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August 2000 - December 2005
Education
January 2006 - July 2010
August 2000 - December 2005
August 1996 - May 2000
Publications
Publications (51)
Carbonate minerals are considered a metastable carbon reservoir under alkaline conditions. Here we demonstrate calcium carbonate as a sole inorganic carbon source at moderately alkaline pH for a methanogenic microbial community enriched from alkaline, saline wetland soil. In reactors amended with calcium carbonate as the sole source of inorganic ca...
Rising global food demand necessitates improved crop yields. Biostimulants offer a potential solution to meet these demands. Among them, antioxidants have shown potential to improve yield, nutritional quality, and resilience to climate change. However, large-scale production of many antioxidants is challenging. Here, we investigate Coenzyme M (CoM)...
Rising global food demand necessitates improved crop yields. Biostimulants offer a potential solution to meet these demands. Among them, antioxidants have shown potential to improve yield, nutritional quality and resilience to climate change. However, large-scale production of many antioxidants is challenging. Here, we investigate Coenzyme M (CoM),...
Methane-producing archaea are key organisms in the anaerobic carbon cycle. These organisms, also called methanogens, grow by converting substrate to methane gas in a process called methanogenesis. Previous research showed that the reduction of the terminal electron acceptor is the rate-limiting step in methanogenesis by Methanosarcina acetivorans....
Carbonate minerals are considered a metastable carbon reservoir under alkaline conditions. Here we demonstrate the use of calcium carbonate as a sole inorganic carbon source at moderately alkaline pH for a methanogenic microbial community enriched from alkaline, saline wetland soil. In reactors amended with calcium carbonate as the sole source of i...
Understanding cellular engagement with its environment is essential to control and monitor metabolism. Molecular Communication theory (MC) offers a computational means to identify environmental perturbations that direct or signify cellular behaviors by quantifying the information about a molecular environment that is transmitted through a metabolic...
Plant growth and resilience require balancing an inherently oxidative metabolism with powerful antioxidant systems that help maintain homeostasis. When the environment changes, reactive oxygen species are potent indicators of that change, allowing adaptation through re-balancing metabolism and antioxidant systems. A large body of evidence supports...
Methanogenic archaea are important organisms in the global carbon cycle that grow by producing methane gas. Methanosarcina acetivorans is a methanogenic archaeum that can grow using methylated compounds, carbon monoxide, or acetate and produces renewable methane as a byproduct. However, there is limited knowledge of how combinations of substrates m...
Methanogens are anaerobic archaea which conserve energy by producing methane. Found in nearly every anaerobic environment on earth, methanogens serve important roles in ecology as key organisms of the global carbon cycle, and in industry as a source of renewable biofuels. Environmentally, methanogenic archaea play an essential role in the reintrodu...
Trophic interactions between microbes are postulated to determine whether a host microbiome is healthy or causes predisposition to disease. Two abundant taxa, the Gram-negative heterotrophic bacterium Bacteroides thetaiotaomicron and the methanogenic archaeon Methanobrevibacter smithii, are proposed to have a synergistic metabolic relationship. Bot...
Advances in quantitative biology data collection and analysis across scales (molecular, cellular, organismal, and ecological) have transformed how we understand, categorize, and predict complex biological systems. This surge of quantitative data creates an opportunity to apply, develop, and evaluate mathematical models of biological systems and exp...
Wastewater biosolids are a promising feedstock for production of value-added renewable chemicals. Methane-producing archaea (methanogens) are already used to produce renewable biogas via the anaerobic treatment of wastewater. The ability of methanogens to efficiently convert dissolved organic carbon into methane makes them an appealing potential pl...
Isoprene is a valuable petrochemical used for a wide variety of consumer goods such as adhesives and synthetic rubber. We were able to achieve high yield of renewable isoprene by taking advantage of the naturally high-flux mevalonate lipid synthesis pathway in anaerobic methane-producing archaea (methanogens). Our study illustrates that by genetica...
Bacteroides is a highly abundant taxon in the human gut, and Bacteroides thetaiotaomicron ( B. theta ) is a ubiquitous human symbiont that colonizes the host early in development and persists throughout its life span. The phenotypic plasticity of keystone organisms such as B. theta is important to understand in order to predict phenotype(s) and met...
Plasmid vectors and use of plasmid vectors in methods for producing methane and isoprene using Archaea are dis closed. Particularly, plasmid vectors that express isoprene synthase ( ispS ) are prepared and inserted into methanogens, such as Methanosarcina acetivorans , to allow for c -production of methane and isoprene. In one embodiment, the metho...
Plasmid vectors and use of plasmid vectors in methods for producing methane and isoprene using Archaea are disclosed . Particularly, plasmid vectors that express isoprene synthase ( ispS ) are prepared and inserted into methanogens, such as Methanosarcina acetivorans, to allow for co - production of methane and isoprene. In one embodiment , the met...
Synopsis
Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversio...
Biological systems are staggeringly complex. To untangle this complexity and make predictions about biological systems is a continuous goal of biological research. One approach to achieve these goals is to emphasize the use of quantitative measures of biological processes. Advances in quantitative biology data collection and analysis across scales...
Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioenergetics b...
The opportunity to control and fine-tune the behavior of biological cells is a fascinating possibility for many diverse disciplines, ranging from medicine and ecology, to chemical industry and space exploration. While synthetic biology is providing novel tools to reprogram cell behavior from their genetic code, many challenges need to be solved bef...
Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role...
Years of research in software engineering has given us novel ways to reason about, test, and predict the behavior of complex software systems that contain hundreds of thousands of lines of code. Many of these techniques have been inspired by nature such as genetic algorithms, swarm intelligence, and ant colony optimization. In this paper we reverse...
Microbial strains are provided, as are methods of making and using Such microbial strains.
Microbial strains are provided, as are methods of making and using such microbial strains. Methane is an increasingly important global energy Source, both as the primary component of natural gas and as a biologically produced fuel. Currently, Sweden uses 100% renewable methane (biogas) in place of compressed natural gas (CNG) for transportation fue...
The opportunity to control and fine-tune the behavior of biological cells is a fascinating possibility for many diverse disciplines, ranging from medicine and ecology, to chemical industry and space exploration. While synthetic biology is providing novel tools to reprogram cell behavior from their genetic code, many challenges need to be solved bef...
Years of research in software engineering have given us novel ways to reason about, test, and predict the behavior of complex software systems that contain hundreds of thousands of lines of code. Many of these techniques have been inspired by nature such as genetic algorithms, swarm intelligence, and ant colony optimization. In this paper we revers...
Bacterial and archaeal genomes can contain 30% or more hypothetical genes with no predicted function. Phylogenetically deep-branching microbes, such as methane-producing archaea (methanogens), contain up to 50% genes with unknown function. In order to formulate hypotheses about the function of hypothetical gene functions in the strict anaerobe, Met...
Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit the...
Methane is an energy-dense fuel but is also a greenhouse gas 25 times more detrimental to the environment than CO2. Methane can be produced abiotically by serpentinization, chemically by Sabatier or Fisher-Tropsh chemistry, or biotically by microbes (Berndt et al., 1996; Horita and Berndt, 1999; Dry, 2002; Wolfe, 1982; Thauer, 1998; Metcalf et al.,...
Gene deletion and protein expression are cornerstone procedures for studying metabolism in any organism, including methane-producing archaea (methanogens). Methanogens produce coenzymes and cofactors not found in most bacteria, therefore it is sometimes necessary to express and purify methanogen proteins from the natural host. Protein expression in...
Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit the...
Methanogens are anaerobic archaea that grow by producing methane, a gas that is both an efficient renewable fuel and a potent greenhouse gas. We observed that overexpression of the cytoplasmic heterodisulfide reductase enzyme, HdrABC, increased methane production rate from methanol by 30% without affecting growth rate relative to the parent strain....
Multienzyme complexes catalyze important metabolic reactions in many organisms, but little is known about the complexes involved in biological methane production (methanogenesis). A crosslinking-mass spectrometry (XL-MS) strategy was employed to identify proteins associated with coenzyme M-coenzyme B heterodisulfide reductase (Hdr), an essential en...
Unlike most methanogenic microorganisms, Methanosarcina species are capable of utilizing a variety of growth substrates, a trait that greatly simplifies genetic analysis of the methanogenic process. The genetic tools and techniques discussed in this chapter form the basis for all genetic experiments in Methanosarcina acetivorans C2A and Methanosarc...
Cobamides are unique cyclic tetrapyrroles because their structures include an upper (Coβ) and a lower (Coα) axial ligand. The Coα and Coβ ligands are important for the interaction of the cobamide with enzymes, and for the chemistry of the reaction catalyzed by
the enzyme. B12 (5,6-dimethylbenzimidazolylcobamide, cobalamin) is the best-known cobamid...
Biochemical studies have revealed two distinct classes of Coenzyme B-Coenzyme M heterodisulfide (CoB-S-S-CoM) reductase (Hdr), a key enzyme required for anaerobic respiration in methane-producing archaea. A cytoplasmic HdrABC enzyme complex is found in most methanogens, whereas a membrane-bound HdrED complex is found exclusively in members of the o...
Aiming at the use of vitamin B12 as a drug delivery carrier for cytotoxic agents, we have reacted vitamin B12 with trans-[PtCl(NH3)2(H2O)]+, [PtCl3(NH3)](-) and [PtCl4](2-). These Pt(II) precursors coordinated directly to the Co(III)-bound cyanide, giving the conjugates [(Co)-CN-(trans-PtCl(NH3)2)]+ (5), [(Co)-CN-(trans-PtCl2(NH3))] (6), [(Co)-CN-(...
–8, 31P-NMR of 5 in phosphate buffer at pH 0.4 and crystallographic data for 5 and 7.
ATP:cob(I)alamin adenosyltransferase (EutT) of Salmonella enterica was overproduced and enriched to ∼70% homogeneity, and its basic kinetic parameters were determined. Abundant amounts of
EutT protein were produced, but all of it remained insoluble. Soluble active EutT protein (∼70% homogeneous) was obtained
after treatment with detergent. Under co...
Although methanogenic archaea use B(12) extensively as a methyl carrier for methanogenesis, little is known about B(12) metabolism in these prokaryotes or any other archaea. To improve our understanding of how B(12) metabolism differs between bacteria and archaea, the gene encoding the ATP:co(I)rrinoid adenosyltransferase in Methanosarcina mazei st...
The activity of the housekeeping ATP:co(I)rrinoid adenosyltransferase (CobA) enzyme of Salmonella enterica sv. Typhimurium is required to adenosylate de novo biosynthetic intermediates of adenosylcobalamin and to salvage incomplete and complete corrinoids from the environment of this bacterium. In vitro, reduced flavodoxin (FldA) provides an electr...
CobA from Salmonella enterica is a member of an enzymatic system responsible for the de novo biosynthesis of adenosylcobalamin (AdoCbl), catalyzing the formation of the essential Co-C bond by transferring the adenosyl group from a molecule of ATP to a transient Co(1+)corrinoid species generated in the enzyme active site. A particularly fascinating...
The eutT gene of Salmonella enterica was cloned and overexpressed, and the function of its product was established in vivo and in vitro. The EutT protein has an oxygen-labile, metal-containing ATP:co(I)rrinoid adenosyltransferase activity associated with it. Functional redundancy between EutT and the housekeeping ATP: co(I)rrinoid adenosyltransfera...
The eutT gene of Salmonella enterica was cloned and overexpressed, and the function of its product was established in vivo and in vitro. The EutT protein has
an oxygen-labile, metal-containing ATP:co(I)rrinoid adenosyltransferase activity associated with it. Functional redundancy
between EutT and the housekeeping ATP:co(I)rrinoid adenosyltransferas...
Co(2+)cobalmain (Co(2+)Cbl) is implicated in the catalytic cycles of all adenosylcobalamin (AdoCbl)-dependent enzymes, as in each case catalysis is initiated through homolytic cleavage of the cofactor's Co-C bond. The rate of Co-C bond homolysis, while slow for the free cofactor, is accelerated by 12 orders of magnitude when AdoCbl is bound to the...
The small heat shock proteins (sHSPs) are a ubiquitous class of ATP-independent chaperones believed to prevent irreversible
protein aggregation and to facilitate subsequent protein renaturation in cooperation with ATP-dependent chaperones. Although
sHSP chaperone activity has been studied extensively in vitro, understanding the mechanism of sHSP fu...
Small heat shock proteins (sHSPs) are dynamic oligomeric proteins that bind unfolding proteins and protect them from irreversible aggregation. This binding results in the formation of sHSP-substrate complexes from which substrate can later be refolded. Interactions between sHSP and substrate in sHSP-substrate complexes and the mechanism by which su...
The B(12) cofactors methylcobalamin (MeCbl) and 5'-deoxyadenosylcobalamin (AdoCbl) have long fascinated chemists because of their complex structures and unusual reactivities in biological systems; however, their electronic absorption (Abs) spectra have remained largely unassigned. In this study, we have used Abs, circular dichroism (CD), magnetic C...
The specificity of the ATP:corrinoid adenosyltransferase (CobA) enzyme of Salmonella entericaserovar Typhimurium LT2 for its nucleotide substrate was tested using ATP analogs and alternative nucleotide donors. The enzyme
showed broad specificity for the nucleotide base and required the 2′-OH group of the ribosyl moiety of ATP for activity. 31P NMR...