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1.
Microb Cell Fact ; 20(1): 180, 2021 Sep 09.
Article in English | MEDLINE | ID: mdl-34503517

ABSTRACT

BACKGROUND: 2,5-Furandicarboxylic acid (FDCA) is a precursor for green plastics due to its structural similarity to terephthalic acid, a common precursor of oil-derived polymers, and its potential production from sugars obtained from plant biomass. Hydroxymethylfurfural oxidase (HMFO) has been reported as a promising biocatalyst for FDCA production since it can convert bio-based 5-hydroxymethylfurfural (HMF) into FDCA building block. This three-step oxidation reaction occurs through the diformylfuran and 2,5-formylfurancarboxylic acid (FFCA) intermediates. Several efforts have been made for the development of HMFO variants that increase FDCA yields by improving their activities over the reaction intermediates. However, there is still limited insight into how operational conditions can influence these enzymatic reactions. The setup of optimal reaction conditions would enable to understand potential problems hampering the effective industrial production of this bioplastic precursor using HMFO as biocatalyst. RESULTS: In this work, several parameters affecting the performance of Methylovorus sp HMFO oxidizing HMF have been analyzed for the wild-type enzyme, and its V367R and W466F single variants, V367R/W466F double variant, and I73V/H74Y/G356H/V367R/T414K/A419Y/A435E/W466F (8BxHMFO) octuple variant. Our results show how the oxidation of HMF by HMFO enzymes is highly influenced by pH, with different optimal pH values for the different improved variants. Moreover, the enzymes are not stable at high hydrogen peroxide concentrations and their activity is inhibited by the FFCA intermediate in a pH-dependent way. These limitations can be efficiently overcome with the addition of catalase to the reaction medium, which removes the hydrogen peroxide formed during the oxidations, and the controlled dosage of the substrate to limit the amount of FFCA accumulated in the reaction. The different behavior of wild-type HMFO and its variants against pH, hydrogen peroxide and FFCA highlights the importance of considering each variant as an individual enzyme with its own operational conditions for an eventual industrial FDCA production. CONCLUSIONS: This work provides information of those parameters that condition a high production of FDCA by HMFO. Unraveling these factors allowed to increase the FDCA yields by using the most stable enzymes at their optimal pH for HMF oxidation, removing the peroxide with catalase, and avoiding FFCA accumulation by controlling substrate and/or enzyme concentration. These above findings will be useful when planning a future scale-up of these conversions and will provide new viewpoints for the design of HMFO variants that render a more effective performance during HMF conversion into FDCA.


Subject(s)
Dicarboxylic Acids/metabolism , Furans/metabolism , Methylophilaceae/metabolism , Oxidoreductases/metabolism , Oxidation-Reduction
2.
Appl Environ Microbiol ; 86(16)2020 08 03.
Article in English | MEDLINE | ID: mdl-32503910

ABSTRACT

The enzymatic production of 2,5-furandicarboxylic acid (FDCA) from 5-hydroxymethylfurfural (HMF) has gained interest in recent years, as FDCA is a renewable precursor of poly(ethylene-2,5-furandicarboxylate) (PEF). 5-Hydroxymethylfurfural oxidases (HMFOs) form a flavoenzyme family with genes annotated in a dozen bacterial species but only one enzyme purified and characterized to date (after heterologous expression of a Methylovorus sp. HMFO gene). This oxidase acts on both furfuryl alcohols and aldehydes and, therefore, is able to catalyze the conversion of HMF into FDCA through 2,5-diformylfuran (DFF) and 2,5-formylfurancarboxylic acid (FFCA), with only the need of oxygen as a cosubstrate. To enlarge the repertoire of HMFO enzymes available, genetic databases were screened for putative HMFO genes, followed by heterologous expression in Escherichia coli After unsuccessful trials with other bacterial HMFO genes, HMFOs from two Pseudomonas species were produced as active soluble enzymes, purified, and characterized. The Methylovorus sp. enzyme was also produced and purified in parallel for comparison. Enzyme stability against temperature, pH, and hydrogen peroxide, three key aspects for application, were evaluated (together with optimal conditions for activity), revealing differences between the three HMFOs. Also, the kinetic parameters for HMF, DFF, and FFCA oxidation were determined, the new HMFOs having higher efficiencies for the oxidation of FFCA, which constitutes the bottleneck in the enzymatic route for FDCA production. These results were used to set up the best conditions for FDCA production by each enzyme, attaining a compromise between optimal activity and half-life under different conditions of operation.IMPORTANCE HMFO is the only enzyme described to date that can catalyze by itself the three consecutive oxidation steps to produce FDCA from HMF. Unfortunately, only one HMFO enzyme is currently available for biotechnological application. This availability is enlarged here by the identification, heterologous production, purification, and characterization of two new HMFOs, one from Pseudomonas nitroreducens and one from an unidentified Pseudomonas species. Compared to the previously known Methylovorus HMFO, the new enzyme from P. nitroreducens exhibits better performance for FDCA production in wider pH and temperature ranges, with higher tolerance for the hydrogen peroxide formed, longer half-life during oxidation, and higher yield and total turnover numbers in long-term conversions under optimized conditions. All these features are relevant properties for the industrial production of FDCA. In summary, gene screening and heterologous expression can facilitate the selection and improvement of HMFO enzymes as biocatalysts for the enzymatic synthesis of renewable building blocks in the production of bioplastics.


Subject(s)
Bacterial Proteins/metabolism , Dicarboxylic Acids/metabolism , Furaldehyde/analogs & derivatives , Furans/metabolism , Methylophilaceae/genetics , Oxidoreductases/metabolism , Pseudomonas/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Furaldehyde/metabolism , Methylophilaceae/metabolism , Microorganisms, Genetically-Modified/genetics , Microorganisms, Genetically-Modified/metabolism , Pseudomonas/metabolism
3.
Environ Microbiol ; 21(10): 3780-3795, 2019 10.
Article in English | MEDLINE | ID: mdl-31267680

ABSTRACT

The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment-water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13 C-methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalysing the first reaction step to methanol. We observed a transfer of carbon to methanol-oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment per day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment-water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane-oxidizing community supported a complex trophic network. Our results provide valuable eco-physiological insights into this specialized microbial community performing an ecosystem function of global relevance.


Subject(s)
Geologic Sediments/microbiology , Methane/metabolism , Methylococcaceae/metabolism , Methylophilaceae/metabolism , Italy , Metagenomics , Microbiota/physiology , Oxidation-Reduction , Phylogeny
4.
Curr Issues Mol Biol ; 33: 149-172, 2019.
Article in English | MEDLINE | ID: mdl-31166190

ABSTRACT

Chloromethane is a halogenated volatile organic compound, produced in large quantities by terrestrial vegetation. After its release to the troposphere and transport to the stratosphere, its photolysis contributes to the degradation of stratospheric ozone. A better knowledge of chloromethane sources (production) and sinks (degradation) is a prerequisite to estimate its atmospheric budget in the context of global warming. The degradation of chloromethane by methylotrophic communities in terrestrial environments is a major underestimated chloromethane sink. Methylotrophs isolated from soils, marine environments and more recently from the phyllosphere have been grown under laboratory conditions using chloromethane as the sole carbon source. In addition to anaerobes that degrade chloromethane, the majority of cultivated strains were isolated in aerobiosis for their ability to use chloromethane as sole carbon and energy source. Among those, the Proteobacterium Methylobacterium (recently reclassified as Methylorubrum) harbours the only characterisized 'chloromethane utilization' (cmu) pathway, so far. This pathway is not representative of chloromethane-utilizing populations in the environment as cmu genes are rare in metagenomes. Recently, combined 'omics' biological approaches with chloromethane carbon and hydrogen stable isotope fractionation measurements in microcosms, indicated that microorganisms in soils and the phyllosphere (plant aerial parts) represent major sinks of chloromethane in contrast to more recently recognized microbe-inhabited environments, such as clouds. Cultivated chloromethane-degraders lacking the cmu genes display a singular isotope fractionation signature of chloromethane. Moreover, 13CH3Cl labelling of active methylotrophic communities by stable isotope probing in soils identify taxa that differ from the taxa known for chloromethane degradation. These observations suggest that new biomarkers for detecting active microbial chloromethane-utilizers in the environment are needed to assess the contribution of microorganisms to the global chloromethane cycle.


Subject(s)
Energy Metabolism/physiology , Methanol/metabolism , Methyl Chloride/metabolism , Proteobacteria/classification , Proteobacteria/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Biodegradation, Environmental , Geologic Sediments/microbiology , Metabolic Networks and Pathways/genetics , Methylobacterium/classification , Methylobacterium/metabolism , Methylophilaceae/classification , Methylophilaceae/metabolism , Methyltransferases/genetics , Methyltransferases/metabolism , Soil Microbiology
5.
Biosystems ; 172: 37-42, 2018 Oct.
Article in English | MEDLINE | ID: mdl-30125625

ABSTRACT

Methylovorus sp. MP688 is a methylotrophic bacterium that can be used as a pyrroloquinolone quinone (PQQ) producer. To obtain a comprehensive understanding of its metabolic capabilities, we constructed a genome-scale metabolic model (iWZ583) of Methylovorus sp. MP688, based on its genome annotations, data from public metabolic databases, and literature mining. The model includes 772 reactions, 764 metabolites, and 583 genes. Growth of Methylovorus sp. MP688 was simulated using different carbon and nitrogen sources, and the results were consistent with experimental data. A core metabolic essential gene set of 218 genes was predicted by gene essentiality analysis on minimal medium containing methanol. Based on in silico predictions, the addition of aspartate to the medium increased PQQ production by 4.6- fold. Deletion of three reactions associated with four genes (MPQ_1150, MPQ_1560, MPQ_1561, MPQ_1562) was predicted to yield a PQQ production rate of 0.123 mmol/gDW/h, while cell growth decreased by 2.5%. Here, model iWZ583 represents a useful platform for understanding the phenotype of Methylovorus sp. MP688 and improving PQQ production.


Subject(s)
Bacterial Proteins/genetics , Computational Biology/methods , Metabolic Networks and Pathways , Metabolome , Methylophilaceae/genetics , Methylophilaceae/metabolism , PQQ Cofactor/metabolism , Computer Simulation , Genome, Bacterial , Methylophilaceae/growth & development , Models, Biological
6.
Environ Microbiol ; 20(3): 1204-1223, 2018 03.
Article in English | MEDLINE | ID: mdl-29411502

ABSTRACT

Recently, it has been found that two types of methanol dehydrogenases (MDHs) exist in Gram-negative bacterial methylotrophs, calcium-dependent MxaFI-MDH and lanthanide-dependent XoxF-MDH and the latter is more widespread in bacterial genomes. We aimed to isolate and characterize lanthanide-dependent methylotrophs. The growth of strain La2-4T on methanol, which was isolated from rice rhizosphere soil, was strictly lanthanide dependent. Its 16S rRNA gene sequence showed only 93.4% identity to that of Methylophilus luteus MimT , and the name Novimethylophilus kurashikiensis gen. nov. sp. nov. is proposed. Its draft genome (ca. 3.69 Mbp, G + C content 56.1 mol%) encodes 3579 putative CDSs and 84 tRNAs. The genome harbors five xoxFs but no mxaFI. XoxF4 was the major MDH in the cells grown on methanol and methylamine, evidenced by protein identification and quantitative PCR analysis. Methylamine dehydrogenase gene was absent in the La2-4T genome, while genes for the glutamate-mediated methylamine utilization pathway were detected. The genome also harbors those for the tetrahydromethanopterin and ribulose monophosphate pathways. Additionally, as known species, isolates of Burkholderia ambifaria, Cupriavidus necator and Dyadobacter endophyticus exhibited lanthanide dependent growth on methanol. Thus, lanthanide can be used as an essential growth factor for methylotrophic bacteria that do not harbor MxaFI-MDH.


Subject(s)
Alcohol Oxidoreductases/genetics , DNA, Bacterial/genetics , Lanthanoid Series Elements/metabolism , Methanol/metabolism , Methylophilaceae , Bacterial Typing Techniques , Base Composition/genetics , Fatty Acids/analysis , Genome, Bacterial/genetics , Genomics , Methylamines/metabolism , Methylophilaceae/classification , Methylophilaceae/genetics , Methylophilaceae/isolation & purification , Methylophilaceae/metabolism , Oxidoreductases Acting on CH-NH Group Donors/genetics , Phylogeny , RNA, Ribosomal, 16S/genetics , Rhizosphere , Sequence Analysis, DNA
7.
ISME J ; 12(1): 87-100, 2018 01.
Article in English | MEDLINE | ID: mdl-28949325

ABSTRACT

Massive biofilms have been discovered in the cave of an iodine-rich former medicinal spring in southern Germany. The biofilms completely cover the walls and ceilings of the cave, giving rise to speculations about their metabolism. Here we report on first insights into the structure and function of the biofilm microbiota, combining geochemical, imaging and molecular analytics. Stable isotope analysis indicated that thermogenic methane emerging into the cave served as an important driver of biofilm formation. The undisturbed cavern atmosphere contained up to 3000 p.p.m. methane and was microoxic. A high abundance and diversity of aerobic methanotrophs primarily within the Methylococcales (Gammaproteobacteria) and methylotrophic Methylophilaceae (Betaproteobacteria) were found in the biofilms, along with a surprising diversity of associated heterotrophic bacteria. The highest methane oxidation potentials were measured for submerged biofilms on the cavern wall. Highly organized globular structures of the biofilm matrix were revealed by fluorescent lectin staining. We propose that the extracellular matrix served not only as an electron sink for nutrient-limited biofilm methylotrophs but potentially also as a diffusive barrier against volatilized iodine species. Possible links between carbon and iodine cycling in this peculiar habitat are discussed.


Subject(s)
Caves/microbiology , Gammaproteobacteria/metabolism , Methane/metabolism , Methylophilaceae/metabolism , Biofilms , Carbon/metabolism , Caves/chemistry , Gammaproteobacteria/classification , Gammaproteobacteria/genetics , Gammaproteobacteria/isolation & purification , Germany , Methylophilaceae/classification , Methylophilaceae/genetics , Methylophilaceae/isolation & purification , Microbiota , Minerals/analysis , Minerals/metabolism , Oxidation-Reduction , Phylogeny
8.
ISME J ; 11(10): 2379-2390, 2017 10.
Article in English | MEDLINE | ID: mdl-28763056

ABSTRACT

Dimethylsulfide (DMS) is an environmentally important trace gas with roles in sulfur cycling, signalling to higher organisms and in atmospheric chemistry. DMS is believed to be predominantly produced in marine environments via microbial degradation of the osmolyte dimethylsulfoniopropionate (DMSP). However, significant amounts of DMS are also generated from terrestrial environments, for example, peat bogs can emit ~6 µmol DMS m-2 per day, likely via the methylation of methanethiol (MeSH). A methyltransferase enzyme termed 'MddA', which catalyses the methylation of MeSH, generating DMS, in a wide range of bacteria and some cyanobacteria, may mediate this process, as the mddA gene is abundant in terrestrial metagenomes. This is the first study investigating the functionality of MeSH-dependent DMS production (Mdd) in a wide range of aerobic environments. All soils and marine sediment samples tested produced DMS when incubated with MeSH. Cultivation-dependent and cultivation-independent methods were used to assess microbial community changes in response to MeSH addition in a grassland soil where 35.9% of the bacteria were predicted to contain mddA. Bacteria of the genus Methylotenera were enriched in the presence of MeSH. Furthermore, many novel Mdd+ bacterial strains were isolated. Despite the abundance of mddA in the grassland soil, the Mdd pathway may not be a significant source of DMS in this environment as MeSH addition was required to detect DMS at only very low conversion rates.


Subject(s)
Bacteria/metabolism , Soil Microbiology , Sulfhydryl Compounds/metabolism , Sulfides/metabolism , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Geologic Sediments/microbiology , Metagenome , Methylophilaceae/metabolism , Soil/chemistry , Sulfhydryl Compounds/analysis , Sulfonium Compounds/metabolism , Sulfur/metabolism
9.
Mikrobiologiia ; 85(5): 506-511, 2016 Sep.
Article in English | MEDLINE | ID: mdl-29364598

ABSTRACT

Phylogeneticanalysis based,on comparison of the 16S rRNA gene sequences in combination with comparative analysis of physiological, biochemical, and chemotaxonomic characteristics and DNA-DNA hybridization revealed that "Methylobacillusfructoseoxidans" 34 (VKM B-1609 = DSM 5897 and-Methylov- orus glucosotrophus 6B 1T (ATCC 49758T = DSM 6874T = VKM B- 1745T = NCIMB 13222 ) belong to the same Methylovorus species. Extended description of the limited facultative methylotroph Methylovorus gluco- sotrophus is proposed, which includes the fructose-utilizing strain 34. Emended description of Methylovorus glucosotrophus is provided.


Subject(s)
DNA, Bacterial/genetics , Fructose/metabolism , Methanol/metabolism , Methylophilaceae/classification , Phylogeny , RNA, Ribosomal, 16S/genetics , Bacterial Typing Techniques , Culture Media/chemistry , Culture Media/pharmacology , Fatty Acids/chemistry , Fatty Acids/isolation & purification , Fructose/pharmacology , Metabolic Networks and Pathways/genetics , Methanol/pharmacology , Methylophilaceae/drug effects , Methylophilaceae/genetics , Methylophilaceae/metabolism , Phospholipids/chemistry , Phospholipids/isolation & purification , Russia , Sequence Analysis, DNA
10.
ISME J ; 9(1): 195-206, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25050523

ABSTRACT

Movile Cave, Romania, is an unusual underground ecosystem that has been sealed off from the outside world for several million years and is sustained by non-phototrophic carbon fixation. Methane and sulfur-oxidising bacteria are the main primary producers, supporting a complex food web that includes bacteria, fungi and cave-adapted invertebrates. A range of methylotrophic bacteria in Movile Cave grow on one-carbon compounds including methylated amines, which are produced via decomposition of organic-rich microbial mats. The role of methylated amines as a carbon and nitrogen source for bacteria in Movile Cave was investigated using a combination of cultivation studies and DNA stable isotope probing (DNA-SIP) using (13)C-monomethylamine (MMA). Two newly developed primer sets targeting the gene for gamma-glutamylmethylamide synthetase (gmaS), the first enzyme of the recently-discovered indirect MMA-oxidation pathway, were applied in functional gene probing. SIP experiments revealed that the obligate methylotroph Methylotenera mobilis is one of the dominant MMA utilisers in the cave. DNA-SIP experiments also showed that a new facultative methylotroph isolated in this study, Catellibacterium sp. LW-1 is probably one of the most active MMA utilisers in Movile Cave. Methylated amines were also used as a nitrogen source by a wide range of non-methylotrophic bacteria in Movile Cave. PCR-based screening of bacterial isolates suggested that the indirect MMA-oxidation pathway involving GMA and N-methylglutamate is widespread among both methylotrophic and non-methylotrophic MMA utilisers from the cave.


Subject(s)
Carbon-Nitrogen Ligases/metabolism , Glutamates/metabolism , Methylamines/metabolism , Methylophilaceae/metabolism , Animals , Bacteria/classification , Bacteria/genetics , Bacteria/metabolism , Carbon-Nitrogen Ligases/genetics , Caves , Ecosystem , Glutamates/genetics , Methylophilaceae/classification , Methylophilaceae/genetics , Phylogeny , Polymerase Chain Reaction , RNA, Ribosomal, 16S/analysis , RNA, Ribosomal, 16S/genetics , Romania
11.
J Basic Microbiol ; 55(3): 312-23, 2015 Mar.
Article in English | MEDLINE | ID: mdl-23828377

ABSTRACT

Pyrroloquinoline quinone is the third redox cofactor after nicotinamide and flavin in bacteria, and its biosynthesis pathway comprise five steps initiated from a precursor peptide PqqA coded by pqqA gene. Methylovorus sp. MP688 is equipped with five copies of pqqA genes. Herein, the transcription of pqqA genes under different conditions by real-time quantitative PCR and ß-galactosidase reporter genes are reported. Multiple pqqA genes were proved to play significant roles and contribute differently in PQQ synthesis. pqqA1, pqqA2, and pqqA4 were determined to be dominantly transcribed over the others, and correspondingly absence of any of the three genes caused a decrease in PQQ synthesis. Notably, pqqA was up-regulated in low pH and limited oxygen environment, and it is pqqA2 promoter that could be induced when bacteria were transferred from pH 7.0 to pH 5.5. Deletion analysis revealed a region within pqqA2 promoter inhibiting transcription. PQQ concentration was increased by overexpression of pqq genes under control of truncated pqqA2 promoter. The results not only imply there exist negative transcriptional regulators for pqqA2 but also provide us a new approach to achieve higher PQQ production by deleting the target binding sequence.


Subject(s)
Gene Expression Regulation, Bacterial , Genes, Bacterial , Methylophilaceae/genetics , PQQ Cofactor/biosynthesis , PQQ Cofactor/genetics , Bacterial Proteins/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Deletion , Hydrogen-Ion Concentration , Methylophilaceae/metabolism , Multigene Family , Mutation , Promoter Regions, Genetic , Real-Time Polymerase Chain Reaction , Sequence Analysis, DNA
12.
PLoS One ; 9(7): e102458, 2014.
Article in English | MEDLINE | ID: mdl-25058595

ABSTRACT

We describe five novel Methylophilaceae ecotypes from a single ecological niche in Lake Washington, USA, and compare them to three previously described ecotypes, in terms of their phenotype and genome sequence divergence. Two of the ecotypes appear to represent novel genera within the Methylophilaceae. Genome-based metabolic reconstruction highlights metabolic versatility of Methylophilaceae with respect to methylotrophy and nitrogen metabolism, different ecotypes possessing different combinations of primary substrate oxidation systems (MxaFI-type methanol dehydrogenase versus XoxF-type methanol dehydrogenase; methylamine dehydrogenase versus N-methylglutamate pathway) and different potentials for denitrification (assimilatory versus respiratory nitrate reduction). By comparing pairs of closely related genomes, we uncover that site-specific recombination is the main means of genomic evolution and strain divergence, including lateral transfers of genes from both closely- and distantly related taxa. The new ecotypes and the new genomes contribute significantly to our understanding of the extent of genomic and metabolic diversity among organisms of the same family inhabiting the same ecological niche. These organisms also provide novel experimental models for studying the complexity and the function of the microbial communities active in methylotrophy.


Subject(s)
Bacterial Proteins/metabolism , Genome, Bacterial , Lakes/microbiology , Methylophilaceae/metabolism , Nitrogen/metabolism , Phylogeny , Alcohol Oxidoreductases/genetics , Alcohol Oxidoreductases/metabolism , Bacterial Proteins/genetics , Denitrification/genetics , Ecotype , Genetic Variation , Glutamates/metabolism , Methylophilaceae/classification , Methylophilaceae/genetics , Oxidoreductases Acting on CH-NH Group Donors/genetics , Oxidoreductases Acting on CH-NH Group Donors/metabolism , Recombination, Genetic , Washington
13.
Prikl Biokhim Mikrobiol ; 49(2): 203-8, 2013.
Article in Russian | MEDLINE | ID: mdl-23795481

ABSTRACT

Cells of dichloromethane (DChM) bacteria-destructors were immobilized by sorption on different types of membranes, which were fixed on the measuring surface of a pH-sensitive field transistor. The presence of DChM in the medium (0.6-8.8 mM) led to a change in the transistor's output signal, which was determined by the appearance of H+ ions in the medium due to DChM utilization by methylobateria. Among four strains of methylobacteria--Methylobacterium dichloromethanicum DM4, Methylobacterium extorquens DM 17, Methylopila helvetica DM6, and Ancylobacter dichloromethanicus DM 16--the highest and most stable activity toward DChM degradation was observed in the strain M. dichloromethanicum DM4. Among 11 types of membranes for cell immobilization, Millipore nitrocellulose membranes and chromatographic fiber paper GF/A, which allow one to obtain stable biosensor signals for 2 weeks without a bioreceptor change, were chosen as optimal carriers.


Subject(s)
Biosensing Techniques , Cells, Immobilized/chemistry , Methylene Chloride/analysis , Methylobacterium/chemistry , Protons , Adsorption , Cells, Immobilized/metabolism , Electrochemical Techniques , Membranes, Artificial , Methylobacterium/metabolism , Methylobacterium extorquens/chemistry , Methylobacterium extorquens/metabolism , Methylophilaceae/chemistry , Methylophilaceae/metabolism
14.
J Bacteriol ; 195(10): 2207-11, 2013 May.
Article in English | MEDLINE | ID: mdl-23475964

ABSTRACT

We investigated phenotypes of mutants of Methylotenera mobilis JLW8 with lesions in genes predicted to encode functions of the denitrification pathway, as well as mutants with mutations in methanol dehydrogenase-like structural genes xoxF1 and xoxF2, in order to obtain insights into denitrification and methanol metabolism by this bacterium. By monitoring the accumulation of nitrous oxide, we demonstrate that a periplasmic nitrate reductase, NAD(P)-linked and copper-containing nitrite reductases, and a nitric oxide reductase are involved in the denitrification pathway and that the pathway must be operational in aerobic conditions. However, only the assimilatory branch of the denitrification pathway was essential for growth on methanol in nitrate-supplemented medium. Mutants with mutations in each of the two xoxF genes maintained their ability to grow on methanol, but not the double XoxF mutant, suggesting that XoxF proteins act as methanol dehydrogenase enzymes in M. mobilis JLW8. Reduced levels of nitrous oxide accumulated by the XoxF mutants compared to the wild type suggest that these enzymes must be capable of donating electrons for denitrification.


Subject(s)
Denitrification/physiology , Methanol/metabolism , Methylophilaceae/metabolism , Alcohol Oxidoreductases/genetics , Alcohol Oxidoreductases/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Mutation
16.
J Bacteriol ; 193(18): 4758-65, 2011 Sep.
Article in English | MEDLINE | ID: mdl-21764938

ABSTRACT

Methylotenera species, unlike their close relatives in the genera Methylophilus, Methylobacillus, and Methylovorus, neither exhibit the activity of methanol dehydrogenase nor possess mxaFI genes encoding this enzyme, yet they are able to grow on methanol. In this work, we integrated a genome-wide proteomics approach, shotgun proteomics, and a genome-wide transcriptomics approach, shotgun transcriptome sequencing (RNA-seq), of Methylotenera mobilis JLW8 to identify genes and enzymes potentially involved in methanol oxidation, with special attention to alternative nitrogen sources, to address the question of whether nitrate could play a role as an electron acceptor in place of oxygen. Both proteomics and transcriptomics identified a limited number of genes and enzymes specifically responding to methanol. This set includes genes involved in oxidative stress response systems, a number of oxidoreductases, including XoxF-type alcohol dehydrogenases, a type II secretion system, and proteins without a predicted function. Nitrate stimulated expression of some genes in assimilatory nitrate reduction and denitrification pathways, while ammonium downregulated some of the nitrogen metabolism genes. However, none of these genes appeared to respond to methanol, which suggests that oxygen may be the main electron sink during growth on methanol. This study identifies initial targets for future focused physiological studies, including mutant analysis, which will provide further details into this novel process.


Subject(s)
Electrons , Gene Expression Profiling , Metabolic Networks and Pathways/genetics , Methanol/metabolism , Methylophilaceae/metabolism , Oxygen/metabolism , Proteome/analysis , Methylophilaceae/chemistry , Methylophilaceae/genetics , Methylophilaceae/growth & development , Nitrates/metabolism , Oxidation-Reduction
17.
J Bacteriol ; 193(15): 3757-64, 2011 Aug.
Article in English | MEDLINE | ID: mdl-21622745

ABSTRACT

The genomes of three representatives of the family Methylophilaceae, Methylotenera mobilis JLW8, Methylotenera versatilis 301, and Methylovorus glucosetrophus SIP3-4, all isolated from a single study site, Lake Washington in Seattle, WA, were completely sequenced. These were compared to each other and to the previously published genomes of Methylobacillus flagellatus KT and an unclassified Methylophilales strain, HTCC2181. Comparative analysis revealed that the core genome of Methylophilaceae may be as small as approximately 600 genes, while the pangenome may be as large as approximately 6,000 genes. Significant divergence between the genomes in terms of both gene content and gene and protein conservation was uncovered, including the varied presence of certain genes involved in methylotrophy. Overall, our data demonstrate that metabolic potentials can vary significantly between different species of Methylophilaceae, including organisms inhabiting the very same environment. These data suggest that genetic divergence among the members of this family may be responsible for their specialized and nonredundant functions in C1 cycling, which in turn suggests means for their successful coexistence in their specific ecological niches.


Subject(s)
Evolution, Molecular , Genome, Bacterial , Methylophilaceae/genetics , Methylophilaceae/metabolism , Fresh Water/microbiology , Methanol/metabolism , Methylophilaceae/classification , Methylophilaceae/isolation & purification , Molecular Sequence Data
18.
J Bacteriol ; 193(4): 1012-3, 2011 Feb.
Article in English | MEDLINE | ID: mdl-21148725

ABSTRACT

Methylotrophic bacteria are widespread microbes which can use one carbon compound as their only carbon and energy sources. Here we report the finished, annotated genome sequence of the methylotrophic bacterium Methylovorus sp. strain MP688, which was isolated from soil for high-level production of pyrroloquinolone quinone (PQQ) in our lab.


Subject(s)
Genome, Bacterial , Methylophilaceae/genetics , Methylophilaceae/metabolism , PQQ Cofactor/metabolism , Methylophilaceae/isolation & purification , Molecular Sequence Data , Soil Microbiology
19.
Int J Mol Sci ; 12(12): 8913-23, 2011.
Article in English | MEDLINE | ID: mdl-22272111

ABSTRACT

Pyrroloquinoline quinone (PQQ) was produced by fermentation of the Methylovorus sp. MP688 strain and purified by ion-exchange chromatography, crystallization and recrystallization. The yield of PQQ reached approximately 125 mg/L and highly pure PQQ was obtained. To determine the optimum dose of PQQ for radioprotection, three doses (2 mg/kg, 4 mg/kg, 8 mg/kg) of PQQ were orally administrated to the experimental animals subjected to a lethal dose of 8.0 Gy in survival test. Survival of mice in the irradiation + PQQ (4 mg/kg) group was found to be significantly higher in comparison with the irradiation and irradiation + nilestriol (10 mg/kg) groups. The numbers of hematocytes and bone marrow cells were measured for 21 days after sublethal 4 Gy gamma-ray irradiation with per os of 4 mg/kg of PQQ. The recovery of white blood cells, reticulocytes and bone marrow cells in the irradiation + PQQ group was faster than that in the irradiation group. Furthermore, the recovery of bone marrow cell in the irradiation + PQQ group was superior to that in irradiation + nilestriol group. Our results clearly indicate favourable effects on survival under higher lethal radiation doses and the ability of pyrroloquinoline quinine to enhance haemopoietic recovery after sublethal radiation exposure.


Subject(s)
Bone Marrow Cells/drug effects , Gamma Rays , Leukocytes/drug effects , PQQ Cofactor/pharmacology , Radiation-Protective Agents/pharmacology , Acute Radiation Syndrome/drug therapy , Administration, Oral , Animals , Bone Marrow Cells/radiation effects , Drug Therapy, Combination , Estriol/administration & dosage , Estriol/analogs & derivatives , Estriol/pharmacology , Estriol/therapeutic use , Fermentation , Leukocytes/radiation effects , Methylophilaceae/chemistry , Methylophilaceae/metabolism , Mice , PQQ Cofactor/administration & dosage , PQQ Cofactor/therapeutic use , Quinestrol/analogs & derivatives , Radiation-Protective Agents/administration & dosage , Radiation-Protective Agents/therapeutic use
20.
Aviakosm Ekolog Med ; 44(1): 54-8, 2010.
Article in Russian | MEDLINE | ID: mdl-20804000

ABSTRACT

Stability of Chinese cabbage crop colonization by methanolic bacteria Methylovorus mays, Methylomonas methanica and Methylosinus trichosporium inoculated using a space-applicable method was evaluated. Besides, trends of methane and methanol concentrations in the pressurized chamber with inoculated and uninoculated crops were calculated. Methylovorus mays and Methylosinus trichosporium were shown to establish more stable colonization as compared to Methylomonas methanica. Also, stable association of methanolic bacteria with plants reduced airborne methanol 75% faster owing to its uptake by bacteria. Therefore, inoculation of these microorganisms can be viewed as a promising method of controlling volatile pollutants in space vehicle atmosphere. Methane drop after 6-hour exposure to inoculated control and test crops was not significant.


Subject(s)
Air Pollutants, Occupational/analysis , Air/analysis , Brassica/microbiology , Methane/analysis , Methanol/analysis , Methylomonas/metabolism , Methylophilaceae/metabolism , Methylosinus/metabolism , Spacecraft , Symbiosis , Air Pollutants, Occupational/metabolism , Brassica/physiology , Methane/metabolism , Methanol/metabolism
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