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International audience; Recently, Comte et al. (2022) re-examined the natural degradation of chlordecone (CLD) in the soils of the French West Indies (FWI) by introducing an additional ‘dissipation parameter’ into the WISORCH model developed by Cabidoche et al. (2009). Recent data sets of CLD concentrations in FWI soils obtained by Comte et al. enabled them optimizing the model parameters, resulting in significantly shorter estimates of pollution persistence than in the original model. Their conclusions jeopardize the paradigm of a very limited degradation of CLD in FWI soils, which may lead to an entire revision of the management of CLD contamination. However, we believe that their study is questionable on several important aspects. This includes potential biases in the data sets and in the modeling approach. It results in an inconsistency between the estimated dissipation half-life time (DT50) of five years that the authors determined for CLD and the fate of CLD in soil from the application period 1972–1993 until nowadays. Most importantly, a rapid dissipation of CLD in the field as proposed by Comte et al. is not sufficiently supported by data and estimates. Hence, the paradigm of long-term persistence of CLD in FWI soils is still to be considered.

Chlordecone (CLD) is a very persistent synthetic organochlorine pesticide found in the French West Indies. Recently published work has demonstrated the potential of zero-valent iron to dechlorinate CLD by in situ chemical reduction (ISCR) in soils under water-saturated conditions, forming mono- to penta-dechlorinated CLD transformation products. These transformation products are more mobile than CLD and less toxic; however, nothing is known about their further degradation, although increasing evidence of CLD biodegradation by bacteria is being found. The present study began with the enrichment from wastewater sludge of a CLD-transforming community which was then inoculated into fresh media in the presence of either CLD or two of the main ISCR transformation products, 10-monohydroCLD (-1Cl-CLD) and tri-hydroCLD (-3Cl-CLD). Carried out in triplicate batches and incubated at 38°C under anoxic conditions and in the dark, the cultures were sampled regularly during 3 months and analyzed for CLD, -1Cl-CLD, -3Cl-CLD, and possible transformation products by gas chromatography coupled to mass spectrometry. All batches showed a decrease in the amended substrates (CLD or hydroCLD). CLD degradation occurred with concomitant formation of a nine-carbon compound (pentachloroindene) and two sulfur-containing transformation products (chlordecthiol, CLD-SH; methyl chlordecsulfide, CLD-SCH3), demonstrating competing transformation pathways. In contrast, -1Cl-CLD and -3Cl-CLD only underwent a sequential reductive sulfidation/S-methylation process resulting in -1Cl-CLD-SH and -1Cl-CLD-SCH3 on the one hand, and -3Cl-CLD-SH, -3Cl-CLD-SCH3 on the other hand. Some sulfur-containing transformation products have been reported previously with single bacterial strains, but never in the presence of a complex microbial community. At the end of the experiment, bacterial and archaeal populations were investigated by 16S rRNA gene amplicon sequencing. The observed diversity was mostly similar in the CLD and -1Cl-CLD conditions to the inoculum with a dominant archaea genus, Methanobacterium, and four OTU affiliated to bacteria, identified at the family (Spirochaetaceae) or genus level (Desulfovibrio, Aminobacterium, and Soehngenia). On the other hand, in the -3Cl-CLD condition, although the same OTU were found, Clostridium sensu stricto 7, Candidatus Cloacimonas, and Proteiniphilum were also present at > 2% sequences. Presence of methanogens and sulfate-reducing bacteria could contribute to sulfidation and S-methylation biotransformations. Overall, these results contribute to increasing our knowledge on the biodegradability of CLD and its transformation products, helping to progress toward effective remediation solutions.

International audience; The insecticide chlordecone has been used in the French West Indies for decades, resulting in long term pollution, human health problems and social crisis. In addition to bacterial consortia and Citrobacter sp.86 previously described to transform chlordecone into three families of transformation products (A: hydrochlordecones, B: polychloroindenes and C: polychloroindenecarboxylic acids), another bacterium Desulfovibrio sp.86, showing the same abilities has been isolated and its genome was sequenced. Ring-opening dechlorination, leading to A, B and C families, was observed as previously described. changing operating conditions in the presence of chlordecone gave rise to the formation of an unknown sulfur-containing transformation product instead of the aforementioned ones. Its structural elucidation enabled to conclude to a thiol derivative, which corresponds to an undocumented bacterial reductive sulfidation. Microbial experiments pointed out that the chlordecone thiol derivative was observed in anaerobiosis, and required the presence of an electron acceptor containing sulfur or hydrogen sulfide, in a confined atmosphere. It seems that this new reaction is also active on hydrochlordecones, as the 10-monohydrochlordecone A1 was transformed the same way. Moreover, the chlordecone thiol derivative called F1 was detected in several chlordecone contaminated mangrove bed sediments from Martinique Island, highlighting the environmental relevance of these results. Chlordecone is a highly recalcitrant organochlorine pesticide that has been added to the Stockholm convention list of persistent organic pollutants in 2009. Several pest control products containing chlordecone (Kepone, Curlone) or a functionalized derivative (Kelevan) have been manufactured in the US, Brazil and France and applied in the Caribbean, Central America, West Africa, and Europe over an extended period of forty years 1. To date, chlordecone has caused two major environmental disasters: (1) acute exposure of workers at the Hopewell (US) chlordecone production plant in 1975 and massive pollution of the James River, extending over 100 miles that lasted for decades 2 , (2) ongoing impregnation of the French West Indies (FWI) population due to extensive agricultural use of chlordecone from 1972 to 1993 that has resulted in long-term pollution of environmental compartments (soils, water resources, coastal areas) and subsequently of some local food production (vegetables, farmed animals, and seafood). Until now, no remediation strategy has been proven satisfactory in the FWI environment whereas the population has to deal with health troubles (increased risk of cancer, motor and cognitive development disorders in young children, premature births) and social difficulties (disappearance of local economy activities) 1 .

Two molecular cages have been tested as receptors for the persistent organic pollutant chlordecone. Whereas the host bearing amide functions displays a moderate binding constant (126 M−1), the receptor with a tris(2-aminoethyl)amine moiety exhibits a higher association constant (2.1 × 104 M−1). The recognition process was investigated by NMR experiments and DFT calculations.

International audience; Production and use of the insecticide chlordecone has caused long-term environmental pollution in the James River area and the French West Indies (FWI) that has resulted in acute human-health problems and a social crisis. High levels of chlordecone in FWI soils, even after its ban decades ago, and the absence of detection of transformation products (TPs), have suggested that chlordecone is virtually nonbiodegradable in the environment. Here, we investigated laboratory biodegradation, consisting of bacterial liquid cultures and microcosms inoculated with FWI soils, using a dual nontargeted GC-MS and LC-HRMS approach. In addition to previously reported, partly characterized hydrochlordecones and polychloroindenes (families A and B), we discovered 14 new chlordecone TPs, assigned to four families (B, C, D, and E). Organic synthesis and NMR analyses allowed us to achieve the complete structural elucidation of 19 TPs. Members of TP families A, B, C, and E were detected in soil, sediment, and water samples from Martinique and include 17 TPs not initially found in commercial chlordecone formulations. 2,4,5,6,7-Pentachloroindene was the most prominent TP, with levels similar to those of chlordecone. Overall, our results clearly show that chlordecone pollution extends beyond the parent chlordecone molecule and includes a considerable number of previously undetected TPs. Structural diversity of the identified TPs illustrates the complexity of chlordecone degradation in the environment and raises the possibility of extensive worldwide pollution of soil and aquatic ecosystems by chlordecone TPs.

International audience; Introduction Metabolite identification remains a major bottleneck in the understanding of metabolism. Many metabolomics studies end up with unknown compounds, leaving a landscape of metabolites and metabolic pathways to be unraveled. Therefore, identifying novel compounds within a metabolome is an entry point into the 'dark side' of metabolism. Objectives This work aimed at elucidating the structure of a novel metabolite that was first detected in the soil bacterium Acinetobacter baylyi ADP1 (ADP1). Methods We used high resolution multi-stage tandem mass spectrometry for characterizing the metabolite within the metabolome. We purified the molecule for 1D-and 2D-NMR (1 H, 13 C, 1 H-1 H-COSY, 1 H-13 C-HSQC, 1 H-13 C-HMBC and 1 H-15 N-HMBC) analyses. Synthetic standards were chemically prepared from MS and NMR data interpretation. Results We determined the de novo structure of a previously unreported metabolite: 3-((3-aminopropyl)amino)-4-hydroxy-benzoic acid. The proposed structure was validated by comparison to a synthetic standard. With a concentration in the mil-limolar range, this compound appears as a major metabolite in ADP1, which we anticipate to participate to an unsuspected metabolic pathway. This novel metabolite was also detected in another γ-proteobacterium. Conclusion Structure elucidation of this abundant and novel metabolite in ADP1 urges to decipher its biosynthetic pathway and cellular function.

International audience; Trigonelline (TG; N-methylnicotinate) is a ubiquitous osmolyte. Although it is known that it can be degraded, the enzymes and metabolites have not been described so far. In this work, we challenged the laboratory model soil-borne, gram-negative bacterium Acinetobacter baylyi ADP1 (ADP1) for its ability to grow on TG and we identified a cluster of catabolic, transporter, and regulatory genes. We dissected the pathway to the level of enzymes and metabolites, and proceeded to in vitro reconstruction of the complete pathway by six purified proteins. The four enzymatic steps that lead from TG to methylamine and succinate are described, and the structures of previously undescribed metabolites are provided. Unlike many aromatic compounds that undergo hydroxylation prior to ring cleavage, the first step of TG catabolism proceeds through direct cleavage of the C5-C6 bound, catalyzed by a flavin-dependent, two-component oxygenase, which yields (Z)-2-((N-methylformamido)methylene)-5-hydroxy-butyrolactone (MFMB). MFMB is then oxidized into (E)-2-((N-methylformamido) methylene) succinate (MFMS), which is split up by a hydrolase into carbon dioxide, methylamine, formic acid, and succinate semialdehyde (SSA). SSA eventually fuels up the TCA by means of an SSA dehydrogenase, assisted by a Conserved Hypothetical Protein. The cluster is conserved across marine, soil, and plant-associated bacteria. This emphasizes the role of TG as a ubiquitous nutrient for which an efficient microbial catabolic toolbox is available. bacterial metabolism | functional genomics | LC/MS-Orbitrap | trigonelline | N-heterocycle degradation E xtensive and accurate bacterial genome annotation is critical for developing a comprehensive and detailed understanding of cellular physiology, and is therefore a major concern in biological research. As a result, 30-40% of genes of a typical ge-nome remain unannotated or associated with a putative function (1, 2). In many cases, function is extrapolated from a small number of characterized proteins (3). In this context, the need for a global effort of experimental assignation, validation, or correction of function is major. Experimental work guided by bioinformatics has proved to be an invaluable tool for assigning new functions (4-7). However, investigations on catabolic pathways are still often conducted in a few model organisms and with a restricted set of nutrients. Given the vast array of natural secondary metabolites and their underrepresentation in metabolic maps, the full range of transformations afforded by bacteria is clearly underestimated. Thus, simply varying the range of organisms tested and the set of nutrients remains a useful tactic for elucidating hidden latent microbial catabolic pathways and providing access to gene function (8-10). Trigonelline (TG; N-methylnicotinate) is a metabolite of nic-otinamide involved in plant cell cycle regulation and oxidative stress (11). Released by legume roots and seeds, such as in alfalfa , it activates nodulation genes in Rhizobium meliloti (12). It is one of the most widely distributed betaines in higher plants (12, 13), and it is also present with different concentration ranges in organisms such as reef-building corals (14, 15), algae (16), and marine plankton, in which it can reach the millimolar range (17, 18). It is likely released in the environment through the death of these organisms. As a consequence, numerous heterotrophic prokaryotes probably use this compound as a nutrient. Surprisingly , the soil bacterium R. meliloti RCR2011 is the only organism reported to use TG as a carbon, nitrogen, and energy source (19). Although an inducible genetic region involved in the degradation of this compound was specified (20, 21), investigations aimed at deciphering this metabolic pathway did not go further. Therefore, the complete set of genes and catabolites involved in this process is not reported. Acinetobacter baylyi ADP1 (ADP1) is a nutritionally versatile strictly aerobic bacterium capable of metabolizing a wide range of aromatic compounds (22). Its extraordinary competence for natural transformation and the ease with which it can be genetically engineered (23, 24) make ADP1 a key organism for the study of soil bacteria metabolism of natural compounds. In this work, we show that ADP1 can use TG as the sole source of carbon, nitrogen, and energy. A gene cluster responsible for TG degradation, which we called tgn (for trigonelline), was revealed Significance The experimental dissection of novel metabolic pathways, from genes and enzymes to metabolites, is a key issue for improving our knowledge of the enzymatic capabilities of the microbial world and providing accurate functional annotation of genomes. We used an integrative methodology combining the phenotyping of a complete genome-scale mutant collection of Acinetobacter baylyi ADP1 with an untargeted liquid chromatography/MS-based approach to uncover the degradation pathway of trigonelline (TG), a widespread osmolyte. We provide extensive information about this unusual N-heterocyclic aromatic degradation route that expands the metabolite repertoire. The occurrence of conserved gene clusters for TG dis-similation in soil, plant-associated, and marine bacteria underlines its environmental abundance.

International audience; Chlordecone is a synthetic organochlorine pesticide, extensively used in banana plantations of the French West Indies from 1972 to 1993. Due to its environmental persistence and bioaccumulation, it has dramatic public health and socio-economic impact. Here we describe a method for carbon-directed compound specific isotope analysis (CSIA) for chlordecone and apply it to monitor biotic and abiotic reductive transformation reactions, selected on the basis of their distinct product profiles (polychloroindenes versus lower chlorinated hydrochlordecones). Significant carbon isotopic enrichments were observed for all microbially mediated transformations (epsilon(bulk) = -6.8 parts per thousand with a Citrobacter strain and epsilon(bulk) = -4.6 parts per thousand with a bacterial consortium) and for two abiotic transformations (epsilon(bulk) = -4.1 parts per thousand with zerovalent iron and epsilon(bulk) = -2.6 parts per thousand with sodium sulfide and vitamin B-12). The reaction with titanium(III) citrate and vitamin B-12 which shows the product profile most similar to that observed in biotic transformation, led to low carbon isotope enrichment (epsilon(bulk) = -0.8 parts per thousand). The CSIA protocol was also applied on representative chlordecone formulations previously used in the French West Indies, giving similar chlordecone delta C-13 values from -31.1 +/- 0.2 parts per thousand to -34.2 +/- 0.2 parts per thousand for all studied samples. This allows the in situ application of CSIA for the assessment of chlordecone persistence.

Amino alcohols are a very common structural motif in natural and synthetic molecules. Starting from l-lysine and hydroxy-l-lysine, a straightforward biocatalytic synthesis of beta- and gamma-amino alcohols is presented. Diastereoselective C–H oxidation catalyzed by an alpha-keto acid-dependent oxygenase followed by cleavage of the carboxylic acid moiety of the corresponding chiral hydroxy amino acid by a pyridoxal phosphate-dependent decarboxylase enabled the formation of the target amino alcohols with moderate to complete conversions. Four beta- and gamma-amino alcohols were obtained on a small scale in excellent yields and stereoselectivities.

International audience; Chlordecone (Kepone®) is a synthetic organochlorine insecticide (C10Cl10O) used worldwide mostly during the 1970 and 1980s. Its intensive application in the French West Indies to control the banana black weevil Cosmopolites sordidus led to a massive environmental pollution. Persistence of chlordecone in soils and water for numerous decades even centuries causes global public health and socio-economic concerns. In order to investigate the biodegradability of chlordecone, microbial enrichment cultures from soils contaminated by chlordecone or other organochlorines and from sludge of a wastewater treatment plant have been conducted. Different experimental procedures including original microcosms were carried out anaerobically over long periods of time. GC-MS monitoring resulted in the detection of chlorinated derivatives in several cultures, consistent with chlordecone biotransformation. More interestingly, disappearance of chlordecone (50 μg/mL) in two bacterial consortia was concomitant with the accumulation of a major metabolite of formula C9Cl5H3 (named B1) as well as two minor metabolites C10Cl9HO (named A1) and C9Cl4H4 (named B3). Finally, we report the isolation and the complete genomic sequences of two new Citrobacter isolates, closely related to Citrobacter amalonaticus, and that were capable of reproducing chlordecone transformation. Further characterization of these Citrobacter strains should yield deeper insights into the mechanisms involved in this transformation process.

International audience; Application of known dialkyl ketene di- and trimerization to more complex precursors could readily open the route to highly functionalized symmetrical cyclobuta-1,3-diones and cyclohexa-1,3,5-triones. We report herein the results on three substrates containing either a C=C double bond or a protected glycol moiety as illustrative functionalized groups. The nature of the substituents is found to be crucial: while cyclopentenyl and more constrained dioxolanocyclopentenyl precursors efficiently dimerize, a diallylic derivative fails. At the millimolar scale, methoxide-catalyzed trimerization shows limited reproducibility, even for the reported substrate tetramethylcyclobuta-1,3-dione. However, systematic studies, including the use of microwaves, demonstrate that formation of symmetrical trimers is favored under solvent-free conditions and conventional heating, which allowed us to isolate and characterize trispiro[4.1.4.1.4.1]octadeca-2,9,15-triene-6,12,18-trione.

International audience; Iron(II)/$\alpha$-ketoacid-dependent oxygenases ($\alpha$KAOs) are enzymesthat mainly catalyse hydroxylation reaction. By usinga genomic approach combining sequence comparison andprotein-domain sharing, a set of 131 $\alpha$KAO enzymes was prepared.The screening of various substrates revealed five new$\alpha$KAOs. Four $\alpha$KAOs were found to be active towards L-lysine,L-ornithine and L-arginine with total regio- and stereoselectivitiesand yielding the corresponding 3- or 4-hydroxyaminoacids. The enzymatic cascade reaction with two stereoselectiveregiodivergent $\alpha$ KAOs enabled the synthesis of 3,4-dihydroxy-L-lysine.

Skyllamycin is a non-ribosomally synthesized cyclic depsipeptide from Streptomyces sp. Acta 2897 that inhibits PDGF-signaling. The peptide scaffold contains an N-terminal cinnamoyl moiety, a β-methylation of aspartic acid, three β-hydroxylated amino acids and one rarely occurring α-hydroxy glycine. With the exception of α-hydroxy glycine, the stereochemistry of the amino acids was assigned by comparison to synthetic reference amino acids applying chiral GC-MS and Marfey-HPLC analysis. The stereochemistry of α-hydroxy glycine, which is unstable under basic and acidic conditions, was determined by conformational analysis, employing a combination of data from NOESY-NMR spectroscopy, simulated annealing and free MD simulations. The simulation procedures were applied for both R- and S-configured α-hydroxy glycine of the skyllamycin structure and compared to the NOESY data. Both methods, simulated annealing and free MD simulations independently support S-configured α-hydroxy glycine thus enabling the assignment of all stereocenters in the structure of skyllamycin and devising the role of two-component flavin dependent monooxygenase (Sky39) as S-selective.

International audience; In the presence of bases, trifluoroacetone is known to trimerize leading to configurationally labile 6-methyl-2,4,6-tris(trifluoromethyl)tetrahydro 2H-pyran-2,4-diols 1a,b and 2a,b, structurally close to fluorinated carbohydrates. We report herein a complete study of their behavior in solution. The remarkable solvent effect on the two equilibria (1a double left right arrow 1b; 2a double left right arrow 2b) was rationalized using solvent basicity measures and polarity scales. Solvents of weak donor number were found to favor the diastereoisomers 1a and 2a, which were subsequently isolated. According to their X-ray analyses, they both possess a concave structure with 1,3-cis-diaxial hydroxyl groups. A complementary kinetic study illustrated that acidic conditions can drastically reduce the equilibration rate, allowing the use of a wide range of solvents. Finally, a reexamination of previously published trimerization conditions using sodium or magnesium amalgam revealed that, contrary to the suggestion by two independent reports, 1,3,5-tris(trifluoromethyl)cyclohexane-1,3,5-triol 3/4 was neither formed as the principal product in place of 1a,b and 2a,b nor could it be detected as a minor product.

International audience; The title compound, C9H3F18O4P, was synthesized by condensation of sodium hexafluoroisopropanolate and phosphoryl chloride. The P atom is in a distorted tetrahedral environment. The molecules are stabilized by weak O center dot center dot center dot H and F center dot center dot center dot H hydrogen- bond interactions as well as F center dot center dot center dot F interactions.

A simplified synthesis of a previously reported Cd 2 Cu 2 complex 4 was developed in order to have a more readily available source of 1,3,5-tris(trifluoromethyl)-cyclohexane- cis , cis -1,3,5-triol 1 , a unique tridentate ligand, only tentatively identified elsewhere. Attempts to liberate the ligand from 4 resulted in the sole formation of 2,4,6-tris(trifluoromethyl)-tetrahydropyran- cis , cis -2,4,6-triol ( 2 ); no traces of 1 were detected. A newly conducted X-ray analysis of complex 4 led to diffraction data that could be explained either by the previously reported structure for 4 or by the statistically disordered structure 5 , containing ligand 2 rather than 1 . Whereas refinement of both models led to equivalent merit factors, mass spectral data and elemental analysis of the crystals revealed unequivocally the sole presence of the tetrahydropyran derivative within the complex and proved thus the erroneous structure assignment 4 previously published for compound 5 .

With proper activation of the leaving group, sulfur mustards react with Grignard reagents with neighboring group participation of the sulfur atom. 2,6-Dichloro-9-thiabicyclo[3.3.1]nonane is especially useful in this regard, providing clean reactivity with organomagnesium nucleophiles on a topologically constrained scaffold.