Distribution of transition metal ions in multiple forms of Methanosarcina hydrogenase

There were significant levels of in vitro hydrogenase activity in Methanosarcina strains. The multiple forms of hydrogenase were observed in cell free extracts of cells grown on methanol. Strains having poor growth on H₂ : CO₂ had four forms while strains having normal growth on all substrates contained two forms of hydrogenase. These multiple forms differ in their charges as well as in their composition of transition metal ions. The strain having normal growth showed higher incorporation of ⁶³Ni²⁺ and ⁶⁵Zn²⁺. Both hydrogenases, A and D, of strain P₃ had methylviologen and F₄₂₀-reducing activity and contained Zn²⁺ and Co²⁺ respectively. Hydrogenases A and D of strains P₁ and P₄ also had similar characteristics whereas hydrogenases B and C had only methylviologen reducing activity.     

Microbial growth by a net heat up-take: a calorimetric and thermodynamic study on acetotrophic methanogenesis by Methanosarcina barkeri

To answer the intriguing question whether or not endothermic microbial growth exists, and in particular, to verify Heijnen and van Dijken's prediction (1992), acetotrophic methanogen, Methanosarcina barkeri, has been cultivated in a highly sensitive bench-scale calorimeter (an improved Bio-RC1 reaction calorimeter) in a pH auxostat fashion. A growth yield of 0.043 C-mol C-mol(-1) has been obtained and a cell density as high as 3 g L(-1) was attained. Heat uptake during growth has indeed been quantitatively measured with calorimetry, resulting in a heat yield of +145 kJ C-mol(-1). Thermodynamics of the growth of acetotrophic methanogens was analyzed in detail. The changes in Gibbs energy, enthalpy, and entropy during growth of M. barkeri were compared with some typical aerobic and anaerobic growth processes of different microorganisms on various substrates. In the growth of M. barkeri on acetate, the retarding effect of the positive enthalpy change on the driving force of growth is overcompensated by the large positive entropy change, resulting from converting one organic molecule (acetic acid) to two gaseous products, CH(4) and CO(2). Both the enthalpy and the entropy increases are due partially to the transition of these two products into the gaseous phase. The thermodynamic role of this phase transition for the growth process is analyzed. Microbial growth characterized by enthalpy increase and correspondingly by a large increase in entropy may be called enthalpy-retarded growth.     

Single replication origin of the archaeon Methanosarcina mazei revealed by the Z curve method

The genomic sequence of the archaeon Methanosarcina mazei has been analyzed by the Z curve method. The Z curve is a three-dimensional curve that uniquely represents the given DNA sequence. The three-dimensional Z curve and its x and y components for the genome of M. mazei show a sharp peak and relatively broad peak, respectively. The cdc6 gene is located exactly at the position of the sharp peak. Based on the known behavior of the Z curves for the archaea whose replication origins have been identified, we hypothesize that the replication origin and termination sites correspond to the positions of the sharp peak and broad peak, respectively. We have located an intergenic region that is between the cdc6 gene (MM1314) and the gene for an adjacent protein (MM1315), which shows strong characteristics of the known replication origins. This region is highly rich in AT and contains multiple copies of consecutive repeats. Our results strongly suggest that the single replication origin of M. mazei is situated at the intergenic region between the cdc6 gene and the gene for the adjacent protein, from 1,564,657 to 1,566,241 bp of the genome.     

Genetic and proteomic analyses of CO utilization by <Emphasis Type="Italic">Methanosarcina acetivorans</Emphasis>

Methanosarcina acetivorans, a member of the methanogenic archaea, can grow with carbon monoxide (CO) as the sole energy source and generates, unlike other methanogens, substantial amounts of acetate and formate in addition to methane. Phenotypic analyses of mutant strains lacking the cooS1F operon and the cooS2 gene suggest that the monofunctional carbon monoxide dehydrogenase (CODH) system contributes to, but is not required for, carboxidotrophic growth of M. acetivorans. Further, qualitative proteomic analyses confirm a recent report (Lessner et al., Proc Natl Acad Sci USA, 103:17921–17926, 2006) in showing that the bifunctional CODH/acetyl-CoA synthase (ACS) system, two enzymes involved in CO₂-reduction, and a peculiar protein homologous to both corrinoid proteins and methyltransferases are synthesized at elevated levels in response to CO; however, the finding that the latter protein is also abundant when trimethylamine serves as growth substrate questions its proposed involvement in the reduction of methyl-groups to methane. Potential catabolic mechanisms and metabolic adaptations employed by M. acetivorans to effectively utilize CO are discussed.     

Membrane-bound F420H2-dependent heterodisulfide reduction in Methanococcus voltae

Washed membranes prepared from H₂+CO₂- or formate-grown cells of Methanococcus voltae catalyzed the oxidation of coenzyme F₄₂₀H₂ and the reduction of the heterodisulfide (CoB–S–S–CoM) of 2-mercaptoethanesulfonate and 7-mercaptoheptanoylthreonine phosphate, which is the terminal electron acceptor of the methanogenic pathway. The reaction followed a 1:1 stoichiometry according to the equation: F₄₂₀H₂ + COB–S–S–CoM → F₄₂₀ + CoM–SH + CoB–SH. These findings indicate that the reaction depends on a membrane-bound F₄₂₀H₂-oxidizing enzyme and on the heterodisulfide reductase, which remains partly membrane-bound after cell lysis. To elucidate the nature of the F₄₂₀H₂-oxidizing protein, washed membranes were solubilized with detergent, and the enzyme was purified by sucrose density centrifugation, anion-exchange chromatography, and gel filtration. Several lines of evidence indicate that F₄₂₀H₂ oxidation is catalyzed by a membrane-associated F₄₂₀-reducing hydrogenase. The purified protein catalyzed the H₂-dependent reduction of methyl viologen and F₄₂₀. The apparent molecular mass and the subunit composition (43, 37, and 27 kDa) are almost identical to those of the F₄₂₀-reducing hydrogenase that has already been purified from Mc. voltae. Moreover, the N-terminus of the 37-kDa subunit is identical to the amino acid sequence deduced from the fruG gene of the operon encoding the selenium-containing F₄₂₀-reducing hydrogenase from Mc. voltae. A distinct F₄₂₀H₂ dehydrogenase, which is present in methylotrophic methanogens, was not found in this organism. Received: 18 September 1998 / Accepted: 2 November 1998     

γ -Ray-Induced DNA Damage and Repair in Methanosarcina barkeri

The capacity of the mesophilic archaeon, Methanosarcina barkeri (DSM 804) for DNA double strand break repair following⁶⁰Co- γ irradiation was investigated. The genome (1.9 Mb) of Methanosarcina barkeri was largely fragmented and was found to be repaired on incubation in medium under anaerobic conditions at 37°C for 4 h. To get an insight into its repair process a set of inhibitors were used. The methanogenesis inhibitor, bromoethanesulfonate showed partial inhibition of repair in Methanosarcina barkeri but not in Escherichia coli or human peripheral blood mononuclear cells. The Methanosarcina barkeri cells could also partially repair the DNA damage in a non-nutrient medium. Arabinosine-CTP, a nucleoside analogue and a polymerase inhibitor, completely inhibited repair in this archaeon. Arabinosine-CTP did not affect DSB (double-strand break) repair in human peripheral blood mononuclear cells but completely inhibited repair in Escherichia coli (a bacterium). The involvement of polymerase indicates recombination to be the underlying mechanism in DSB repair of Methanosarcina barkeri. 3-Aminobenzamide, a poly (ADP-ribose) polymerase inhibitor, completely inhibited repair in this archaeon as well as in eukarya but not in Escherichia coli showing the involvement of poly (ADP-ribose) polymerase in the DSB repair of Methanosarcina barkeri.     

Acetate threshold values and acetate activating enzymes in methanogenic bacteria

Abstract The minimum threshold concentrations of acetate utilization and the enzymes responsible for acetate activation of several methanogenic bacteria were investigated and compared with literature data. The minimum acetate concentrations reached by hydrogenotrophic methane bacteria, which require acetate as carbon source, were between 0.4 and 0.6 mM. The acetoclastic Methanosarcina achieves acetate concentrations between 0.2 and 1.2 mM and Methanothrix between 7 and 70 μM. For the activation of acetate most of the hydrogenotrophic methane bacteria investigated use an acetyl-CoA synthetase with a relatively low K _m (40–90 μM) for acetate. although the affinity for acetate was high, the hydrogenotrophic methane bacteria were not able to remove acetate to lower concentrations than the acetoclastic methane bacteria, neither in pure cultures nor in anaerobic granular sludge samples. Based on these observations, it is not likely that hydrogenotrophic methanogens compete strongly for acetate with the acetoclastic methane bacteria.     

Kinetic mechanism for the ability of sulfate reducers to out-compete methanogens for acetate

Methanosarcina barkeri and Desulfobacter postgatei are ubiquitous anaerobic bacteria which grow on acetate or acetate plus sulfate, respectively, as sole energy sources. Their apparent K _s values for acetate were determined and found to be approximately 0.2 mM for the sulfate-reducing bacterium and 3 mM for the methanogenic bacterium. In mixed cell suspensions of the two bacteria (adjusted to equal V _max) the rate of acetate consumption by D. postgatei approached 15-fold the rate of M. barkeri at low acetate concentrations. The apparent inhibition of methanogenesis was of the same order as expected from the different K _s value for acetate. Difference in substrate affinities can thus account for the inhibition of methanogenesis from acetate in sulfate-rich environments, where the acetate concentration is well below 1 mM.