dimitri Juillot) 06 Mar 2024
https://hal.inrae.fr/hal-04492600v1
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[hal-01003421] Co-evolution of segregation guide DNA motifs and the FtsK translocase in bacteria: identification of the atypical Lactococcus lactis KOPS motif
Bacteria use the global bipolarization of their chromosomes into replichores to control the dynamics and segregation of their genome during the cell cycle. This involves the control of protein activities by recognition of specific short DNA motifs whose orientation along the chromosome is highly skewed. The KOPS motifs act in chromosome segregation by orienting the activity of the FtsK DNA translocase towards the terminal replichore junction. KOPS motifs have been identified in gamma-Proteobacteria and in Bacillus subtilis as closely related G-rich octamers. We have identified the KOPS motif of Lactococcus lactis, a model bacteria of the Streptococcaceae family harbouring a compact and low GC% genome. This motif, 5'-GAAGAAG-3, was predicted in silico using the occurrence and skew characteristics of known KOPS motifs. We show that it is specifically recognized by L. lactis FtsK in vitro and controls its activity in vivo. L. lactis KOPS is thus an A-rich heptamer motif. Our results show that KOPS-controlled chromosome segregation is conserved in Streptococcaceae but that KOPS may show important variation in sequence and length between bacterial families. This suggests that FtsK adapts to its host genome by selecting motifs with convenient occurrence frequencies and orientation skews to orient its activity.
ano.nymous@ccsd.cnrs.fr.invalid (Sophie Nolivos) 29 May 2020
https://hal.science/hal-01003421v1
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[hal-01001538] Direct involvement of DprA, the transformation-dedicated RecA loader, in the shut-off of pneumococcal competence
Natural bacterial transformation is a genetically programmed process allowing genotype alterations that involves the internalization of DNA and its chromosomal integration catalyzed by the universal recombinase RecA, assisted by its transformation-dedicated loader. DNA processing protein A (DprA). In Streptococcus pneumoniae, the ability to internalize DNA, known as competence, is transient, developing suddenly and stopping as quickly. Competence is induced by the comC-encoded peptide, competence stimulating peptide (CSP), via a classic two-component regulatory system ComDE. Upon CSP binding, ComD phosphorylates the ComE response-regulator, which then activates transcription of comCDE and the competence-specific sigma(x), leading to a sudden rise in CSP levels and rendering all cells in a culture competent. However, how competence stops has remained unknown. We report that DprA, under sigma(x) control, interacts with ComE similar to P to block ComE-driven transcription, chiefly impacting sigma(x) production. Mutations of dprA specifically disrupting interaction with ComE were isolated and shown to map mainly to the N-terminal domain of DprA. Wild-type DprA but not ComE interaction mutants affected in vitro binding of ComE to its promoter targets. Once introduced at the dprA chromosomal locus, mutations disrupting DprA interaction with ComE altered competence shut-off. The absence of DprA was found to negatively impact growth following competence induction, highlighting the importance of DprA for pneumococcal physiology. DprA has thus two key roles: ensuring production of transformants via interaction with RecA and competence shut-off via interaction with ComE, avoiding physiologically detrimental consequences of prolonged competence. Finally, phylogenetic analyses revealed that the acquisition of a new function by DprA impacted its evolution in streptococci relying on ComE to regulate comX expression.
ano.nymous@ccsd.cnrs.fr.invalid (Nicolas N. Mirouze) 28 May 2020
https://hal.science/hal-01001538v1
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[hal-02822191] The dynamic protein partnership of RNA polymerase in <em>Bacillus subtilis</em>
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Olivier Delumeau) 06 Jun 2020
https://hal.inrae.fr/hal-02822191v1
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[hal-03761115] The dynamic protein partnership of RNA polymerase in Bacillus subtilis
In prokaryotes, transcription results from the activity of a 400 kDa RNA polymerase (RNAP) protein complex composed of at least five subunits (2a,b,b0,o). To ensure adequateresponses to changing environmental cues, RNAP activity is tightly controlled by means ofinteracting regulatory proteins. Here, we report the affinity-purification of the Bacillus subtilis RNAP complexes from cells in different growth states and stress conditions, and the quantitative assessment by mass spectrometry of the dynamic changes in the composition of the RNAP complex. The stoichiometry of RNA polymerase was determined by a comparison of two mass spectrometry-based quantification methods : a label-based and a label-free method. The validated label-free method was then used to quantify the proteins associated with RNAP.The levels of sigma factors bound to RNAP varied during growth and exposure to stress. Elongation factors, helicases such as HelD and PcrA, and novel unknown proteins were also associated with RNAP complexes. The content in 6S RNAs of purified RNAP complexes increased at the onset of the stationary phase. These quantitative variations in the protein and RNA composition of the RNAP complexes well correlate with the known physiology of B. subtilis cells under different conditions.
ano.nymous@ccsd.cnrs.fr.invalid (Olivier Delumeau) 25 Aug 2022
https://hal.inrae.fr/hal-03761115v1
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[hal-03065267] A Key Presynaptic Role in Transformation for a Widespread Bacterial Protein: DprA Conveys Incoming ssDNA to RecA
Natural transformation is a mechanism for genetic exchange in many bacterial genera. It proceeds through the uptake of exogenous DNA and subsequent homology-dependent integration into the genome. In Streptococcus pneumoniae, this integration requires the ubiquitous recombinase, RecA, and DprA, a protein of unknown function widely conserved in bacteria. To unravel the role of DprA, we have studied the properties of the purified S. pneumoniae protein and its Bacillus subtilis ortholog (Smf). We report that DprA and Smf bind cooperatively to single-stranded DNA (ssDNA) and that these proteins both self-interact and interact with RecA. We demonstrate that DprA-RecA-ssDNA filaments are produced and that these filaments catalyze the homology-dependent formation of joint molecules. Finally, we show that while the Escherichia coli ssDNA-binding protein SSB limits access of RecA to ssDNA, DprA lowers this barrier. We propose that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation.
ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Mortier-Barrière) 14 Dec 2020
https://hal.science/hal-03065267v1
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[hal-00636313] The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment.
Ramlibacter tataouinensis TTB310(T) (strain TTB310), a betaproteobacterium isolated from a semi-arid region of South Tunisia (Tataouine), is characterized by the presence of both spherical and rod-shaped cells in pure culture. Cell division of strain TTB310 occurs by the binary fission of spherical "cyst-like" cells ("cyst-cyst" division). The rod-shaped cells formed at the periphery of a colony (consisting mainly of cysts) are highly motile and colonize a new environment, where they form a new colony by reversion to cyst-like cells. This unique cell cycle of strain TTB310, with desiccation tolerant cyst-like cells capable of division and desiccation sensitive motile rods capable of dissemination, appears to be a novel adaptation for life in a hot and dry desert environment. In order to gain insights into strain TTB310's underlying genetic repertoire and possible mechanisms responsible for its unusual lifestyle, the genome of strain TTB310 was completely sequenced and subsequently annotated. The complete genome consists of a single circular chromosome of 4,070,194 bp with an average G+C content of 70.0%, the highest among the Betaproteobacteria sequenced to date, with total of 3,899 predicted coding sequences covering 92% of the genome. We found that strain TTB310 has developed a highly complex network of two-component systems, which may utilize responses to light and perhaps a rudimentary circadian hourglass to anticipate water availability at the dew time in the middle/end of the desert winter nights and thus direct the growth window to cyclic water availability times. Other interesting features of the strain TTB310 genome that appear to be important for desiccation tolerance, including intermediary metabolism compounds such as trehalose or polyhydroxyalkanoate, and signal transduction pathways, are presented and discussed.
ano.nymous@ccsd.cnrs.fr.invalid (Gilles de Luca) 27 Apr 2012
https://hal.science/hal-00636313v1
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[hal-01204238] The complete genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy actinobacterium with food and probiotic applications
Background: Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and is also considered for its probiotic use [1]. This species exhibits slow growth, low nutritional requirements, and hardiness in many habitats. It belongs to the taxonomic group of dairy propionibacteria, in contrast to the cutaneous species P. acnes. The genome of the type strain, P. freudenreichii subsp. shermanii CIRM-BIA1 (CIP 103027T), was sequenced with an 11-fold coverage. Methodology/Principal Findings: The circular chromosome of 2.7 Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different insertion sequences (3.5% of the genome in base pairs). Using a proteomic approach, 490 of the 2439 predicted proteins were confirmed. The annotation revealed the genetic basis for the hardiness of P. freudenreichii, as the bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of aminoacids and vitamins (except panthotenate and biotin) as well as sequences involved in metabolism of various carbon sources, immunity against phages, duplicated chaperone genes and, interestingly, genes involved in the management of polyphosphate, glycogen and trehalose storage. The complete biosynthesis pathway for a bifidogenic compound is described, as well as a high number of surface proteins involved in interactions with the host and present in other probiotic bacteria. By comparative genomics, no pathogenicity factors found in P. acnes or in other pathogenic microbial species were identified in P. freudenreichii, which is consistent with the Generally Recognized As Safe and Qualified Presumption of Safety status of P. freudenreichii. Various pathways for formation of cheese flavor compounds were identified: the Wood-Werkman cycle for propionic acid formation, amino acid degradation pathways resulting in the formation of volatile branched chain fatty acids, and esterases involved in the formation of free fatty acids and esters. Conclusions/Significance: With the exception of its ability to degrade lactose, P. freudenreichii seems poorly adapted to dairy niches. This genome annotation opens up new prospects for the understanding of the P. freudenreichii probiotic activity.
ano.nymous@ccsd.cnrs.fr.invalid (Hélène Falentin) 31 May 2020
https://hal.science/hal-01204238v1
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[hal-01895330] Sulfur Amino Acid Metabolism and Its Control in Lactococcus lactis IL1403
Cysteine and methionine availability influences many processes in the cell. In bacteria, transcription of the specific genes involved in the synthesis of these two amino acids is usually regulated by different mechanisms or regulators. Pathways for the synthesis of cysteine and methionine and their interconversion were experimentally determined for Lactococcus lactis, a lactic acid bacterium commonly found in food. A new gene, yhcE, was shown to be involved in methionine recycling to cysteine. Surprisingly, 18 genes, representing almost all genes of these pathways, are under the control of a LysR-type activator, FhuR, also named CmbR. DNA microarray experiments showed that FhuR targets are restricted to this set of 18 genes clustered in seven transcriptional units, while cysteine starvation modifies the transcription level of several other genes potentially involved in oxidoreduction processes. Purified FhuR binds a 13-bp box centered 46 to 53 bp upstream of the transcriptional starts from the seven regulated promoters, while a second box with the same consensus is present upstream of the first binding box, separated by 8 to 10 bp. O-Acetyl serine increases FhuR binding affinity to its binding boxes. The overall view of sulfur amino acid metabolism and its regulation in L. lactis indicates that CysE could be a master enzyme controlling the activity of FhuR by providing its effector, while other controls at the enzymatic level appear to be necessary to compensate the absence of differential regulation of the genes involved in the interconversion of methionine and cysteine and other biosynthesis genes.
ano.nymous@ccsd.cnrs.fr.invalid (Brice Sperandio) 15 Oct 2018
https://hal.science/hal-01895330v1
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[hal-04314416] Investigating the Links between Transformation and Cell Division in Streptococcus pneumoniae
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Dimitri Juillot) 29 Nov 2023
https://hal.inrae.fr/hal-04314416v1
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[hal-01004530] Structure-function analysis of pneumococcal DprA protein reveals that dimerization is crucial for loading RecA recombinase onto DNA during transformation
Transformation promotes genome plasticity in bacteria via RecA-driven homologous recombination. In the Gram-positive human pathogen Streptococcus pneumoniae, the transformasome a multiprotein complex, internalizes, protects, and processes transforming DNA to generate chromosomal recombinants. Double-stranded DNA is internalized as single strands, onto which the transformation-dedicated DNA processing protein A (DprA) ensures the loading of RecA to form presynaptic filaments. We report that the structure of DprA consists of the association of a sterile alpha motif domain and a Rossmann fold and that DprA forms tail-to-tail dimers. The isolation of DprA self-interaction mutants revealed that dimerization is crucial for the formation of nucleocomplexes in vitro and for genetic transformation. Residues important for DprA-RecA interaction also were identified and mutated, establishing this interaction as equally important for transformation. Positioning of key interaction residues on the DprA structure revealed an overlap of DprA-DprA and DprA-RecA interaction surfaces. We propose a model in which RecA interaction promotes rearrangement or disruption of the DprA dimer, enabling the subsequent nucleation of RecA and its polymerization onto ssDNA.
ano.nymous@ccsd.cnrs.fr.invalid (Sophie S. Quevillon-Cheruel) 29 May 2020
https://hal.science/hal-01004530v1
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[hal-04314427] Investigating the Links between Transformation and Cell Division in Streptococcus pneumoniae
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Dimitri Juillot) 29 Nov 2023
https://hal.inrae.fr/hal-04314427v1
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[hal-03028340] RNA processing machineries in Archaea: the 5′-3′ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3′-5′ exoribonucleolytic RNA exosome machinery
A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
ano.nymous@ccsd.cnrs.fr.invalid (Duy Khanh Phung) 09 Dec 2020
https://hal.science/hal-03028340v1
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[hal-01000647] The dynamic protein partnership of RNA polymerase in Bacillus subtilis
In prokaryotes, transcription results from the activity of a 400 kDa RNA polymerase (RNAP) protein complex composed of at least five subunits (2 alpha, beta, beta', omega). To ensure adequate responses to changing environmental cues, RNAP activity is tightly controlled by means of interacting regulatory proteins. Here, we report the affinity-purification of the Bacillus subtilis RNAP complexes from cells in different growth states and stress conditions, and the quantitative assessment by mass spectrometry of the dynamic changes in the composition of the RNAP complex. The stoichiometry of RNA polymerase was determined by a comparison of two mass spectrometry-based quantification methods: a label-based and a label-free method. The validated label-free method was then used to quantify the proteins associated with RNAP. The levels of sigma factors bound to RNAP varied during growth and exposure to stress. Elongation factors, helicases such as HelD and PcrA, and novel unknown proteins were also associated with RNAP complexes. The content in 6S RNAs of purified RNAP complexes increased at the onset of the stationary phase. These quantitative variations in the protein and RNA composition of the RNAP complexes well correlate with the known physiology of B. subtilis cells under different conditions.
ano.nymous@ccsd.cnrs.fr.invalid (Olivier O. Delumeau) 04 Jun 2014
https://hal.science/hal-01000647v1
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[hal-01190796] Comparaison des deux sites expérimentaux de longue durée pour l’étude de l’impact des fertilisants sur les propriétés physiques et chimiques des sols
absent
ano.nymous@ccsd.cnrs.fr.invalid (Veronique Chaplain) 01 Sep 2015
https://hal.science/hal-01190796v1
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[hal-01867992] Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass
Background: Plant biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of plant biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of P. brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a biomass feedstock worldwide. Results: We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multiomics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners. Conclusion: As a peculiar feature of P. brumalis, we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.
ano.nymous@ccsd.cnrs.fr.invalid (Shingo Miyauchi) 04 Sep 2018
https://hal.science/hal-01867992v1
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[hal-02315852] Investigating Host Microbiota Relationships Through Functional Metagenomics
The human Intestinal mucus is formed by glycoproteins, the O- and N-linked glycans which constitute a crucial source of carbon for commensal gut bacteria, especially when deprived of dietary glycans of plant origin. In recent years, a dozen carbohydrate-active enzymes from cultivated mucin degraders have been characterized. But yet, considering the fact that uncultured species predominate in the human gut microbiota, these biochemical data are far from exhaustive. In this study, we used functional metagenomics to identify new metabolic pathways in uncultured bacteria involved in harvesting mucin glycans. First, we performed a high-throughput screening of a fosmid metagenomic library constructed from the ileum mucosa microbiota using chromogenic substrates. The screening resulted in the isolation of 124 clones producing activities crucial in the degradation of human O- and N-glycans, namely sialidases, beta-D-N-acetyl-glucosaminidase, beta-D-N-acetyl-galactosaminidase, and/or beta-D-mannosidase. Thirteen of these clones were selected based on their diversified functional profiles and were further analyzed on a secondary screening. This step consisted of lectin binding assays to demonstrate the ability of the clones to degrade human intestinal mucus. In total, the structural modification of several mucin motifs, sialylated mucin ones in particular, was evidenced for nine clones. Sequencing their metagenomic loci highlighted complex catabolic pathways involving the complementary functions of glycan sensing, transport, hydrolysis, deacetylation, and deamination, which were sometimes associated with amino acid metabolism machinery. These loci are assigned to several Bacteroides and Feacalibacterium species highly prevalent and abundant in the gut microbiome and explain the metabolic flexibility of gut bacteria feeding both on dietary and human glycans.
ano.nymous@ccsd.cnrs.fr.invalid (Elisabeth Laville) 14 Oct 2019
https://hal.science/hal-02315852v1
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[hal-02868456] Conserved white rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus
White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood decaying activity within the Basidiomycota genus Pycnoporus. We observed strong conservation in the genome structures and the repertoires of protein coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analyzed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2 producing enzymes with H2O2 consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 LPMO gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood decaying process.
ano.nymous@ccsd.cnrs.fr.invalid (Shingo Miyauchi) 05 Jan 2024
https://amu.hal.science/hal-02868456v2
