Papers by stephane vuilleumier
Microorganisms
Metformin is one of the most prescribed antidiabetic agents worldwide and is also considered for ... more Metformin is one of the most prescribed antidiabetic agents worldwide and is also considered for other therapeutic applications including cancer and endocrine disorders. It is largely unmetabolized by human enzymes and its presence in the environment has raised concern, with reported toxic effects on aquatic life and potentially also on humans. We report on the isolation and characterisation of strain MD1, an aerobic methylotrophic bacterium growing with metformin as its sole carbon, nitrogen and energy source. Strain MD1 degrades metformin into dimethylamine used for growth, and guanylurea as a side-product. Sequence analysis of its fully assembled genome showed its affiliation to Aminobacter niigataensis. Differential proteomics and transcriptomics, as well as mini-transposon mutagenesis of the strain, point to genes and proteins essential for growth with metformin and potentially associated with hydrolytic C-N cleavage of metformin or with cellular transport of metformin and guan...
Environmental Science & Technology, 2001
The main aim of the study was to evaluate hydrogen and carbon isotope fractionation during biodeg... more The main aim of the study was to evaluate hydrogen and carbon isotope fractionation during biodegradation of benzene as a possible tool to trace the process in contaminated environments. Aerobic biodegradation of benzene by two bacterial isolates, Acinetobacter sp. and Burkholderia sp., was accompanied by significant hydrogen and carbon isotope fractionation with hydrogen isotope enrichment factors of-12.8 (0.7‰ and-11.2 (1.8‰, respectively, and average carbon isotope enrichment factors of-1.46 (0.06‰ and-3.53 (0.26‰, respectively. Inorganic carbon produced by Acinetobacter sp. was depleted in 13 C by 3.6-6.2‰ as compared to the initial δ 13 C of benzene, while the produced biomass was enriched in 13 C by 3.8‰. The secondary aim was to determine isotope ratios of benzenes from different manufacturers with regard to the use of isotopes for source differentiation. While two of the four analyzed benzenes had similar δ 13 C values, each of them had a distinct δ 2 H-δ 13 C pair and δ 2 H values spread over a range of 66.5‰. Thus, combined analyses of hydrogen and carbon isotopes may be a more promising approach to trace sources and/or biodegradation of benzene than measuring carbon isotopes only.
2016 Molecular Basis of Microbial One-Carbon Metabolism GRC/GRS
U.S. Department of Energy Office of Scientific and Technical Information - OSTI OAI, Jul 30, 2016
Frontiers in Microbiology, 2019
Microcosm experiments with CE-contaminated groundwater from a former industrial site were setup t... more Microcosm experiments with CE-contaminated groundwater from a former industrial site were setup to evaluate the relationships between biological CE dissipation, dehalogenase genes abundance and bacterial genera diversity. Impact of high concentrations of PCE on organohalide respiration was also evaluated. Complete or partial dechlorination of PCE, TCE, cis-DCE and VC was observed independently of the addition of a reducing agent (Na 2 S) or an electron donor (acetate). The addition of either 10 or 100 µM PCE had no effect on organohalide respiration. qPCR analysis of reductive dehalogenases genes (pceA, tceA, vcrA, and bvcA) indicated that the version of pceA gene found in the genus Dehalococcoides [hereafter named pceA(Dhc)] and vcrA gene increased in abundance by one order of magnitude during the first 10 days of incubation. The version of the pceA gene found, among others, in the genus Dehalobacter, Sulfurospirillum, Desulfuromonas, and Geobacter [hereafter named pceA(Dhb)] and bvcA gene showed very low abundance. The tceA gene was not detected throughout the experiment. The proportion of pceA(Dhc) or vcrA genes relative to the universal 16S ribosomal RNA (16S rRNA) gene increased by up to 6-fold upon completion of cis-DCE dissipation. Sequencing of 16S rRNA amplicons indicated that the abundance of Operational Taxonomic Units (OTUs) affiliated to dehalogenating genera Dehalococcoides, Sulfurospirillum, and Geobacter represented more than 20% sequence abundance in the microcosms. Among organohalide respiration associated genera, only abundance of Dehalococcoides spp. increased up to fourfold upon complete dissipation of PCE and cis-DCE, suggesting a major implication of Dehalococcoides in CEs organohalide respiration. The relative abundance of pceA and vcrA genes correlated with the occurrence of Dehalococcoides and with dissipation extent of PCE, cis-DCE and CV. A new type of dehalogenating Dehalococcoides sp. phylotype affiliated to the Pinellas group, and suggested to contain both pceA(Dhc) and vcrA genes, may be involved in organohalide
Bacterial Tolerance in Contaminated Soils
Environmental and Ecological Risk Assessment, 2011
Microbiology, 2001
Dichloromethane dehalogenase/glutathione S-transferase allows methylotrophic bacteria to grow wit... more Dichloromethane dehalogenase/glutathione S-transferase allows methylotrophic bacteria to grow with dichloromethane (DCM), a predominantly man-made compound. Bacteria growing with DCM by virtue of this enzyme have been readily isolated in the past. So far, the sequence of the dcmA gene encoding DCM dehalogenase has been determined for Methylobacterium dichloromethanicum DM4 and Methylophilus sp. DM11. DCM dehalogenase genes closely related to that of strain DM4 were amplified by PCR and cloned from total DNA from 14 different DCM-degrading strains, enrichment cultures and sludge samples from wastewater treatment plants. In total, eight different sequences encoding seven different protein sequences were obtained. Sequences of different origin were identical in several instances. Sequence variation was limited to base substitutions ; strikingly, 16 of the 19 substitutions in the dcmA gene itself encoded amino acids that were different from those of the DM4 sequence. The kinetic parameters k cat and K m , the pH optimum and the stability of representative DCM dehalogenase variants were investigated, revealing minor differences between the properties of DCM dehalogenases related to that from strain DM4.
Background: Chloromethane (CH3Cl) is the most abundant chlorinated volatile organic compound in t... more Background: Chloromethane (CH3Cl) is the most abundant chlorinated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH3Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH3Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. Results and Conclusions: We investigated chloromethane-degrading taxa associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with 13C-labelled CH3Cl combined with metagenomic DNA sequencing. Metagenome assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH3Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH3Cl degradation in the fern rhizosphere....
The genome sequence of Hyphomicrobium sp. strain GJ21, isolated in the Netherlands from samples o... more The genome sequence of Hyphomicrobium sp. strain GJ21, isolated in the Netherlands from samples of environments contaminated with halogenated pollutants and capable of using dichloromethane as its sole carbon and energy source,
Microorganisms, 2020
Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using ... more Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using the conserved dehalogenase DcmA, the only system for DCM degradation characterised at the sequence level so far. Using differential proteomics, we rapidly identified key determinants of DCM degradation for Hyphomicrobium sp. MC8b, an unsequenced facultative methylotrophic DCM-degrading strain. For this, we designed a pan-proteomics database comprising the annotated genome sequences of 13 distinct Hyphomicrobium strains. Compared to growth with methanol, growth with DCM induces drastic changes in the proteome of strain MC8b. Dichloromethane dehalogenase DcmA was detected by differential pan-proteomics, but only with poor sequence coverage, suggesting atypical characteristics of the DCM dehalogenation system in this strain. More peptides were assigned to DcmA by error-tolerant search, warranting subsequent sequencing of the genome of strain MC8b, which revealed a highly divergent set of dc...
Methyl halides are volatile one-carbon compounds responsible for substantial depletion of stratos... more Methyl halides are volatile one-carbon compounds responsible for substantial depletion of stratospheric ozone. Among them, chloromethane (CH 3 Cl) is the most abundant halogenated hydrocarbon in the atmosphere. Global budgets of methyl halides in the environment are still poorly understood due to uncertainties in their natural sources, mainly from vegetation, and their sinks, which include chloromethane-degrading bacteria. A bacterial bioreporter for the detection of methyl halides was developed on the basis of detailed knowledge of the physiology and genetics of Methylobacterium extorquens CM4, an aerobic alphaproteobacterium which utilizes chloromethane as the sole source of carbon and energy. A plasmid construct with the promoter region of the chloromethane dehalogenase gene cmuA fused to a promotorless yellow fluorescent protein gene cassette resulted in specific methyl halide-dependent fluorescence when introduced into M. extorquens CM4. The bacterial whole-cell bioreporter allowed detection of methyl halides at femtomolar levels and quantification at concentrations above 10 pM (approximately 240 ppt). As shown for the model chloromethane-producing plant Arabidopsis thaliana in particular, the bioreporter may provide an attractive alternative to analytical chemical methods to screen for natural sources of methyl halide emissions.
Applied and Environmental Microbiology, 1998
Methylobacterium sp. strain DM4 andMethylophilus sp. strain DM11 can grow with dichloromethane (D... more Methylobacterium sp. strain DM4 andMethylophilus sp. strain DM11 can grow with dichloromethane (DCM) as the sole source of carbon and energy by virtue of homologous glutathione-dependent DCM dehalogenases with markedly different kinetic properties (the k cat values of the enzymes of these strains are 0.6 and 3.3 s−1, respectively, and theKm values are 9 and 59 μM, respectively). These strains, as well as transconjugant bacteria expressing the DCM dehalogenase gene (dcmA) from DM11 or DM4 on a broad-host-range plasmid in the background of dcmA mutant DM4-2cr, were investigated by growing them under growth-limiting conditions and in the presence of an excess of DCM. The maximal growth rates and maximal levels of dehalogenase for chemostat-adapted bacteria were higher than the maximal growth rates and maximal levels of dehalogenase for batch-grown bacteria. The substrate saturation constant of strain DM4 was much lower than theKm of its associated dehalogenase, suggesting that this str...
Scientific Reports, 2017
Chloromethane (CH 3 Cl) is a toxic gas mainly produced naturally, in particular by plants, and it... more Chloromethane (CH 3 Cl) is a toxic gas mainly produced naturally, in particular by plants, and its emissions contribute to ozone destruction in the stratosphere. Conversely, CH 3 Cl can be degraded and used as the sole carbon and energy source by specialised methylotrophic bacteria, isolated from a variety of environments including the phyllosphere, i.e. the aerial parts of vegetation. The potential role of phyllospheric CH 3 Cl-degrading bacteria as a filter for plant emissions of CH 3 Cl was investigated using variants of Arabidopsis thaliana with low, wild-type and high expression of HOL1 methyltransferase previously shown to be responsible for most of CH 3 Cl emissions by A. thaliana. Presence and expression of the bacterial chloromethane dehalogenase cmuA gene in the A. thaliana phyllosphere correlated with HOL1 genotype, as shown by qPCR and RT-qPCR. Production of CH 3 Cl by A. thaliana paralleled HOL1 expression, as assessed by a fluorescence-based bioreporter. The relation between plant production of CH 3 Cl and relative abundance of CH 3 Cl-degrading bacteria in the phyllosphere suggests that CH 3 Cl-degrading bacteria co-determine the extent of plant emissions of CH 3 Cl to the atmosphere. The phyllosphere, defined as the aerial part of plants and especially leaves, is a crucial if perhaps still overlooked ecosystem, with leaf surfaces estimated to total 1 × 10 9 km², i.e. twice the land surface area. The phyllosphere represents a major habitat for microorganisms. Bacteria, in particular, are present at 10 6-10 7 cells per cm² of leaf surface, as determined by both culture-dependent and culture-independent studies 1. Availability of carbon is an important factor for microbial colonisation of the phyllosphere 2. Methanol (global estimates of 100 Tg /y for plant emissions 3) and photosynthates such as fructose, sucrose and glucose, are prominent carbon sources on leaves 2. Methanol represents a privileged growth substrate for methylotrophic bacteria, and such microorganisms , in particular from the Alphaproteobacterial genus Methylobacterium, are dominant in the phyllosphere 4. Chloromethane is another volatile one-carbon compound produced by plant leaves 5 , with global production currently estimated at approximately 1-5 Tg/y 6. Although quantitatively far less important than methanol, chloromethane has environmental significance as the most abundant halogenated hydrocarbon in the atmosphere (~550 ppt), and because it is responsible for about 15% of chlorine-catalysed destruction of stratospheric ozone 6. The best characterised mechanism for chloromethane production involves a methyltransferase-catalysed reaction, first demonstrated in Brassica oleracea 7. In Arabidopsis thaliana, the methyltransferase gene HOL1 (Harmless to Ozone Layer) was identified by a knockout mutation leading to loss of chloromethane production 8. A halide methyltransferase gene homolog of HOL1 in Raphanus sativus (daikon radish, another member of Brassicaceae family) was since also shown to be involved in methyl halide emissions 9. Some specialised methylotrophic bacteria utilise chloromethane as their only source of carbon and energy for growth 10,11 , and may thus represent natural sinks for chloromethane emissions. In this context, methylotrophic chloromethane-degrading strains from the phyllosphere of A. thaliana were isolated 12. These isolates feature
Journal of Bacteriology, 1997
Genome Announcements, 2017
The genomes of the aerobic methanotrophs “ Methyloterricola oryzae ” strain 73a T and Methylomagn... more The genomes of the aerobic methanotrophs “ Methyloterricola oryzae ” strain 73a T and Methylomagnum ishizawai strain 175 were sequenced. Both strains were isolated from rice plants. Methyloterricola oryzae strain 73a T represents the first isolate of rice paddy cluster I, and strain 175 is the second representative of the recently described genus Methylomagnum .
PloS one, 2017
Hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. Curren... more Hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. Currently, the physiological role of hopanoids is not well understood, and this represents one of the major limitations in interpreting the significance of their presence in ancient or contemporary sediments. Previous analyses of mutants lacking hopanoids in a range of bacteria have revealed a range of phenotypes under normal growth conditions, but with most having at least an increased sensitivity to toxins and osmotic stress. We employed hopanoid-free strains of Methylobacterium extorquens DM4, uncovering severe growth defects relative to the wild-type under many tested conditions, including normal growth conditions without additional stressors. Mutants overproduce carotenoids-the other major isoprenoid product of this strain-and show an altered fatty acid profile, pronounced flocculation in liquid media, and lower growth yields than for the wild-type strain. The flocculation phenotype can b...
Frontiers in microbiology, 2016
Chloromethane (CM) is an ozone-depleting gas, produced predominantly from natural sources, that p... more Chloromethane (CM) is an ozone-depleting gas, produced predominantly from natural sources, that provides an important carbon source for microbes capable of consuming it. CM catabolism has been difficult to study owing to the challenging genetics of its native microbial hosts. Since the pathways for CM catabolism show evidence of horizontal gene transfer, we reproduced this transfer process in the laboratory to generate new CM-catabolizing strains in tractable hosts. We demonstrate that six putative accessory genes improve CM catabolism, though heterologous expression of only one of the six is strictly necessary for growth on CM. In contrast to growth of Methylobacterium strains with the closely related compound dichloromethane (DCM), we find that chloride export does not limit growth on CM and, in general that the ability of a strain to grow on DCM is uncorrelated with its ability to grow on CM. This heterologous expression system allows us to investigate the components required for...
Dichloromethane Mediated in Vivo Section and Functional Characterization of Rat Glutathione S-Transferase Theta 1-1 Variants
European Journal of Biochemistry, 2001
The glutathione S-transferase OrfE3 of the dioxin-degrading bacterium Sphingomonas sp. RW1 displays maleylpyruvate isomerase activity
Chemico Biological Interactions, 2001
A GST gene of unknown function, orfE3, was earlier detected in one of the gene clusters responsib... more A GST gene of unknown function, orfE3, was earlier detected in one of the gene clusters responsible for dibenzofuran degradation by Sphingomonas sp. RW1 The degradation pathway for dibenzofuran in strain RW1 proceeds through salicylate and gentisate into intermediate metabolism. Using gentisate dioxygenase from Sphingomonas sp. RW5 to generate maleylpyruvate from gentisate, the OrfE3 protein of strain RW1 was shown to display maleylpyruvate isomerase activity. However, data obtained with an orfE3-specific chromosomal knockout mutant of strain RW1 suggest that the orfE3 GST gene is not essential for growth of strain RW1 with dibenzofuran, salicylate or gentisate. © 2001 Elsevier Science Ireland Ltd. All rights reserved.
Chloromethane-Induced Genes Define a Third C[sub 1] Utilization Pathway in Methylobacterium chloromethanicum CM4
Journal of Bacteriology, 2002
Microbiology and molecular biology reviews : MMBR, 2016
Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophor... more Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a peptide precursor that undergoes a series of posttranslational modifications, including (i) ring formation, (ii) cleavage of a leader peptide sequence, and (iii) in some cases, addition of a sulfate group. Functionally, mbs represent the extracellular component of a copper acquisition system. Consistent with this role in copper acquisition, mbs have a high affinity for copper ions. Following binding, ...
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Papers by stephane vuilleumier