Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

Characterization of L-Carnitine Metabolism in Sinorhizobium meliloti

International audienceL-Carnitine is a trimethylammonium compound mostly known for its contribution to fatty acid transport into mitochondria. In bacteria, it is synthesized from ␥-butyrobetaine (GBB) and can be used as a carbon source. L-Carnitine can be formed directly by GBB hydroxylation or synthesized via a biosynthetic route analogous to fatty acid degradation. However, this multistep pathway has not been experimentally characterized. In this work, we identified by gene context analysis a cluster of L-carnitine anabolic genes next to those involved in its catabolism and proceeded to the complete in vitro characterization of L-carnitine biosynthesis and degradation in Sinorhizobium meliloti. The five enzymes catalyzing the seven steps that convert GBB to glycine betaine are described. Metabolomic analysis confirmed the multistage synthesis of L-carnitine in GBB-grown cells but also revealed that GBB is synthesized by S. meliloti. To our knowledge, this is the first report of aerobic GBB synthesis in bacteria. The conservation of L-carnitine metabolism genes in different bacterial taxonomic classes underscores the role of L-carnitine as a ubiquitous nutrient. IMPORTANCE The experimental characterization of novel metabolic pathways is essential for realizing the value of genome sequences and improving our knowledge of the enzymatic capabilities of the bacterial world. However, 30% to 40% of genes of a typical genome remain unannotated or associated with a putative function. We used enzyme kinetics, liquid chromatography-mass spectroscopy (LC-MS)-based metabolomics, and mutant phenotyping for the characterization of the metabolism of L-carnitine in Sinorhizobium meliloti to provide an accurate annotation of the corresponding genes. The occurrence of conserved gene clusters for carnitine metabolism in soil, plant-associated, and marine bacteria underlines the environmental abundance of carnitine and suggests this molecule might make a significant contribution to ecosystem nitrogen and carbon cycling

Characterization of L­-Serine O-succinyltransferases involved in l-cysteine biosynthesis in prokaryotes

International audienceUntil very recently, acetylation was the only known way for activating L-serine in the penultimate step of L-cysteine biosynthesis, in bacteria and fungi. This reaction is catalyzed by L-serine O-acetyl transferases (SAT), encoded by cysE and srpH, and belonging to the transferase hexapeptide repeat family. Nevertheless, we demonstrated that L-serine is succinylated in Schizosaccharomyces pombe by an enzyme unrelated to the classical SAT (Bastard and Perret et al., Nat. Chem. Biol., 2017). This unique class of L-serine succinyl-CoA transferases (SST), called Cys2, is encoded by metX homologs whereas these latter are known to only be involved in L-methionine biosynthesis. The conservation of Cys2 in fungi suggests that the biosynthesis of L-cysteine via the novel metabolite O-succinyl L-serine (OSS) is a common treat in this kingdom. In contrast, few Cys2 homologs have been identified in bacteria, particularly in Xanthomonadales species. The phylogenetic proximity of these enzymes, along with the structural similarity of their active site suggest they share the same function. To support the in vivo role for OSS in Xanthomonadales, we kinetically characterized Cys2 from both Xanthomonas campestris and Frateuria aurantia. Their catalytic efficiency (kcat/Km) is in favor of the formation of OSS. We also report that their L-cysteine synthase (the next enzyme in L-cysteine biosynthesis pathway) are actually O-succinyl-L-serine sulfhydrylases. This new metabolite was detected in the metabolome of X. campestris. Together, these results demonstrate the role for this novel metabolite in L-cysteine biosynthesis in bacteria, too

Characterization of L­-Serine O-succinyltransferases involved in l-cysteine biosynthesis in prokaryotes

Until very recently, acetylation was the only known way for activating L-serine in the penultimate step of L-cysteine biosynthesis, in bacteria and fungi. This reaction is catalyzed by L-serine O-acetyl transferases (SAT), encoded by cysE and srpH, and belonging to the transferase hexapeptide repeat family. Nevertheless, we demonstrated that L-serine is succinylated in Schizosaccharomyces pombe by an enzyme unrelated to the classical SAT (Bastard and Perret et al., Nat. Chem. Biol., 2017). This unique class of L-serine succinyl-CoA transferases (SST), called Cys2, is encoded by metX homologs whereas these latter are known to only be involved in L-methionine biosynthesis. The conservation of Cys2 in fungi suggests that the biosynthesis of L-cysteine via the novel metabolite O-succinyl L-serine (OSS) is a common treat in this kingdom. In contrast, few Cys2 homologs have been identified in bacteria, particularly in Xanthomonadales species. The phylogenetic proximity of these enzymes, along with the structural similarity of their active site suggest they share the same function. To support the in vivo role for OSS in Xanthomonadales, we kinetically characterized Cys2 from both Xanthomonas campestris and Frateuria aurantia. Their catalytic efficiency (kcat/Km) is in favor of the formation of OSS. We also report that their L-cysteine synthase (the next enzyme in L-cysteine biosynthesis pathway) are actually O-succinyl-L-serine sulfhydrylases. This new metabolite was detected in the metabolome of X. campestris. Together, these results demonstrate the role for this novel metabolite in L-cysteine biosynthesis in bacteria, too

Cephalosporin Hypersensitivity: Descriptive Analysis, Cross-Reactivity, and Risk Factors

International audienc

Cephalosporin Hypersensitivity: Descriptive Analysis, Cross-reactivity, and Risk Factors

International audienceBackground: Cephalosporins, which belong to the beta-lactam therapeutic class, are increasingly used throughout the world. Few large studies on this issue have been conducted, and most of them have been performed as part of penicillin hypersensitivity studies.Objective: We described our 26-year experience exploring cephalosporin drug hypersensitivity, from which we identified epidemiological and cross-reactivity data.Methods: We included 476 patients who reported drug hypersensitivity reaction (DHR) to cephalosporin and underwent an allergy workup between January 1992 and July 2018 in the Allergy Unit of the University Hospital of Montpellier (France). According to their structural side chain R1 homology, we worked with 4 classes of cephalosporins. Logistic regression analysis was used to search for risk factors for hypersensitivity to cephalosporin (positive skin test [ST] or drug provocation test [DPT] results).Results: Cephalosporin hypersensitivity was proven in 22.3% of the patients referred in our Unit, according to positive ST (51.9%) or DPT to the culprit drug (48.1%). One in 5 patients were children, and cephalosporin hypersensitivity was confirmed in 15% (47.6% of them by means of ST). In the cephalosporin hypersensitive population, initial reactions were mostly immediate (68.9%) and anaphylactic (72.7%). Cross-reactivity with aminopenicillins was the most frequent pattern of cross-reactivity. In multivariate analysis, immediate reactions (odds ratio [OR] = 3, 95% confidence interval [CI] [1.6-5.5], P < .001), anaphylactic shock (OR = 6.5, 95% CI [3.3-13.1], P < .001) and anaphylaxis (OR = 3.1, 95% CI [1.6-6.1], P < .001), and multiple reactions to the same or several cephalosporins (OR = 2.0, 95% CI [1-3.5], P = .04) were statistically associated with confirmed DHR. DPT was generally safe, but elicited anaphylaxis in 20% of patients. Systemic reactions during skin testing occurred in 9.1% of positive patients, almost always related to anaphylactic index reactions. Nonimmediate confirmed DHR to cephalosporins were rare and occurred in less than 10% of the positive patients.Conclusion: Almost a quarter of the tested patients were confirmed as hypersensitive to cephalosporins; sensitivity of skin testing was 51.9%, and thus, half of the positive patients needed a DPT to prove the diagnosis

Le « C-type Natriuretic Peptide » (CNP) comme arme dans la lutte contre les biofilms de Pseudomonas aeruginosa : Présentation du mécanisme d’action

International audienc

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems.ISSN:2052-446

What is the optimal treatment for T1N0 anal squamous cell carcinoma? Analysis of current practices in the prospective French FFCD ANABASE cohort

International audienceIntroduction: for localized T1N0 squamous cell carcinoma of the anus (SCCA) standard radiotherapy (RT) may result in overtreatment and alternative strategies are debated. Methods: T1N0M0 SCCA treated between 2015 and 2020 by local excision (LE) or RT were analyzed from the French prospective FFCD ANABASE cohort. Treatment strategies, recurrence-free and colostomy-free survivals (RFS, CFS) and prognostic factors were reported. Results: among 1135 SCCA patients, 99 T1N0M0 were treated by LE(n = 17,17.2%), or RT ( n = 82,82.8%) including RT alone ( n = 65,79.2%) or chemo-RT ( n = 17, 20.7%). Median follow-up was 27.2 months [0.03 and ndash;54.44]. Median tumor size were 11.4 mm [0.9 and ndash;20] and 15.3 mm [2 and ndash;20] in the LE and RT groups respectively. Mean RT tumor dose was 59.4 Gy [18 and ndash;69.4 Gy]. One patient in LE group and 9 in RT group had a pelvic recurrence, either local (60%), nodal (10%) or both (30%). RFS and CFS at 24 months were 92.2%[95%CI,83.4 and ndash;96.4] and 94.6%[95%CI,86.1 and ndash;98.0], at 36 months 88.1%[95%CI,77.1 and ndash; 94.2] and 88.5%[95%CI,77.0 and ndash;94.5], in LE and RT group respectively, without any significative difference (HR = 0.57;[95%CI,0.07 and ndash;4.45];p= 0.60). By univariate analysis, male gender was the only prognostic fac-tor(HR = 5.57;95%CI, 1.76 and ndash;17.63; p = 0.004). Conclusion: this cohort confirms the heterogeneity of T1N0M0 SCCA management, questioning the place of RT alone, reduced dose or RT volume, and the safety of LE. (c) 2021 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved

Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis

See also corrigendum :Corrigendum: Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis (Nature Chemical Biology volume 13, page 1137 (2017))International audienceExperimental validation of enzyme function is crucial for genome interpretation, but it remains challenging because it cannot be scaled up to accommodate the constant accumulation of genome sequences. We tackled this issue for the MetA and MetX enzyme families, phylogenetically unrelated families of acyl-L-homoserine transferases involved in L-methionine biosynthesis. Members of these families are prone to incorrect annotation because MetX and MetA enzymes are assumed to always use acetyl-CoA and succinyl-CoA, respectively. We determined the enzymatic activities of 100 enzymes from diverse species, and interpreted the results by structural classification of active sites based on protein structure modeling. We predict that >60% of the 10,000 sequences from these families currently present in databases are incorrectly annotated, and suggest that acetyl-CoA was originally the sole substrate of these isofunctional enzymes, which evolved to use exclusively succinyl-CoA in the most recent bacteria. We also uncovered a divergent subgroup of MetX enzymes in fungi that participate only in L-cysteine biosynthesis as O-succinyl-L-serine transferases