Levels of coenzyme F420, coenzyme M, hydrogenase, and methylcoenzyme M methylreductase in acetate-grown Methanosarcina

Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea

Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.

Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions

5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420 in methanogenic archaea in processes such as substrate oxidation, C1 pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Fo and F420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.

Production and Consumption of H(2) during Growth of Methanosarcina spp. on Acetate

Methanosarcina sp. strain TM-1 and Methanosarcina acetivorans produced and consumed H(2) to maintain H(2) partial pressures of 16 to 92 Pa in closed cultures during growth on acetate. Strain TM-1 produced H(2) continuously when H(2) was continuously removed from the culture. The potential physiological significance of H(2) in acetate metabolism to methane is discussed.

Interactions in syntrophic associations of endospore-forming, butyrate-degrading bacteria and h(2)-consuming bacteria

Butyrate is an important intermediate in the anaerobic degradation of organic matter. In sulfate-depleted environments butyrate is oxidized to acetate and hydrogen by obligate proton reducers, in syntrophic association with hydrogen-consuming methanogens. This paper describes two enrichments of endospore-forming bacteria degrading butyrate in consortia with methanogens. The isolates are readily established in coculture with H(2)-consuming, sulfate-reducing bacteria by pasteurizing the culture. The two original enrichments differed in that one grew to an optically dense culture while the second grew in clumps. Examination by scanning electron microscopy showed that clumping resulted from the production of large amounts of extracellular polymer. Several H(2)-consuming methanogens were identified in the enrichments. Some of them grew closely associated to the butyrate degraders. This attachment to the hydrogen producer may permit some methanogens to compete for the growth substrate against other bacteria having higher substrate affinity.

Isolation and Characterization of a Methylotrophic Marine Methanogen, Methanococcoides methylutens gen. nov., sp. nov

A new genus of marine methanogenic bacteria is described that utilizes trimethylamine, diethylamine, monomethylamine, and methanol as substrates for growth and methanogenesis. Methane was not produced from H(2)-CO(2), sodium formate, or sodium acetate. Growth on trimethylamine was stimulated by yeast extract, Trypticase (BBL Microbiology Systems, Cockeysville, Md.), rumen fluid, or B vitamins. The optimal growth temperature was 30 to 35 degrees C. The maximum growth rate was between pH 7.0 and 7.5. Na (0.4 M) and MgSO(4) (0.05 M) were required for maximum growth. Colonies of the type strain, TMA-10, were yellow, circular, and convex with entire edges. Cells were nonmotile, nonsporeforming, irregular cocci 1 mum in diameter which stained gram negative and occurred singly or in pairs. Micrographs of thin sections revealed a monolayered cell wall approximately 10-nm thick which consisted of protein. Cells were lysed in 0.01% sodium dodecyl sulfate or 0.001% Triton X-100. The DNA base composition was 42 mol% guanine plus cytosine. Methanococcoides is the proposed genus and Methanococcoides methylutens is the type species. TMA-10 is the type strain (ATCC 33938).

Methanogenesis in marine sediments

The anaerobic conversion of complex organic matter to CH(4) is an essential link in the global carbon cycle. In freshwater anaerobic environments, the organic matter is decomposed to CH(4) and CO(2) by a microbial food chain that terminates with methanogens that produce methane primarily by reduction of the methyl group of acetate and also reduction of CO(2). The process also occurs in marine environments, particularly those receiving large loads of organic matter, such as coastal sediments. The great majority of research on methanogens has focused on marine and freshwater CO(2)-reducing species, and freshwater acetate-utilizing species. Recent molecular, biochemical, bioinformatic, proteomic, and microarray analyses of the marine isolate Methanosarcina acetivorans has revealed that the pathway for acetate conversion to methane differs significantly from that in freshwater methanogens. Similar experimental approaches have also revealed striking contrasts with freshwater species for the pathway of CO-dependent CO(2) reduction to methane by M. acetivorans. The differences in both pathways reflect an adaptation by M. acetivorans to the marine environment.

Intensive aerobic bioconversion of sewage sludge and food waste into fertiliser

The aim of this research was to verify the possibility of recovering the nutrients present in sewage sludge and vegetable food waste as fertiliser after aerobic thermophilic intensive bioconversion. The process was performed in a closed reactor under controlled conditions of aeration, stirring and pH, at a temperature of 60 degrees C, after addition of a starter bacterial culture of Bacillus thermoamylovorans SW25. End product with the best fertilising properties was obtained when sewage sludge, mixed with food waste, CaCO3 and an artificial bulking agent was thermally pretreated. The content of volatile solids and organic carbon decreased from 82.8% to 62.3% and from 37.7% to 32.5% of total solids (TS) respectively, during 12 days of bioconversion. The stable organic fertiliser produced was a powder with moisture content of 5%. Furthermore, 3.4% of nitrogen, 0.4% of phosphorus and 2.9% of potassium were also present. Addition of 10-15g of this fertiliser to 1 kg of poor fertility soil increased the growth of different plants by 113-164%.

Reactor-scale cultivation of the hyperthermophilic methanarchaeon Methanococcus jannaschii to high cell densities

For the hyperthermophilic and barophilic methanarchaeon Methanococcus jannaschii, we have developed a medium and protocols for reactor-scale cultivation that improved the final cell yield per liter from approximately 0.5 to approximately 7.5 g of packed wet cells ( approximately 1.8 g dry cell mass) under autotrophic growth conditions and to approximately 8.5 g of packed wet cells ( approximately 2 g dry cell mass) with yeast extract (2 g liter(-1)) and tryptone (2 g liter(-1)) as medium supplements. For growth in a sealed bottle it was necessary to add Se to the medium, and a level of 2 microM for added Se gave the highest final cell yield. In a reactor M. jannaschii grew without added Se in the medium; it is plausible that the cells received Se as a contaminant from the reactor vessel and the H(2)S supply. But, for the optimal performance of a reactor culture, an addition of Se to a final concentration of 50 to 100 microM was needed. Also, cell growth in a reactor culture was inhibited at much higher Se concentrations. These observations and the data from previous work with methanogen cell extracts (B. C. McBride and R. S. Wolfe, Biochemistry 10:4312-4317, 1971) suggested that from a continuously sparged reactor culture Se was lost in the exhaust gas as volatile selenides, and this loss raised the apparent required level of and tolerance for Se. In spite of having a proteinaceous cell wall, M. jannaschii withstood an impeller tip speed of 235.5 cms(-1), which was optimal for achieving high cell density and also was the higher limit for the tolerated shear rate. The organism secreted one or more acidic compounds, which lowered pH in cultures without pH control; this secretion continued even after cessation of growth.

Conditions for vigorous growth on sulfide and reactor-scale cultivation protocols for the thermophilic green sulfur bacterium chlorobium tepidum

We describe a reactor-scale cultivation protocol for the fastest-growing and only known thermophilic member of the family Chlorobiaceae, Chlorobium tepidum. We discovered that C. tepidum would grow with sulfide as the sole electron source at rates and with final cell yields comparable to those found with thiosulfate only if the sulfide concentration was maintained below 0.1 mM and the culture redox potential was at -300 +/- 20 mV. Such was also the requirement for growth in a photobioreactor when thiosulfate (optimum level, 12 mM) was used as the preferred electron source. For cultivation of C. tepidum on a 5- to 500-ml scale, we used the system of Balch and Wolfe (Appl. Environ. Microbiol. 32:781-791, 1976) using stopper-sealed serum tubes and bottles as an alternative to the methods commonly used for the cultivation of phototrophic anaerobes and obtained consistent results.

Reductive dechlorination of 1,2-dichloroethane and chloroethane by cell suspensions of methanogenic bacteria

Concentrated cell suspensions of methanogenic bacteria reductively dechlorinated 1,2-dichloroethane via two reaction-mechanisms: a dihalo-elimination yielding ethylene and two hydrogenolysis reactions yielding chloroethane and ethane, consecutively. The transformation of chloroethane to ethane was inhibited by 1,2-dichloroethane. Stimulation of methanogenesis caused an increase in the amount of dechlorination products formed, whereas the opposite was found when methane formation was inhibited. Cells of Methanosarcina barkeri grown on H2/CO2 converted 1,2-dichloroethane and chloroethane at higher rates than acetate or methanol grown cells.

Changes in concentrations of coenzyme F420 analogs during batch growth of Methanosarcina barkeri and Methanosarcina mazei

Coenzyme F420 has been assayed by high-performance liquid chromatography with fluorimetric detection; this permits quantification of individual coenzyme F420 analogs whilst avoiding the inclusion of interfering material. The total intracellular coenzyme F420 content of Methanosarcina barkeri MS cultivated on methanol and on H2-CO2 and of Methanosarcina mazei S-6 cultured on methanol remained relatively constant during batch growth. The most abundant analogs in M. barkeri were coenzymes F420-2 and F420-4, whilst in M. mazei coenzymes F420-2 and F420-3 predominated. Significant changes in the relative proportions of the coenzyme F420 analogs were noted during batch growth, with coenzymes F420-2 and F420-4 showing opposite responses to each other and the same being also true for coenzymes F420-3 and F420-5. This suggests that an enzyme responsible for transferring pairs of glutamic acid residues may be active. The degradation fragment FO was also detected in cells in late exponential and stationary phase. Coenzyme F420 analogs were present in the culture supernatant of both methanogens, in similar proportions to that in the cells, except for FO which was principally located in the supernatant.

Presence of an Unusual Methanogenic Bacterium in Coal Gasification Waste

Methanogenic bacteria growing on a pilot-scale, anaerobic filter processing coal gasification waste were enriched in a mineral salts medium containing hydrogen and acetate as potential energy sources. Transfer of the enrichments to methanol medium resulted in the initial growth of a strain of Methanosarcina barkeri, but eventually small cocci became dominant. The cocci growing on methanol produced methane and exhibited the typical fluorescence of methanogenic bacteria. They grew in the presence of the cell wall synthesis-inhibiting antibiotics d -cycloserine, fosfomycin, penicillin G, and vancomycin as well as in the presence of kanamycin, an inhibitor of protein synthesis in eubacteria. The optimal growth temperature was 37°C, and the doubling time was 7.5 h. The strain lysed after reaching stationary phase. The bacterium grew poorly with hydrogen as the energy source and failed to grow on acetate. Morphologically, the coccus shared similarities with Methanosarcina sp. Cells were 1 μm wide, exhibited the typical thick cell wall and cross-wall formation, and formed tetrads. Packets and cysts were not formed.

Relationship of Intracellular Coenzyme F 420 Content to Growth and Metabolic Activity of Methanobacterium bryantii and Methanosarcina barkeri

The use of F 420 as a parameter for growth or metabolic activity of methanogenic bacteria was investigated. Two representative species of methanogens were grown in batch culture: Methanobacterium bryantii (strain M.o.H.G.) on H 2 and CO 2 , and Methanosarcina barkeri (strain Fusaro) on methanol or acetate. The total intracellular content of coenzyme F 420 was followed by high-resolution fluorescence spectroscopy. F 420 concentration in M. bryantii ranged from 1.84 to 3.65 μmol · g of protein −1 ; and in M. barkeri grown with methanol it ranged from 0.84 to 1.54 μmol · g −1 depending on growth conditions. The content of F 420 in M. barkeri was influenced by a factor of 2 depending on the composition of the medium (minimal or complex) and by a factor of 3 to 4 depending on whether methanol or acetate was used as the carbon source. A comparison of F 420 content with protein, cell dry weight, optical density, and specific methane production rate showed that the intracellular content of F 420 approximately followed the increase in biomass in both strains. In contrast, no correlation was found between specific methane production rate and intracellular F 420 content. However, qCH 4 (F 420 ), calculated by dividing the methane production rate by the coenzyme F 420 concentration, almost paralleled qCH 4 (protein). These results suggest that F 420 may be used as a specific parameter for estimating the biomass, but not the metabolic activity, of methanogens; hence qCH 4 (F 420 ) determined in mixed populations with complex carbon substrates must be considered as measure of the actual methanogenic activity and not as a measure of potential activity.

Acetate catabolism by Methanosarcina barkeri: evidence for involvement of carbon monoxide dehydrogenase, methyl coenzyme M, and methylreductase

The pathway of acetate catabolism in Methanosarcina barkeri strain MS was studied by using a recently developed assay for methanogenesis from acetate by soluble enzymes in cell extracts. Extracts incubated with [2-14C]acetate, hydrogen, and ATP formed 14CH4 and [14C]methyl coenzyme M as products. The apparent Km for acetate conversion to methane was 5 mM. In the presence of excess acetate, both the rate and duration of methane production was dependent on ATP. Acetyl phosphate replaced the cell extract methanogenic requirement for both acetate and ATP (the Km for ATP was 2 mM). Low concentrations of bromoethanesulfonic acid and cyanide, inhibitors of methylreductase and carbon monoxide dehydrogenase, respectively, greatly reduced the rate of methanogenesis. Precipitation of CO dehydrogenase in cell extracts by antibodies raised to 95% purified enzyme inhibited both CO dehydrogenase and acetate-to-methane conversion activity. The data are consistent with a model of acetate catabolism in which methylreductase, methyl coenzyme M, CO dehydrogenase, and acetate-activating enzymes are components. These results are discussed in relation to acetate uptake and rate-limiting transformation mechanisms in methane formation.

Growth substrate effects on acetate and methanol catabolism in Methanosarcina sp. strain TM-1

When Methanosarcina sp. strain TM-1 is grown in medium in which both methanol and acetate are present, growth is biphasic, with methanol used as the primary catabolic substrate during the first phase. To better understand this phenomenon, we grew cells on methanol or on acetate or on both and examined the abilities of anaerobically washed cells to catabolize these substrates. Washed acetate-grown cells incubated with 10 mM acetate, 10 mM methanol, or both substrates together produced methane at initial rates of 325, 3, and 315 nmol min-1 mg of protein-1, respectively. Although the initial rate of methanogenesis from both substrates was nearly identical to the rate for acetate alone, after several hours of incubation the rate was greater for cells provided with both substrates. Studies with 14C-labeled methanol indicated that methanol was catabolized to methane at increasing rates by acetate-grown cells in a manner reminiscent of an induction curve, but only when cells were provided with acetate as a cosubstrate. Acetate was presumably providing energy and carbon for induction of methanol-catabolic enzymes. Methanol-grown cells showed a pattern of substrate utilization significantly different from that of acetate-grown cells, producing methane from 10 mM acetate, 10 mM methanol, or both substrates at initial rates of 10, 280, and 450 nmol min-1 mg of protein-1, respectively. There was significant oxidation of the methyl group of acetate during metabolism of both substrates. Cells grown on methanol-acetate and harvested before methanol depletion (methanol phase) showed catabolic patterns nearly identical to those of methanol-grown cells, including a low rate of methanogenesis from acetate. Cells harvested from methanol-acetate cultures in the acetate phase were capable of significant methanogenesis from either methanol or acetate alone, and the rate from both substrates together was nearly equal to the sum of the rates for the single substrates. When both 10 mM methanol and 10 mM acetate were presented to the acetate-phase cells, there was a preference for the methanol. These results are consistent with a model for regulation in Methanosarcina sp. strain TM-1 in which methanol represses acetate catabolism while methanol catabolism is inducible.

Inhibition of methanogenesis and carbon metabolism in Methanosarcina sp. by cyanide

NaCN was tested for its inhibitory effects on growth of and metabolism by Methanosarcina barkeri 227. NaCN (10 microM) inhibited catabolism of acetate methyl groups to CH4 and CO2 but did not inhibit methanogenesis from methanol, CO2, methylamine, or trimethylamine. NaCN also inhibited the assimilation of methanol or CO2 (as the sole carbon source) into cell carbon and stimulated the assimilation of acetate. These results suggest that inhibition by NaCN was a result of its action as an inhibitor of in vivo CO dehydrogenase. The results also implicate CO dehydrogenase in the oxidation of acetate but not methanol methyl groups to CO2.

Identification of methyl coenzyme M as an intermediate in methanogenesis from acetate in Methanosarcina spp

The transfer of the methyl group of acetate to coenzyme M (2-mercaptoethanesulfonic acid; HS-CoM) during the metabolism of acetate to methane was investigated in cultures of Methanosarcina strain TM-1. The organism metabolized CD3COO- to 83% CD3H and 17% CD2H2 and produced no CDH3 or CH4. The isotopic composition of coenzyme M in cells grown on CD3COO- was analyzed with a novel gas chromatography-mass spectrometry technique. The cells contained CD3-D-CoM and CD2H-S-CoM) in a proportion similar to that of CD3H to CD2H2. These results, in conjunction with a report (J.K. Nelson and J.G. Ferry, J. Bacteriol. 160:526-532, 1984) that extracts of acetate-grown strain TM-1 contain high levels of CH3-S-CoM methylreductase, indicate that CH3-S-CoM is an intermediate in the metabolism of acetate to methane in this organism.

Carbon monoxide-dependent methyl coenzyme M methylreductase in acetotrophic Methosarcina spp

Cell extracts of acetate-grown Methanosarcina strain TM-1 and Methanosarcina acetivorans both contained CH3-S-CoM methylreductase activity. The methylreductase activity was supported by CO and H2 but not by formate as electron donors. The CO-dependent activity was equivalent to the H2-dependent activity in strain TM-1 and was fivefold higher than the H2-dependent activity of M. acetivorans. When strain TM-1 was cultured on methanol, the CO-dependent activity was reduced to 5% of the activity in acetate-grown cells. Methanobacterium formicicum grown on H2-CO2 contained no CO-dependent methylreductase activity. The CO-dependent methylreductase of strain TM-1 had a pH optimum of 5.5 and a temperature optimum of 60 degrees C. The activity was stimulated by the addition of MgCl2 and ATP. Both acetate-grown strain TM-1 and acetate-grown M. acetivorans contained CO dehydrogenase activities of 9.1 and 3.8 U/mg, respectively, when assayed with methyl viologen. The CO dehydrogenase of acetate-grown cells rapidly reduced FMN and FAD, but coenzyme F420 and NADP+ were poor electron acceptors. No formate dehydrogenase was detected in either organism when grown on acetate. The results suggest that a CO-dependent CH3-S-CoM methylreductase system is involved in the pathway of the conversion of acetate to methane and that free formate is not an intermediate in the pathway.

Methanogenic cleavage of acetate by lysates of Methanosarcina barkeri

Cell lysates of acetate-grown Methanosarcina barkeri 227 were found to cleave acetate to CH4 and CO2. The aceticlastic reaction was identified by using radioactive methyl-labeled acetate. Cell lysates decarboxylated acetate in a nitrogen atmosphere, conserving the methyl group in methane. The rate of methanogenesis from acetate in the cell lysates was comparable to that observed with whole cells. Aceticlastic activity was found in the particulate fraction seperate from methylcoenzyme M methylreductase activity, which occurs in the soluble fraction. Pronase treatment eliminated methylcoenzyme M methylreductase activity in lysates and stimulated aceticlastic activity, indicating the aceticlastic activity was not derived from unbroken cells, which are unaffected by proteolytic treatment.

Inhibition of the methylcoenzyme M methylreductase system by NAD+ and NADP+ in cell-extracts of Methanosarcina barkeri

In cell extracts of Methanosarcina barkeri, the methylcoenzyme M methylreductase system with H2 as the electron donor was inhibited by NAD+ and NADP+, but NADH and NADPH had no effect on enzyme activity. NAD+ (4 and 8 mM) shifted the saturation curve for methylcoenzyme M from hyperbolic (Hill coefficient [nH] = 1.0; concentration of substrate giving half maximal velocity [Km] = 0.21 mM) to sigmoidal (nH = 1.5 and 2.0), increased Km (Km = 0.25 and 0.34 mM), and slightly decreased Vmax. Similarly NADP+ at 4m and 8 mM increased nH to 1.6 and 1.85 respectively, but the Km values (0.3 and 0.56 mM) indicated that NADP+ was a more efficient inhibitor than NAD+.

Reversal of 2-bromoethanesulfonate inhibition of methanogenesis in Methanosarcina sp

2-Bromoethanesulfonate (BES) inhibition of methanogenesis from methanol by resting-cell suspensions or cell extracts of Methanosarcina was reversed by coenzyme M. BES inhibition of methylcoenzyme M methylreductase activity in cell-free extracts was reversed by methylcoenzyme M but not by coenzyme M. Methanol/coenzyme M methyltransferase activity was not inhibited by 10 microM BES. Inhibition of methylreductase by BES and 3-bromopropionate was competitive with methylcoenzyme M, but inhibition by 2-bromoethanol exhibited mixed kinetics. The Ki values for the inhibitors in cell-free extracts were similar to the concentrations which inhibited intact cells. BES-resistant mutants of strain 227 were apparently permeability mutants because in vitro assays showed that mutant and parent strain methylreductases were equally sensitive to BES.