A5068195631- Microbial metabolism and enzyme function
- Microbial Metabolic Engineering and Bioproduction
- Methane Hydrates and Related Phenomena
- Microbial bioremediation and biosurfactants
- Amino Acid Enzymes and Metabolism
- Biofuel production and bioconversion
- Alcohol Consumption and Health Effects
- Microbial Community Ecology and Physiology
- Porphyrin Metabolism and Disorders
- Anaerobic Digestion and Biogas Production
- Metal-Catalyzed Oxygenation Mechanisms
- Enzyme Structure and Function
- Wastewater Treatment and Nitrogen Removal
- Metabolism and Genetic Disorders
- Metalloenzymes and iron-sulfur proteins
- Atmospheric and Environmental Gas Dynamics
- Metabolomics and Mass Spectrometry Studies
- Polyamine Metabolism and Applications
- Analytical Chemistry and Sensors
- Microfluidic and Capillary Electrophoresis Applications
- Bacterial Genetics and Biotechnology
- Biochemical Acid Research Studies
- Microbial Fuel Cells and Bioremediation
- Enzyme Catalysis and Immobilization
- Mass Spectrometry Techniques and Applications
University of Washington
2014-2024
Seattle University
1983-2015
Joint Genome Institute
2013
Lawrence Livermore National Laboratory
2013
University of Michigan–Ann Arbor
2013
Microscale (United States)
2003-2010
Czech Academy of Sciences, Institute of Microbiology
2009
Environmental Molecular Sciences Laboratory
2005
Pacific Northwest National Laboratory
2005
Institute of Chemical Engineering
2002
Genes encoding paniculate methane monooxygenase and ammonia share high sequence identity. Degenerate oligonucleotide primers were designed, based on regions of shared amino acid between the 27-kDa polypeptides, which are believed to contain active sites, particulate monooxygenase. A 525-bp internal DNA fragment genes these polypeptides (pmoA amoA) from a variety methanotrophic nitrifying bacteria was amplified by PCR, cloned sequenced. Representatives each phylogenetic groups both...
ABSTRACT The 16S rRNA and pmoA genes from natural populations of methane-oxidizing bacteria (methanotrophs) were PCR amplified total community DNA extracted Lake Washington sediments obtained the area where peak methane oxidation occurred. Clone libraries constructed for each genes, approximately 200 clones library analyzed by using restriction fragment length polymorphism (RFLP) tetrameric enzymes Msp I, Hae III, Hha I. products grouped based on their RFLP patterns, representatives group...
Methylamine dehydrogenase (MADH), an α 2 β enzyme from numerous methylotrophic soil bacteria, contains a novel quinonoid redox prosthetic group that is covalently bound to its small subunit through two amino acyl residues. A comparison of the acid sequence deduced gene for Methylobacterium extorquens AM1 with published obtained by Edman degradation method, allowed identification constituents cofactor as tryptophyl This information was crucial interpreting 1 Hand 13 C nuclear magnetic...
We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence FLS enables design new carbon fixation pathway, consisting small number thermodynamically favorable chemical transformations that convert formate sugar in central metabolism. pathway is predicted to use more efficiently and with less backward flux than any naturally occurring assimilation...
Trichloroethylene (TCE), a common groundwater contaminant, is suspected carcinogen that highly resistant to aerobic biodegradation. An aerobic, methane-oxidizing bacterium was isolated degrades TCE in pure culture at concentrations commonly observed contaminated groundwater. Strain 46-1, type I methanotrophic bacterium, degraded if grown on methane or methanol, producing CO 2 and water-soluble products. Gas chromatography 14 C radiotracer techniques were used determine the rate, dependence,...
The utilization of methane, a potent greenhouse gas, is an important component local and global carbon cycles that characterized by tight linkages between methane-utilizing (methanotrophic) nonmethanotrophic bacteria. It has been suggested the methanotroph sustains these nonmethanotrophs cross-feeding, because subsequent products methane oxidation pathway, such as methanol, represent alternative sources. We established cocultures in microcosm model system to determine mechanism substrate...
The rapid increase of the potent greenhouse gas methane in atmosphere creates great urgency to develop and deploy technologies for mitigation. One approach removing is use bacteria which their carbon energy source (methanotrophs). Such naturally convert CO 2 biomass, a value-added product cobenefit removal. Typically, methanotrophs grow best at around 5,000 10,000 ppm methane, but 1.9 ppm. Air above emission sites such as landfills, anaerobic digestor effluents, rice paddy oil wells contains...
Full exploitation of the information available in bacterial genome sequences requires availability facile tools for rapid genetic manipulation. One bacterium which new are needed is methylotroph Methylobacterium extorquens AM1. IncQ and small IncP vectors were shown to be unsuitable use this bacterium, but a spontaneous mutant plasmid was isolated that functioned efficiently M. This sequenced used as base developing improved broad-host-range cloning vectors. These found replicate wide...
Complete genome sequences are now available for many bacterial species that lack sophisticated genetic tools. We describe the development of a broad-host-range cre-lox system allows antibiotic marker recycling in variety gram-negative bacteria. This consists an allelic exchange vector bearing kanamycin cassette flanked by loxP sites and tetracycline-resistant IncP plasmid provides expression Cre recombinase. demonstrate this generating unmarked deletions genes two different bacteria,...
Methanogenic and sulfate-reducing Archaea are considered to have an energy metabolism involving C 1 transfer coenzymes enzymes unique for this group of strictly anaerobic microorganisms. An aerobic methylotrophic bacterium, Methylobacterium extorquens AM1, was found contain a cluster genes that predicted encode some these shown two the enzyme activities one methanogenic coenzymes. Insertion mutants were all unable grow on compounds, suggesting archaeal function in metabolism. Thus,...
A 45-kDa membrane polypeptide that is associated with activity of the particulate methane monooxygenase (pMMO) has been purified from three methanotrophic bacteria, and N-terminal amino acid sequence was found to be identical in 17 20 positions for all polypeptides 14 N terminus AmoB, 43-kDa subunit ammonia monooxygenase. DNA a variety methanotrophs screened two probes, an oligonucleotide designed Methylococcus capsulatus Bath internal fragment amoA, which encodes 27-kDa In most cases,...
ABSTRACT Profiles of dissolved O 2 and methane with increasing depth were generated for Lake Washington sediment, which suggested the zone oxidation is limited to top 0.8 cm sediment. Methane potentials measured 0.5-cm layers down 1.5 found be relatively constant at 270 350 μmol/liter sediment/h. Approximately 65% was oxidized cell material or metabolites, a signature suggestive type I methanotrophs. Eleven methanotroph strains isolated from lake sediment analyzed. Five these classed as I,...
ABSTRACT Active members of the bacterial community in sediment Lake Washington, with special emphasis on C 1 utilizers, were identified by employing two complementary culture-independent approaches: reverse transcription environmental mRNA and 16S rRNA combined PCR (RT-PCR) stable-isotope probing (SIP) DNA 13 C-labeled substrates methanol, methylamine, formaldehyde, formate. Analysis RT-PCR-amplified fragments rRNA-encoding genes revealed that gammaproteobacterial methanotrophs belonging to...
Background Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes two pink-pigmented facultative methylotrophic bacteria Alpha-proteobacterial genus Methylobacterium, reference species Methylobacterium extorquens strain AM1 and dichloromethane-degrading DM4, were compared. Methodology/Principal Findings 6.88 Mb genome comprises a 5.51 chromosome, 1.26 megaplasmid three plasmids, while 6.12 DM4 features 5.94 chromosome...
It is shown that the particulate methane monooxygenase (pMMO) has an obligate requirement for copper. The MMO activity in fractions obtained from Methylococcus capsulatus (Bath) cells found to increase with increasing copper content of membranes. enzyme membranes grown at low levels can be stimulated further by addition Cu(II) ions assay medium. membrane-bound exist both and Cu(I) forms. EPR magnetic susceptibility characterizations indicate presence exchange-coupled trinuclear cluster when...
ABSTRACT Aerobic methanotrophs oxidize methane at ambient temperatures and pressures are therefore attractive systems for methane-based bioconversions. In this work, we developed validated genetic tools Methylomicrobium buryatense , a haloalkaliphilic gammaproteobacterial (type I) methanotroph. M. was isolated directly on natural gas grows robustly in pure culture with 3-h doubling time, enabling rapid manipulation compared to many other methanotrophic species. As proof of concept, used...
Aerobic oxidation is important in the cycling of methane sediments Lake Washington. About half flux from depth oxidized to CO 2 upper 0.7 cm and remainder escapes into water column. In terms total carbon budget lake, upward insignificant with only about 2% fixed by primary production being returned as methane. The methane, however, does represent 20% organic decomposed within sediments. addition, consumcs 7–10% oxygen Measured kinetic parameters suggest that restricted top 6–7 mm sediment...