Utilisation of low methane concentrations by methanotrophs.

The growing urgency regarding climate change points to methane as a key greenhouse gas for slowing global warming to allow other mitigation measures to take effect. One approach to both decreasing methane emissions and removing methane from air is aerobic methanotrophic bacteria, those bacteria that grow on methane as sole carbon and energy source and require O. A subset of these methanotrophs is able to grow on methane levels of 1000 parts per million (ppm) and below, and these present an opportunity for developing both environmental- and bioreactor-based methane treatment systems.

Direct Methane Removal from Air by Aerobic Methanotrophs.

The rapid pace of climate change has created great urgency for short-term mitigation strategies. Appropriately, the long-term target for intervening in global warming is CO, but experts suggest that methane should be a key short-term target. Methane has a warming impact 34 times greater than CO on a 100-year timescale, and 86 times greater on a 20-year timescale, and its short half-life in the atmosphere provides the opportunity for near-term positive climate impacts.

A methanotrophic bacterium to enable methane removal for climate mitigation.

The rapid increase of the potent greenhouse gas methane in the atmosphere creates great urgency to develop and deploy technologies for methane mitigation. One approach to removing methane is to use bacteria for which methane is their carbon and energy source (methanotrophs). Such bacteria naturally convert methane to CO and biomass, a value-added product and a cobenefit of methane removal.

Enzyme engineering and testing of a formate reduction pathway.

Formate is an attractive feedstock for sustainable microbial production of fuels and chemicals, but its potential is limited by the lack of efficient assimilation pathways. The reduction of formate to formaldehyde would allow efficient downstream assimilation, but no efficient enzymes are known for this transformation. To develop a 2-step formate reduction pathway, we screened natural variants of acyl-CoA synthetase (ACS) and acylating aldehyde dehydrogenase (ACDH) for activity on one-carbon substrates and identified active and highly expressed homologs of both enzymes.

A Computational Framework for Identifying Promoter Sequences in Nonmodel Organisms Using RNA-seq Data Sets.

Engineering microorganisms into biological factories that convert renewable feedstocks into valuable materials is a major goal of synthetic biology; however, for many nonmodel organisms, we do not yet have the genetic tools, such as suites of strong promoters, necessary to effectively engineer them. In this work, we developed a computational framework that can leverage standard RNA-seq data sets to identify sets of constitutive, strongly expressed genes and predict strong promoter signals within their upstream regions. The framework was applied to a diverse collection of RNA-seq data measured for the methanotroph 5GB1 and identified 25 genes that were constitutively, strongly expressed across 12 experimental conditions.

Cultivation techniques to study lanthanide metal interactions in the haloalkaliphilic Type I methanotroph "Methylotuvimicrobium buryatense" 5GB1C.

Lanthanide metals are commonly used in technological devices including batteries, computers, catalysts and magnets. Despite their important properties, mining difficulties and pollution concerns limit the number of mines worldwide. Because of these concerns, biometallurgy is an attractive possibility for lanthanide extraction from recycled materials or from contaminated sites.

The Entner-Doudoroff Pathway Is an Essential Metabolic Route for Methylotuvimicrobium buryatense 5GB1C.

5GB1C, a fast-growing gammaproteobacterial methanotroph, is equipped with two glycolytic pathways, the Entner-Doudoroff (ED) pathway and the Embden-Meyerhof-Parnas (EMP) pathway. Metabolic flux analysis and C-labeling experiments have shown the EMP pathway is the principal glycolytic route in 5GB1C, while the ED pathway appears to be metabolically and energetically insignificant. However, it has not been possible to obtain a null mutant in the - genes encoding the two unique enzymatic reactions in the ED pathway, suggesting the ED pathway may be essential for 5GB1C growth.

The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges.

The long atmospheric residence time of CO creates an urgent need to add atmospheric carbon drawdown to CO regulatory strategies. Synthetic and systems biology (SSB), which enables manipulation of cellular phenotypes, offers a powerful approach to amplifying and adding new possibilities to current land management practices aimed at reducing atmospheric carbon. The participants (in attendance: Christina Agapakis, George Annas, Adam Arkin, George Church, Robert Cook-Deegan, Charles DeLisi, Dan Drell, Sheldon Glashow, Steve Hamburg, Henry Jacoby, Henry Kelly, Mark Kon, Todd Kuiken, Mary Lidstrom, Mike MacCracken, June Medford, Jerry Melillo, Ron Milo, Pilar Ossorio, Ari Patrinos, Keith Paustian, Kristala Jones Prather, Kent Redford, David Resnik, John Reilly, Richard J.

A 6-month randomized, double-blind, placebo-controlled trial of weekly exenatide in adolescents with obesity.

Background: Pharmacological treatment options for adolescents with obesity are very limited. Glucagon-like-peptide-1 (GLP-1) receptor agonist could be a treatment option for adolescent obesity.

Objective: To investigate the effect of exenatide extended release on body mass index (BMI)-SDS as primary outcome, and glucose metabolism, cardiometabolic risk factors, liver steatosis, and other BMI metrics as secondary outcomes, and its safety and tolerability in adolescents with obesity.

Quantifying Methane and Methanol Metabolism of "" 5GB1C under Substrate Limitation.

Methanotrophic bacteria are a group of prokaryotes capable of using methane as their sole carbon and energy source. Although efforts have been made to simulate and elucidate their metabolism via computational approaches or C tracer analysis, major gaps still exist in our understanding of methanotrophic metabolism at the systems level. Particularly, direct measurements of system-wide fluxes are required to understand metabolic network function.

Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph 5GB1.

5GB1 is an obligate methylotroph which grows on methane or methanol with similar growth rates. It has long been assumed that the core metabolic pathways must be similar on the two substrates, but recent studies of methane metabolism in this bacterium suggest that growth on methanol might have significant differences from growth on methane. In this study, both a targeted metabolomics approach and a C tracer approach were taken to understand core carbon metabolism in 5GB1 during growth on methanol and to determine whether such differences occur.

Interspecies Chemical Signaling in a Methane-Oxidizing Bacterial Community.

Multiple species of bacteria oxidize methane in the environment after it is produced by anaerobic ecosystems. These organisms provide reduced carbon substrates for species that cannot oxidize methane themselves, thereby serving a key role in these niches while also sequestering this potent greenhouse gas before it enters the atmosphere. Deciphering the molecular details of how methane-oxidizing bacteria interact in the environment enables us to understand an important aspect that shapes the structures and functions of these communities.

Tundrenone: An Atypical Secondary Metabolite from Bacteria with Highly Restricted Primary Metabolism.

Methane-oxidizing bacteria, aerobes that utilize methane as their sole carbon and energy source, are being increasingly studied for their environmentally significant ability to remove methane from the atmosphere. Their genomes indicate that they also have a robust and unusual secondary metabolism. Bioinformatic analysis of the Methylobacter tundripaludum genome identified biosynthetic gene clusters for several intriguing metabolites, and this report discloses the structural and genetic characterization of tundrenone, one of these metabolites.

A pathway for biological methane production using bacterial iron-only nitrogenase.

Methane (CH) is a potent greenhouse gas that is released from fossil fuels and is also produced by microbial activity, with at least one billion tonnes of CH being formed and consumed by microorganisms in a single year . Complex methanogenesis pathways used by archaea are the main route for bioconversion of carbon dioxide (CO) to CH in nature. Here, we report that wild-type iron-iron (Fe-only) nitrogenase from the bacterium Rhodopseudomonas palustris reduces CO simultaneously with nitrogen gas (N) and protons to yield CH, ammonia (NH) and hydrogen gas (H) in a single enzymatic step.

Oxygen-limited metabolism in the methanotroph 5GB1C.

The bacteria that grow on methane aerobically (methanotrophs) support populations of non-methanotrophs in the natural environment by excreting methane-derived carbon. One group of excreted compounds are short-chain organic acids, generated in highest abundance when cultures are grown under O-starvation. We examined this O-starvation condition in the methanotroph 5GB1.

The oxidative TCA cycle operates during methanotrophic growth of the Type I methanotroph Methylomicrobium buryatense 5GB1.

Methanotrophs are a group of bacteria that use methane as sole carbon and energy source. Type I methanotrophs are gamma-proteobacterial methanotrophs using the ribulose monophosphate cycle (RuMP) cycle for methane assimilation. In order to facilitate metabolic engineering in the industrially promising Type I methanotroph Methylomicrobium buryatense 5GB1, flux analysis of cellular metabolism is needed and C tracer analysis is a foundational tool for such work.

Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions.

The utilization of methane, a potent greenhouse gas, is an important component of local and global carbon cycles that is characterized by tight linkages between methane-utilizing (methanotrophic) and nonmethanotrophic bacteria. It has been suggested that the methanotroph sustains these nonmethanotrophs by cross-feeding, because subsequent products of the methane oxidation pathway, such as methanol, represent alternative carbon sources. We established cocultures in a microcosm model system to determine the mechanism and substrate that underlay the observed cross-feeding in the environment.

Quorum Sensing in a Methane-Oxidizing Bacterium.

Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Dissecting the molecular details of how these organisms interact in the environment may increase our understanding of how they perform this important ecological role. Many bacterial species use quorum sensing (QS) systems to regulate gene expression in a cell density-dependent manner.

MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense.

Many methylotrophs, microorganisms that consume carbon compounds lacking carbon-carbon bonds, use two different systems to oxidize methanol for energy production and biomass accumulation. The MxaFI methanol dehydrogenase (MDH) contains calcium in its active site, while the XoxF enzyme contains a lanthanide in its active site. The genes encoding the MDH enzymes are differentially regulated by the presence of lanthanides.

Difference in C3-C4 metabolism underlies tradeoff between growth rate and biomass yield in Methylobacterium extorquens AM1.

Background: Two variants of Methylobacterium extorquens AM1 demonstrated a trade-off between growth rate and biomass yield. In addition, growth rate and biomass yield were also affected by supplementation of growth medium with different amounts of cobalt. The metabolism changes relating to these growth phenomena as well as the trade-off were investigated in this study.

Comprehensive molecular characterization of Methylobacterium extorquens AM1 adapted for 1-butanol tolerance.

Background: The toxicity of alcohols is one of the major roadblocks of biological fermentation for biofuels production. Methylobacterium extorquens AM1, a facultative methylotrophic α-proteobacterium, has been engineered to generate 1-butanol from cheap carbon feedstocks through a synthetic metabolic pathway. However, M.