Characterization of a Copper-Chelating Natural Product from the Methanotroph Methylosinus sp. LW3.

Methanobactins (Mbns) are ribosomally produced, post-translationally modified peptidic natural products that bind copper with high affinity. Methanotrophic bacteria use Mbns to acquire copper needed for enzymatic methane oxidation. Despite the presence of Mbn operons in a range of methanotroph and other bacterial genomes, few Mbns have been isolated and structurally characterized. Here we report the isolation of a novel Mbn from the methanotroph Methylosinus (Ms.) sp. LW3. Mass spectrometric and nuclear magnetic resonance spectroscopic data indicate that this Mbn, the largest characterized to date, consists of a 13-amino acid backbone modified to include pyrazinedione/oxazolone rings and neighboring thioamide groups derived from cysteine residues. The pyrazinedione ring is more stable to acid hydrolysis than the oxazolone ring and likely protects the Mbn from degradation. The structure corresponds exactly to that predicted on the basis of the Ms. sp. LW3 Mbn operon content, providing support for the proposed role of an uncharacterized biosynthetic enzyme, MbnF, and expanding the diversity of known Mbns.

Repurposed HisC Aminotransferases Complete the Biosynthesis of Some Methanobactins.

Methanobactins (Mbns) are ribosomally produced, post-translationally modified bacterial natural products with a high affinity for copper. MbnN, a pyridoxal 5'-phosphate-dependent aminotransferase, performs a transamination reaction that is the last step in the biosynthesis of Mbns produced by several Methylosinus species. Our bioinformatic analyses indicate that MbnNs likely derive from histidinol-phosphate aminotransferases (HisCs), which play a key role in histidine biosynthesis. A comparison of the HisC active site with the predicted MbnN structure suggests that MbnN's active site is altered to accommodate the larger and more hydrophobic substrates necessary for Mbn biosynthesis. Moreover, we have confirmed that MbnN is capable of catalyzing the final transamination step in Mbn biosynthesis in vitro and in vivo. We also demonstrate that without this final modification, Mbn exhibits significantly decreased stability under physiological conditions. An examination of other Mbns and Mbn operons suggests that N-terminal protection of this family of natural products is of critical importance and that several different means of N-terminal stabilization have evolved independently in Mbn subfamilies.

Biochemical Properties and Phylogeny of Hydroxypyruvate Reductases from Methanotrophic Bacteria with Different C1-Assimilation Pathways.

In the aerobic methanotrophic bacteria Methylomicrobium alcaliphilum 20Z, Methylococcus capsulatus Bath, and Methylosinus trichosporium OB3b, the biochemical properties of hydroxypyruvate reductase (Hpr), an indicator enzyme of the serine pathway for assimilation of reduced C1-compounds, were comparatively analyzed. The recombinant Hpr obtained by cloning and heterologous expression of the hpr gene in Escherichia coli catalyzed NAD(P)H-dependent reduction of hydroxypyruvate or glyoxylate, but did not catalyze the reverse reactions of D-glycerate or glycolate oxidation. The absence of the glycerate dehydrogenase activity in the methanotrophic Hpr confirmed a key role of the enzyme in utilization of C1-compounds via the serine cycle. The enzyme from Ms. trichosporium OB3b realizing the serine cycle as a sole assimilation pathway had much higher special activity and affinity in comparison to Hpr from Mm. alcaliphilum 20Z and Mc. capsulatus Bath assimilating carbon predominantly via the ribulose monophosphate (RuMP) cycle. The hpr gene was found as part of gene clusters coding the serine cycle enzymes in all sequenced methanotrophic genomes except the representatives of the Verrucomicrobia phylum. Phylogenetic analyses revealed two types of Hpr: (i) Hpr of methanotrophs belonging to the Gammaproteobacteria class, which use the serine cycle along with the RuMP cycle, as well as of non-methylotrophic bacteria belonging to the Alphaproteobacteria class; (ii) Hpr of methylotrophs from Alpha- and Betaproteobacteria classes that use only the serine cycle and of non-methylotrophic representatives of Betaproteobacteria. The putative role and origin of hydroxypyruvate reductase in methanotrophs are discussed.

Characterization of Methanobactin from Methylosinus sp. LW4.

Methanobactins (Mbns) are a growing family of ribosomally produced, post-translationally modified natural products. Characteristic nitrogen-containing heterocycles and neighboring thioamides allow these compounds to bind copper with high affinity. Genome mining has enabled the identification of Mbn operons in bacterial genomes and the prediction of diverse Mbn structures from operon content and precursor peptide sequence. Here we report the characterization of Mbn from Methylosinus (Ms.) species (sp.) LW4. The peptide backbone is distinct from all previously characterized Mbns, and the post-translational modifications correspond precisely to those predicted on the basis of the Ms. sp. LW4 Mbn operon. Thus, prediction based on genome analysis combined with isolation and structural characterization represents a phylogenetic approach to finding diverse Mbns and elucidating their biosynthetic pathways.

Comparative enzyme inhibitive methanol production by Methylosinus sporium from simulated biogas.

Methane in a simulated biogas converting to methanol under aerobic condition was comparatively assessed by inhibiting the activity of methanol dehydrogenase (MDH) of Methylosinus sporium using phosphate, NaCl, NH4Cl or EDTA in their varying concentrations. The highest amount of methane was indistinguishably diverted at the typical conditions regardless of the types of inhibitors: 35°C and pH 7 under a 0.4% (v/v) of biogas, specifically for <40 mM phosphate, 50 mM NaCl, 40 mM NH4Cl or 150 µM EDTA. The highest level of methanol was obtained for the addition of 40 mM phosphate, 100 mM NaCl, 40 mM NH4Cl or 50 µM EDTA. In other words, 0.71, 0.60, 0.66 and 0.66 mmol methanol was correspondingly generated by the oxidation of 1.3, 0.67, 0.74 and 1.3 mmol methane. It gave a methanol conversion rate of 54.7%, 89.9%, 89.6% and 47.8%, respectively. Among them, the maximum rate of methanol production was observed at 6.25 µmol/mg h for 100 mM NaCl. Regardless of types or concentrations of inhibitors differently used, methanol production could be nonetheless identically maximized when the MDH activity was limitedly hampered by up to 35%.

Stress resistance and C1 metabolism involved in plant colonization of a methanotroph Methylosinus sp. B4S.

Methanotrophs are widespread and have been isolated from various environments including the phyllosphere. In this study, we characterized the plant colonization by Methylosinus sp. B4S, an α-proteobacterial methanotroph isolated from plant leaf. The gfp-tagged Methylosinus sp. B4S cells were observed to colonize Arabidopsis leaf surfaces by forming aggregates. We cloned and sequenced the general stress response genes, phyR, nepR and ecfG, from Methylosinus sp. B4S. In vitro analysis showed that the phyR expression level was increased after heat shock challenge, and phyR was shown to be involved in resistance to heat shock and UV light. In the phyllospheric condition, the gene expression level of phyR as well as mmoX and mxaF was found to be relatively high, compared with methane-grown liquid cultures. The phyR-deletion strain as well as the wild-type strain inoculated on Arabidopsis leaves proliferated at the initial phase and then gradually decreased during plant colonization. These results have shed light firstly on the importance of general stress resistance and C1 metabolism in methanotroph living in the phyllosphere.

Role of tyrosine residue in methane activation at the dicopper site of particulate methane monooxygenase: a density functional theory study.

Methane hydroxylation at the dinuclear copper site of particulate methane monooxygenase (pMMO) is studied by using density functional theory calculations. The electronic, structural, and reactivity properties of a possible dinuclear copper species (µ-oxo)(µ-hydroxo)Cu(II)Cu(III) are discussed with respect to the C-H bond activation of methane. We propose that the tyrosine residue in the second coordination sphere of the dicopper site donates an H atom to the µ-η(2):η(2)-peroxoCu(II)Cu(II) species and the resultant (µ-oxo)(µ-hydroxo)Cu(II)Cu(III) species can hydroxylate methane. This species for methane hydroxylation is more favorable in reactivity than the bis(µ-oxo)Cu(III)Cu(III) species. The H-atom transfer or proton-coupled electron transfer from the tyrosine residue can reasonably induce the O-O bond dissociation of the µ-η(2):η(2)-peroxoCu(II)Cu(II) species to form the reactive (µ-oxo)(µ-hydroxo)Cu(II)Cu(III) species, which is expected to be an active species for the conversion of methane to methanol at the dicopper site of pMMO. The rate-determining step for the methane hydroxylation is the C-H cleavage, which is in good agreement with experimental KIE values reported so far.

A turn-on fluorescent nano-probe base on methanobactin-AuNPs for simple and efficient detection of nitrite.

Nitrite ions are important markers threatening humans and environmental security. A highly selective method for rapid detection of nitrite needs to be developed. Herein, a novel and rapid fluorescence method for nitrite determination is established on the basis of diazotization-coupling reaction of methanobactin (Mb) extracted by Methylosinus trichosporium OB3b with nitrite on the fluorescence. In the presence of gold nanoparticles (AuNPs), the fluorescence of AuNPs was strongly quenched by the Mb because the sulfhydryl or amino structures on the surface of Mb could be bound to the surface of AuNPs by forming Au-S or Au-N bonds. Upon addition of nitrite, the Mb easily reacts with nitrite to form azo products in the acidic medium. Then, with the increase of nitrite concentration, the Mb-AuNPs fluorescence was gradually recovered, realizing the turn-on fluorescence sensing of nitrite. Under optimal conditions, the proposed method has a good linear relationship with nitrite concentration in the range of 0-8.0 µM and 8.0-50.0 µM, and the detection limit is 16.21 nM. In addition, satisfactory results were obtained for nitrite analysis using milk, ham sausage and leaf mustard as real samples, which demonstrated that the method as-developed would have great practical application prospects.

Distribution of methanotrophs in the phyllosphere.

Plants have been reported to emit methane as well as methanol originating in their cell-wall constituents. We investigated methanotrophs in the phyllosphere by the enrichment culture method with methane as sole carbon source. We enriched methanotrophs from the leaves, flowers, bark, and roots of various plants. Analysis of the pmoA and mxaF genes retrieved from the enrichment cultures revealed that methanotrophs closely related to the genera Methylomonas, Methylosinus, and Methylocystis inhabit not only the rhizosphere but also the phyllosphere, together with methanol-utilizing bacteria.

Elucidation of the electron transfer environment in the MMOR FAD-binding domain from Methylosinus sporium 5.

By facilitating electron transfer to the hydroxylase diiron center, MMOR-a reductase-serves as an essential component of the catalytic cycle of soluble methane monooxygenase. Here, the X-ray structure analysis of the FAD-binding domain of MMOR identified crucial residues and its influence on the catalytic cycle.

[Effect of plant-associated methanolic bacteria on methane and methanol concentration dynamics in atmosphere of pressurized chamber].

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.

Isolation and Genomic Characterization of a Proteobacterial Methanotroph Requiring Lanthanides.

Although the bioavailability of rare earth elements (REEs, including scandium, yttrium, and 15 lanthanides) has not yet been examined in detail, methane-oxidizing bacteria (methanotrophs) were recently shown to harbor specific types of methanol dehydrogenases (XoxF-MDHs) that contain lanthanides in their active site, whereas their well-characterized counterparts (MxaF-MDHs) were Ca2+-dependent. However, lanthanide dependency in methanotrophs has not been demonstrated, except in acidic environments in which the solubility of lanthanides is high. We herein report the isolation of a lanthanide-dependent methanotroph from a circumneutral environment in which lanthanides only slightly dissolved. Methanotrophs were enriched and isolated from pond sediment using mineral medium supplemented with CaCl2 or REE chlorides. A methanotroph isolated from the cerium (Ce) chloride-supplemented culture, Methylosinus sp. strain Ce-a6, was clearly dependent on lanthanide. Strain Ce-a6 only required approximately 30 nM lanthanide chloride for its optimal growth and exhibited the ability to utilize insoluble lanthanide oxides, which may enable survival in circumneutral environments. Genome and gene expression analyses revealed that strain Ce-a6 lost the ability to produce functional MxaF-MDH, and this may have been due to a large-scale deletion around the mxa gene cluster. The present results provide evidence for lanthanide dependency as a novel survival strategy by methanotrophs in circumneutral environments.

MMOD-induced structural changes of hydroxylase in soluble methane monooxygenase.

Soluble methane monooxygenase in methanotrophs converts methane to methanol under ambient conditions. The maximum catalytic activity of hydroxylase (MMOH) is achieved through the interplay of its regulatory protein (MMOB) and reductase. An additional auxiliary protein, MMOD, functions as an inhibitor of MMOH; however, its inhibitory mechanism remains unknown. Here, we report the crystal structure of the MMOH-MMOD complex from Methylosinus sporium strain 5 (2.6 Å). Its structure illustrates that MMOD associates with the canyon region of MMOH where MMOB binds. Although MMOD and MMOB recognize the same binding site, each binding component triggers different conformational changes toward MMOH, which then respectively lead to the inhibition and activation of MMOH. Particularly, MMOD binding perturbs the di-iron geometry by inducing two major MMOH conformational changes, i.e., MMOH ß subunit disorganization and subsequent His147 dissociation with Fe1 coordination. Furthermore, 1,6-hexanediol, a mimic of the products of sMMO, reveals the substrate access route.

Analysis of methanotrophic communities in landfill biofilters using diagnostic microarray.

Biofilters operated for the microbial oxidation of landfill methane at two sites in Northern Germany were analysed for the composition of their methanotrophic community by means of diagnostic microarray targeting the pmoA gene of methanotrophs. The gas emitted from site Francop (FR) contained the typical principal components (CH4, CO2, N2) only, while the gas at the second site Müggenburger Strasse (MU) was additionally charged with non-methane volatile organic compounds (NMVOCs). Methane oxidation activity measured at 22 degrees C varied between 7 and 103 microg CH4 (g dw)(-1) h(-1) at site FR and between 0.9 and 21 microg CH4 (g dw)(-1) h(-1) at site MU, depending on the depth considered. The calculated size of the active methanotrophic population varied between 3 x 10(9) and 5 x 10(11) cells (g dw)(-1) for biofilter FR and 4 x 10(8) to 1 x 10(10) cells (g dw)(-1) for biofilter MU. The methanotrophic community in both biofilters as well as the methanotrophs present in the landfill gas at site FR was strongly dominated by type II organisms, presumably as a result of high methane loads, low copper concentration and low nitrogen availability. Within each biofilter, community composition differed markedly with depth, reflecting either the different conditions of diffusive oxygen supply or the properties of the two layers of materials used in the filters or both. The two biofilter communities differed significantly. Type I methanotrophs were detected in biofilter FR but not in biofilter MU. The type II community in biofilter FR was dominated by Methylocystis species, whereas the biofilter at site MU hosted a high abundance of Methylosinus species while showing less overall methanotroph diversity. It is speculated that the differing composition of the type II population at site MU is driven by the presence of NMVOCs in the landfill gas fed to the biofilter, selecting for organisms capable of co-oxidative degradation of these compounds.

Effect of temperature on composition of the methanotrophic community in rice field and forest soil.

Temperature change affects methane consumption in soil. However, there is no information on possible temperature control of methanotrophic bacterial populations. Therefore, we studied CH(4) consumption and populations of methanotrophs in an upland forest soil and a rice field soil incubated at different temperatures between 5 and 45 degrees C for up to 40 days. Potential methane consumption was measured at 4% CH(4). The temporal progress of CH(4) consumption indicated growth of methanotrophs. Both soils showed maximum CH(4) consumption at 25-35 degrees C, but no activity at >40 degrees C. In forest soil CH(4) was also consumed at 5 degrees C, but in rice soil only at 15 degrees C. Methanotroph populations were assessed by terminal restriction fragment length polymorphism (T-RFLP) targeting particulate methane monooxygenase (pmoA) genes. Eight T-RFs with relative abundance >1% were retrieved from both forest and rice soil. The individual T-RFs were tentatively assigned to different methanotrophic populations (e.g. Methylococcus/Methylocaldum, Methylomicrobium, Methylobacter, Methylocystis/Methylosinus) according to published sequence data. Two T-RFs were assigned to ammonium monooxygenase (amoA) gene sequences. Statistical tests showed that temperature affected the relative abundance of most T-RFs. Furthermore, the relative abundance of individual T-RFs differed between the two soils, and also exhibited different temperature dependence. We conclude that temperature can be an important factor regulating the community composition of methanotrophs in soil.

[Study on the structure and function of a stable methane-oxidizing mixed microbial consortium].

From an agricultural sample taken in Chongqing, a stable methane-oxidizing mixed microbial consortium was established by enrichment culture with methane as a sole source of carbon and energy. The mixed consortium showed high capability of phenol degradation and 1,2-epoxypropane production from propene. More than 99% of phenol at an initial concentration of 600mg/L could be degraded by the mixed microbial consortium after 11 h of cultivation. The productivity of 1, 2-epoxypropane could be increased with the decrease of phosphate concentration. The concentration of 1, 2-epoxypropane produced could reach to 5.0mmol/L. The bacterial structure of the methane-oxidizing mixed microbial consortium was analyzed by pure culture isolation combining with 16S rRNA and PCR of the related MMO functional genes. The results showed that the methane-oxidizing mixed microbial consortium was composed of a type 1U methanotroph identified as Methylosinus trichosporium and at least 4 kinds of heterotrophs ( Comamonas testosteroni, Cupriavidus metallidurans, Acinetobacter junii and Stenotrophomonas maltophilia ). M. trichosporium Y9, isolated from the mixed consortium, harbored both sMMO and pMMO genes.

Ammonium conversion and its feedback effect on methane oxidation of Methylosinus sporium.

Ammonium (NH4+) is not only nitrogen source that can support methanotrophic growth, but also it can inhibit methane (CH4) oxidation by competing with CH4 for the active site of methane monooxygenase. NH4+ conversion and its feedback effect on the growth and activity of methanotrophs were evaluated with Methylosinus sporium used as a model methanotroph. Nitrogen sources could affect the CH4-derived carbon distribution, which varied with incubation time and nitrogen concentrations. More CH4-derived carbon was incorporated into biomass in the media with NH4+-N, compared to nitrate-nitrogen (NO3--N), as sole nitrogen source at the nitrogen concentrations of 10-18 mmol L-1. Although ammonia (NH3) oxidation activity of methanotrophs was considerably lower, only accounting for 0.01-0.06% of CH4 oxidation activity in the experimental cultures, NH4+ conversion could lead to the pH decrease and toxic intermediates accumulation in the their habits. Compared with NH4+, nitrite (NO2-) accumulation in the NH4+ conversion of methanotroph had stronger inhibition on its activity, especially the joint inhibition of NO2- accumulation and the pH decrease during the NH4+-N conversion. These results suggested that more attention should be paid to the feedback effects of NH4+ conversion by methanotrophs to understand effects of NH4+ on CH4 oxidation in the environments.

Enrichment culture and identification of endophytic methanotrophs isolated from peatland plants.

Aerobic methane-oxidizing bacteria (MOB) are an environmentally significant group of microorganisms due to their role in the global carbon cycle. Research conducted over the past few decades has increased the interest in discovering novel genera of methane-degrading bacteria, which efficiently utilize methane and decrease the global warming effect. Moreover, methanotrophs have more promising applications in environmental bioengineering, biotechnology, and pharmacy. The investigations were undertaken to recognize the variety of endophytic methanotrophic bacteria associated with Carex nigra, Vaccinium oxycoccus, and Eriophorum vaginatum originating from Moszne peatland (East Poland). Methanotrophic bacteria were isolated from plants by adding sterile fragments of different parts of plants (roots and stems) to agar mineral medium (nitrate mineral salts (NMS)) and incubated at different methane values (1-20% CH4). Single colonies were streaked on new NMS agar media and, after incubation, transferred to liquid NMS medium. Bacterial growth dynamics in the culture solution was studied by optical density-OD600 and methane consumption. Changes in the methane concentration during incubation were controlled by the gas chromatography technique. Characterization of methanotrophs was made by fluorescence in situ hybridization (FISH) with Mg705 and Mg84 for type I methanotrophs and Ma450 for type II methanotrophs. Identification of endophytes was performed after 16S ribosomal RNA (rRNA) and mmoX gene amplification. Our study confirmed the presence of both types of methanotrophic bacteria (types I and II) with the predominance of type I methanotrophs. Among cultivable methanotrophs, there were different strains of the genus Methylomonas and Methylosinus. Furthermore, we determined the potential of the examined bacteria for methane oxidation, which ranged from 0.463 ± 0.067 to 5.928 ± 0.169 µmol/L CH4/mL/day.

Methylmercury uptake and degradation by methanotrophs.

Methylmercury (CH3Hg+) is a potent neurotoxin produced by certain anaerobic microorganisms in natural environments. Although numerous studies have characterized the basis of mercury (Hg) methylation, no studies have examined CH3Hg+ degradation by methanotrophs, despite their ubiquitous presence in the environment. We report that some methanotrophs, such as Methylosinus trichosporium OB3b, can take up and degrade CH3Hg+ rapidly, whereas others, such as Methylococcus capsulatus Bath, can take up but not degrade CH3Hg+. Demethylation by M. trichosporium OB3b increases with increasing CH3Hg+ concentrations but was abolished in mutants deficient in the synthesis of methanobactin, a metal-binding compound used by some methanotrophs, such as M. trichosporium OB3b. Furthermore, addition of methanol (>5 mM) as a competing one-carbon (C1) substrate inhibits demethylation, suggesting that CH3Hg+ degradation by methanotrophs may involve an initial bonding of CH3Hg+ by methanobactin followed by cleavage of the C-Hg bond in CH3Hg+ by the methanol dehydrogenase. This new demethylation pathway by methanotrophs indicates possible broader involvement of C1-metabolizing aerobes in the degradation and cycling of toxic CH3Hg+ in the environment.

Functional expression of the particulate methane mono-oxygenase gene in recombinant Rhodococcus erythropolis.

In order to construct an expression system for the particulate methane mono-oxygenase (pMMO) gene (pmo), the structural gene cluster pmoCAB amplified from Methylosinus trichosporium OB3b was inserted into a shuttle vector pBS305 under the control of a dsz promoter and transformed into Rhodococcus erythropolis LSSE8-1. A stable transformant was successfully obtained using ethane as the sole carbon source. Fluorescence in situ hybridization results showed that the dsz promoter allowed the pmo genes to be transcribed in the recombinant strain. The effects of Cu2+ and Zn2+ concentrations on cell growth and pMMO activity in ethane-containing medium were examined. It was discovered that 7.5 microM Cu2+ and 1.8 microM Zn2+ were suitable to achieve high cell concentration and pMMO activity, but the amount of methanol accumulated during methane oxidation by the recombinant strain was still low.