A5013272093- Microbial metabolism and enzyme function
- Methane Hydrates and Related Phenomena
- Anaerobic Digestion and Biogas Production
- Enzyme Structure and Function
- Microbial Metabolic Engineering and Bioproduction
- Amino Acid Enzymes and Metabolism
- Porphyrin Metabolism and Disorders
- Microbial Community Ecology and Physiology
- Biofuel production and bioconversion
- CRISPR and Genetic Engineering
- Alcohol Consumption and Health Effects
- Microbial Fuel Cells and Bioremediation
- Heme Oxygenase-1 and Carbon Monoxide
- Radioactive element chemistry and processing
- Microbial Metabolites in Food Biotechnology
- RNA and protein synthesis mechanisms
- Polyamine Metabolism and Applications
- Metabolism and Genetic Disorders
- Epigenetics and DNA Methylation
- Radioactive contamination and transfer
- Transgenic Plants and Applications
- Geochemistry and Elemental Analysis
- Microbial bioremediation and biosurfactants
- Animal Genetics and Reproduction
- Enzyme Production and Characterization
University of California, Berkeley
2023-2025
Berkeley College
2025
Planetary Science Institute
2023
Harvard University
2014-2021
University of Idaho
2015-2021
University of Illinois System
2020-2021
University of Illinois Urbana-Champaign
2017-2020
University of Illinois Chicago
2019
Stanford University
2009
Although Cas9-mediated genome editing has proven to be a powerful genetic tool in eukaryotes, its application Bacteria been limited because of inefficient targeting or repair; and Archaea yet reported. Here we describe the development genome-editing that allows facile manipulation slow-growing methanogenic archaeon
Methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production consumption of potent greenhouse gas methane. The α subunit MCR (McrA) contains several unusual post-translational modifications, including a rare thioamidation glycine. Based on presumed function homologous genes involved biosynthesis thioviridamide, thioamide-containing natural product, we hypothesized that archaeal tfuA ycaO would be responsible for...
Abstract Methanogens are a diverse group of Archaea that obligately couple energy conservation to the production methane. Some methanogens encode alternate pathways for conservation, like anaerobic respiration, but biochemical details this process unknown. We show multiheme c -type cytochrome called MmcA from Methanosarcina acetivorans is important intracellular electron transport during methanogenesis and can also reduce extracellular acceptors soluble Fe 3+ anthraquinone-2,6-disulfonate....
Methyl-coenzyme M reductase (MCR) catalyzes the final step of methanogenesis, microbial metabolism responsible for nearly all biological methane emissions to atmosphere. Decades biochemical and structural research studies have generated detailed insights into MCR function
2-mercaptoethanesulfonate (Coenzyme M, CoM) is an organic sulfur-containing cofactor used for hydrocarbon metabolism in Archaea and Bacteria. In Archaea, CoM serves as alkyl group carrier enzymes belonging to the alkyl-CoM reductase family, including methyl-CoM reductase, which catalyzes methane formation methanogens. Two pathways biosynthesis of are present methanogenic archaea. The initial steps these distinct but last two reactions, leading up formation, universally conserved. final step...
The enzyme methyl-coenzyme M reductase (MCR) plays an important role in mediating global levels of methane by catalyzing a reversible reaction that leads to the production or consumption this potent greenhouse gas methanogenic and methanotrophic archaea. In archaea, alpha subunit MCR (McrA) typically contains four six posttranslationally modified amino acids near active site. Recent studies have identified enzymes performing two these modifications (thioglycine 5-[S]-methylarginine), yet...
Methylobacterium extorquens AM1, a strain serendipitously isolated half century ago, has become the best-characterized model system for study of aerobic methylotrophy (the ability to grow on reduced single-carbon compounds). However, with 5 replicons and 174 insertion sequence (IS) elements in genome as well long history domestication laboratory, genetic genomic analysis M. AM1 face several challenges. On contrary, recently - PA1- is closely related (100% 16S rRNA identity) contains...
Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane, and its activity accounts for nearly all biologically produced methane released into atmosphere. The assembly MCR is an intricate process involving installation a complex set posttranslational modifications unique Ni-containing tetrapyrrole called coenzyme F 430 . Despite decades research, details remain largely unresolved. Here, we report structural characterization in two intermediate states assembly. These lack one or...
ABSTRACT Methylotrophs grow on reduced single-carbon compounds like methylamine as the sole source of carbon and energy. In Methylobacterium extorquens AM1, best-studied aerobic methylotroph, a periplasmic dehydrogenase that catalyzes primary oxidation to formaldehyde has been examined in great detail. However, recent metagenomic data from natural ecosystems are revealing abundance importance lesser-known routes, such N -methylglutamate pathway, for oxidation. this study, we used M. PA1,...
Microorganisms often encode multiple non-orthologous metabolic modules that catalyze the same reaction. However, little experimental evidence actually demonstrates a selective basis for degeneracy. Many methylotrophs—microorganisms grow on reduced single-carbon compounds—like Methylobacterium extorquens AM1 two routes methylamine oxidation: periplasmic dehydrogenase (MaDH) and cytoplasmic N-methylglutamate (NMG) pathway. In AM1, MaDH is essential growth, but NMG pathway has no known...
Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin generated in organisms from bacteria humans. Methylotrophic such as Methylorubrum extorquens face an acute challenge due their production of formaldehyde obligate central intermediate single-carbon metabolism. Mechanisms sense respond were speculated exist methylotrophs for decades but had never been discovered. Here, we identify member the DUF336...
Methylamine plays an important role in the global carbon and nitrogen budget; microorganisms that grow on reduced single compounds, methylotrophs, serve as a major biological sink for methylamine aerobic environments. Two non-orthologous, functionally degenerate routes oxidation have been studied methylotrophic Proteobacteria: dehydrogenase N-methylglutamate pathway. Recent work suggests (NMG) pathway may be more common nature than well-studied (MaDH, encoded by mau gene cluster). However,...
Abstract Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin generated in organisms from bacteria humans. Methylotrophic such as Methylorubrum extorquens face an acute challenge due their production of formaldehyde obligate central intermediate single-carbon metabolism. Mechanisms sense respond were speculated exist methylotrophs for decades but had never been discovered. Here we identify member...
Abstract The stable isotopic composition of biogenic methane varies substantially in the environment and is routinely used to fingerprint its source. However, underlying cause this variation debated. Here, we experimentally manipulate growth rate model methanogen, Methanosarcina acetivorans , using CRISPR mutagenesis generate a tunable version key final enzyme methanogenesis, methyl-coenzyme M reductase (MCR). We demonstrate that carbon hydrogen change as function MCR expression rate. Using...
Abstract The ribosome is the universal translator of genetic code and shared across all life. Despite divergence in structure over course evolution, peptidyl transferase center (PTC), catalytic site ribosome, has been thought to be nearly universally conserved. Here, we identify clades archaea that have highly divergent ribosomal RNA sequences PTC. To understand how these PTC fold, determined cryo-EM structures Pyrobaculum calidifontis ribosome. We find sequence variation leads rearrangement...
ABSTRACT Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane and its activity accounts for nearly all biologically produced released into atmosphere. The assembly MCR is an intricate process involving installation a complex set post-translational modifications unique Ni porphyrin cofactor F 430 . Despite decades research, details remain largely unresolved. Here, we report structural characterization in two intermediate states assembly. These lack one or both cofactors form...
Nearly all biogenic methane is produced by a group of microorganisms called methanogenic archaea (or methanogens). Methanogens can use variety substrates, such as H 2 + CO , acetate, and methylated compounds, for methanogenesis. Previous studies have shown that the stable carbon hydrogen isotopic compositions methanogens vary drastically depending on substrate composition concentration in environment. For instance, environment has substantial impact derived from hydrogenotrophic...
Abstract Methanogens are a diverse group of Archaea that couple energy conservation to the production methane gas. While most methanogens have no alternate mode conservation, strains like Methanosarcina acetivorans known also conserve by dissimilatory metal reduction (DSMR) in presence soluble ferric iron or iron-containing minerals. The ecological ramifications decoupled from substantial, yet molecular details poorly understood. In this work, we conducted vitro and vivo studies with...