Occurrence of coenzyme F420 and its gamma-monoglutamyl derivative in nonmethanogenic archaebacteria

Asymmetric Ene-Reduction by F420 -Dependent Oxidoreductases B (FDOR-B) from Mycobacterium smegmatis

Asymmetric reduction by ene-reductases has received considerable attention in recent decades. While several enzyme families possess ene-reductase activity, the Old Yellow Enzyme (OYE) family has received the most scientific and industrial attention. However, there is a limited substrate range and few stereocomplementary pairs of current ene-reductases, necessitating the development of a complementary class. Flavin/deazaflavin oxidoreductases (FDORs) that use the uncommon cofactor F₄₂₀ have recently gained attention as ene-reductases for use in biocatalysis due to their stereocomplementarity with OYEs. Although the enzymes of the FDOR-As sub-group have been characterized in this context and reported to catalyse ene-reductions enantioselectively, enzymes from the similarly large, but more diverse, FDOR-B sub-group have not been investigated in this context. In this study, we investigated the activity of eight FDOR-B enzymes distributed across this sub-group, evaluating their specific activity, kinetic properties, and stereoselectivity against α,β-unsaturated compounds. The stereochemical outcomes of the FDOR-Bs are compared with enzymes of the FDOR-A sub-group and OYE family. Computational modelling and induced-fit docking are used to rationalize the observed catalytic behaviour and proposed a catalytic mechanism.

Glutamate: A multifunctional amino acid in plants

Glutamate (Glu) is a versatile metabolite and a signaling molecule in plants. Glu biosynthesis is associated with the primary nitrogen assimilation pathway. The conversion between Glu and 2-oxoglutarate connects Glu metabolism to the tricarboxylic acid cycle, carbon metabolism, and energy production. Glu is the predominant amino donor for transamination reactions in the cell. In addition to protein synthesis, Glu is a building block for tetrapyrroles, glutathione, and folate. Glu is the precursor of γ-aminobutyric acid that plays an important role in balancing carbon/nitrogen metabolism and various cellular processes. Glu can conjugate to the major auxin indole 3-acetic acid (IAA), and IAA-Glu is destined for oxidative degradation. Glu also conjugates with isochorismate for the production of salicylic acid. Accumulating evidence indicates that Glu functions as a signaling molecule to regulate plant growth, development, and defense responses. The ligand-gated Glu receptor-like proteins (GLRs) mediate some of these responses. However, many of the Glu signaling events are GLR-independent. The receptor perceiving extracellular Glu as a danger signal is still unknown. In addition to GLRs, Glu may act on receptor-like kinases or receptor-like proteins to trigger immune responses. Glu metabolism and Glu signaling may entwine to regulate growth, development, and defense responses in plants.

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.

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.

The Intersection of Geology, Geochemistry, and Microbiology in Continental Hydrothermal Systems

Decompressional boiling of ascending hydrothermal waters and separation into a vapor (gas) and a liquid phase drive extensive variation in the geochemical composition of hot spring waters. Yet little is known of how the process of phase separation influences the distribution of microbial metabolisms in springs. Here, we determined the variation in protein coding genes in 51 metagenomes from chemosynthetic hot spring communities that span geochemical gradients in Yellowstone National Park. The 51 metagenomes could be divided into 5 distinct groups that correspond to low and high temperatures and acidic and circumneutral/alkaline springs. A fifth group primarily comprised metagenomes from springs with moderate acidity and that are influenced by elevated volcanic gas input. Protein homologs putatively involved in the oxidation of sulfur compounds, a process that leads to acidification of spring waters, in addition to those involved in the reduction of sulfur compounds were enriched in metagenomes from acidic springs sourced by vapor phase gases. Metagenomes from springs with evidence for elevated volcanic gas input were enriched in protein homologs putatively involved in oxidation of those gases, including hydrogen and methane. Finally, metagenomes from circumneutral/alkaline springs sourced by liquid phase waters were enriched in protein homologs putatively involved in heterotrophy and respiration of oxidized nitrogen compounds and oxygen. These results indicate that the geological process of phase separation shapes the ecology of thermophilic communities through its influence on the availability of nutrients in the form of gases, solutes, and minerals. Microbial acidification of hot spring waters further influences the kinetic and thermodynamic stabilities of nutrients and their bioavailability. These data therefore provide an important framework to understand how geological processes have shaped the evolutionary history of chemosynthetic thermophiles and how these organisms, in turn, have shaped their geochemical environments.

A Novel F420-dependent Thioredoxin Reductase Gated by Low Potential FAD: A TOOL FOR REDOX REGULATION IN AN ANAEROBE

A recent report suggested that the thioredoxin-dependent metabolic regulation, which is widespread in all domains of life, existed in methanogenic archaea about 3.5 billion years ago. We now show that the respective electron delivery enzyme (thioredoxin reductase, TrxR), although structurally similar to flavin-containing NADPH-dependent TrxRs (NTR), lacked an NADPH-binding site and was dependent on reduced coenzyme F₄₂₀ (F₄₂₀H₂), a stronger reductant with a mid-point redox potential (E'₀) of -360 mV; E'₀ of NAD(P)H is -320 mV. Because F₄₂₀ is a deazaflavin, this enzyme was named deazaflavin-dependent flavin-containing thioredoxin reductase (DFTR). It transferred electrons from F₄₂₀H₂ to thioredoxin via protein-bound flavin; K_m values for thioredoxin and F₄₂₀H₂ were 6.3 and 28.6 μm, respectively. The E'₀ of DFTR-bound flavin was approximately -389 mV, making electron transfer from NAD(P)H or F₄₂₀H₂ to flavin endergonic. However, under high partial pressures of hydrogen prevailing on early Earth and present day deep-sea volcanoes, the potential for the F₄₂₀/F₄₂₀H₂ pair could be as low as -425 mV, making DFTR efficient. The presence of DFTR exclusively in ancient methanogens and mostly in the early Earth environment of deep-sea volcanoes and DFTR's characteristics suggest that the enzyme developed on early Earth and gave rise to NTR. A phylogenetic analysis revealed six more novel-type TrxR groups and suggested that the broader flavin-containing disulfide oxidoreductase family is more diverse than previously considered. The unprecedented structural similarities between an F₄₂₀-dependent enzyme (DFTR) and an NADPH-dependent enzyme (NTR) brought new thoughts to investigations on F₄₂₀ systems involved in microbial pathogenesis and antibiotic production.

The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria

F₄₂₀ is a low-potential redox cofactor that mediates the transformations of a wide range of complex organic compounds. Considered one of the rarest cofactors in biology, F₄₂₀ is best known for its role in methanogenesis and has only been chemically identified in two phyla to date, the Euryarchaeota and Actinobacteria. In this work, we show that this cofactor is more widely distributed than previously reported. We detected the genes encoding all five known F₄₂₀ biosynthesis enzymes (cofC, cofD, cofE, cofG and cofH) in at least 653 bacterial and 173 archaeal species, including members of the dominant soil phyla Proteobacteria, Chloroflexi and Firmicutes. Metagenome datamining validated that these genes were disproportionately abundant in aerated soils compared with other ecosystems. We confirmed through high-performance liquid chromatography analysis that aerobically grown stationary-phase cultures of three bacterial species, Paracoccus denitrificans, Oligotropha carboxidovorans and Thermomicrobium roseum, synthesized F₄₂₀, with oligoglutamate sidechains of different lengths. To understand the evolution of F₄₂₀ biosynthesis, we also analyzed the distribution, phylogeny and genetic organization of the cof genes. Our data suggest that although the F_o precursor to F₄₂₀ originated in methanogens, F₄₂₀ itself was first synthesized in an ancestral actinobacterium. F₄₂₀ biosynthesis genes were then disseminated horizontally to archaea and other bacteria. Together, our findings suggest that the cofactor is more significant in aerobic bacterial metabolism and soil ecosystem composition than previously thought. The cofactor may confer several competitive advantages for aerobic soil bacteria by mediating their central metabolic processes and broadening the range of organic compounds they can synthesize, detoxify and mineralize.

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.

Convenient synthesis of deazaflavin cofactor FO and its activity in F(420)-dependent NADP reductase

F420 and FO are phenolic 5-deazaflavin cofactors that complement nicotinamide and flavin redox coenzymes in biochemical oxidoreductases and photocatalytic systems. Specifically, these 5-deazaflavins lack the single electron reactivity with O2 of riboflavin-derived coenzymes (FMN and FAD), and, in general, have a more negative redox potential than NAD(P)(+). For example, F420-dependent NADP(+) oxidoreductase (Fno) is critical to the conversion of CO2 to CH4 by methanogenic archaea, while FO functions as a light-harvesting agent in DNA repair. The preparation of these cofactors is an obstacle to their use in biochemical studies and biotechnology. Here, a convenient synthesis of FO was achieved by improving the redox stability of synthetic intermediates containing a polar, electron-rich aminophenol fragment. Improved yields and simplified purification techniques for FO are described. Additionally, Fno activity was restored with FO in the absence of F420. Investigating the FO-dependent NADP(+)/NADPH redox process by stopped-flow spectrophotometry, steady state kinetics were defined as having a Km of 4.00 ± 0.39 μM and a kcat of 5.27 ± 0.14 s(-1). The preparation of FO should enable future biochemical studies and novel uses of F420 mimics.

The many roles of glutamate in metabolism

The amino acid glutamate is a major metabolic hub in many organisms and as such is involved in diverse processes in addition to its role in protein synthesis. Nitrogen assimilation, nucleotide, amino acid, and cofactor biosynthesis, as well as secondary natural product formation all utilize glutamate in some manner. Glutamate also plays a role in the catabolism of certain amines. Understanding glutamate's role in these various processes can aid in genome mining for novel metabolic pathways or the engineering of pathways for bioremediation or chemical production of valuable compounds.

The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations

The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.

A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T

BACKGROUND

Natrialba magadii is an aerobic chemoorganotrophic member of the Euryarchaeota and is a dual extremophile requiring alkaline conditions and hypersalinity for optimal growth. The genome sequence of Nab. magadii type strain ATCC 43099 was deciphered to obtain a comprehensive insight into the genetic content of this haloarchaeon and to understand the basis of some of the cellular functions necessary for its survival.

RESULTS

The genome of Nab. magadii consists of four replicons with a total sequence of 4,443,643 bp and encodes 4,212 putative proteins, some of which contain peptide repeats of various lengths. Comparative genome analyses facilitated the identification of genes encoding putative proteins involved in adaptation to hypersalinity, stress response, glycosylation, and polysaccharide biosynthesis. A proton-driven ATP synthase and a variety of putative cytochromes and other proteins supporting aerobic respiration and electron transfer were encoded by one or more of Nab. magadii replicons. The genome encodes a number of putative proteases/peptidases as well as protein secretion functions. Genes encoding putative transcriptional regulators, basal transcription factors, signal perception/transduction proteins, and chemotaxis/phototaxis proteins were abundant in the genome. Pathways for the biosynthesis of thiamine, riboflavin, heme, cobalamin, coenzyme F420 and other essential co-factors were deduced by in depth sequence analyses. However, approximately 36% of Nab. magadii protein coding genes could not be assigned a function based on Blast analysis and have been annotated as encoding hypothetical or conserved hypothetical proteins. Furthermore, despite extensive comparative genomic analyses, genes necessary for survival in alkaline conditions could not be identified in Nab. magadii.

CONCLUSIONS

Based on genomic analyses, Nab. magadii is predicted to be metabolically versatile and it could use different carbon and energy sources to sustain growth. Nab. magadii has the genetic potential to adapt to its milieu by intracellular accumulation of inorganic cations and/or neutral organic compounds. The identification of Nab. magadii genes involved in coenzyme biosynthesis is a necessary step toward further reconstruction of the metabolic pathways in halophilic archaea and other extremophiles. The knowledge gained from the genome sequence of this haloalkaliphilic archaeon is highly valuable in advancing the applications of extremophiles and their enzymes.

Enumeration of methanogens with a focus on fluorescence in situ hybridization

Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.

Methanogenesis in subglacial sediments

Methanogenic archaea have a unique role in Earth's global carbon cycle as producers of the greenhouse gas methane (CH4 ). However, despite the fact that ice covers 11% of Earth's continental landmass, evidence for methanogenic activity in subglacial environments has yet to be clearly demonstrated. Here we present genetic, biochemical and geochemical evidence indicative of an active population of methanogens associated with subglacial sediments from Robertson Glacier (RG), Canadian Rockies. Porewater CH4 was quantified in two subglacial sediment cores at concentrations of 16 and 29 ppmv. Coenzyme M (CoM), a metabolic biomarker for methanogens, was detected at a concentration of 1.3 nmol g sediment(-1) corresponding to ∼3 × 10(3) active cells g sediment(-1) . Genetic characterization of communities associated with subglacial sediments indicated the presence of several archaeal 16S rRNA and methyl CoM reductase subunit A (mcrA) gene phylotypes, all of which were affiliated with the euryarchaeal order Methanosarcinales. Further, CH4 was produced at 9-51 fmol g dry weight sediment(-1)  h(-1) in enrichment cultures of RG sediments incubated at 4°C. Collectively, these findings have important implications for the global carbon cycle in light of recent estimates indicating that the Earth's subglacial biome ranges from 10(4) to 10(6)  km(3) sediment.

In situ microbial metabolism as a cause of gas anomalies in ice

Isolated spikes of anomalously high concentrations of N(2)O have been reported at depths in Greenland and Antarctic ice cores corresponding to narrow time intervals over the past approximately 10(5) years. Now, using a calibrated spectrofluorimeter to map protein-bound Trp, a proxy for microbes, versus depth in the 3,053-m GISP2 ice core, we find six depths at which localized spikes of high cell concentrations coincide with N(2)O spikes. We show that the excess gases are consistent with accumulation of in situ metabolic wastes during residence times of the excess microbes in the ice. Because of sparseness of N(2)O measurements and our spectrofluorimetry versus depth, the total number of microbially produced N(2)O spikes in GISP2 is probably much larger than six. Spikes of excess methanogens coincident with CH(4) spikes are found at three depths in the bottom 3% of GISP2, most likely because of methanogenic metabolism in the underlying silty ice, followed by turbulent flow of the lowest approximately 90 m of ice. The apparent rates of in situ production of N(2)O and CH(4) spikes by metabolism are observed to be consistent with a single activation energy, U, and maintain proportionality to exp(-U/RT) over the entire temperature range down to -40 degrees C. Fluorescence of nonmicrobial aerosols in GISP2 ice is distinguishable from microbial fluorescence by its different emission spectra. Our spectrofluorimetric scans throughout the GISP2 ice core lead us to conclude that both microbes and nonmicrobial aerosols are deposited in discontinuous bursts, which may provide a tool for studying wind storms in the distant past.

Diffusion-controlled metabolism for long-term survival of single isolated microorganisms trapped within ice crystals

Two known habitats for microbial metabolism in ice are surfaces of mineral grains and liquid veins along three-grain boundaries. We propose a third, more general, habitat in which a microbe frozen in ice can metabolize by redox reactions with dissolved small molecules such as CO(2), O(2), N(2), CO, and CH(4) diffusing through the ice lattice. We show that there is an adequate supply of diffusing molecules throughout deep glacial ice to sustain metabolism for >10(5) yr. Using scanning fluorimetry to map proteins (a proxy for cells) and F420 (a proxy for methanogens) in ice cores, we find isolated spikes of fluorescence with intensity consistent with as few as one microbial cell in a volume of 0.16 microl with the protein mapper and in 1.9 microl with the methanogen mapper. With such precise localization, it should be possible to extract single cells for molecular identification.

Mycobacterium smegmatis mc2 155 fbiC and MSMEG_2392 are involved in triphenylmethane dye decolorization and coenzyme F420 biosynthesis

Mycobacteria can tolerate relatively high concentrations of triphenylmethane dyes such as malachite green and methyl violet. To identify mycobacterial genes involved in the decolorization of malachite green, a transposon mutant library of Mycobacterium smegmatis mc2 155 was screened for mutants unable to decolorize this dye. One of the genes identified was MSMEG_5126, an orthologue of Mycobacterium bovis fbiC encoding a 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) synthase, which is essential for the biosynthesis of the electron carrier coenzyme F420. The other gene identified was MSMEG_2392, encoding an alanine-rich protein with a DUF121 domain. The minimum inhibitory concentrations (MICs) for malachite green and methyl violet of the six fbiC mutants and two MSMEG_2392 mutants were one-third and one-fifth, respectively, of the MIC of the parent strain M. smegmatis mc2 155. Representative fbiC and MSMEG_2392 mutant strains were also sensitive to oxidative stress caused by the redox-cycling agents plumbagin and menadione, and the sensitivity was reversed in the complemented strains. HPLC analysis of representative fbiC and MSMEG_2392 strains revealed that, while the fbiC mutant lacked both coenzyme F420 and FO, the MSMEG_2392 mutant contained FO but not coenzyme F420. These results indicate that MSMEG_2392 is involved in the biosynthesis of coenzyme F420.

Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor

UV exposure of DNA molecules induces serious DNA lesions. The cyclobutane pyrimidine dimer (CPD) photolyase repairs CPD-type - lesions by using the energy of visible light. Two chromophores for different roles have been found in this enzyme family; one catalyzes the CPD repair reaction and the other works as an antenna pigment that harvests photon energy. The catalytic cofactor of all known photolyases is FAD, whereas several light-harvesting cofactors are found. Currently, 5,10-methenyltetrahydrofolate (MTHF), 8-hydroxy-5-deaza-riboflavin (8-HDF) and FMN are the known light-harvesting cofactors, and some photolyases lack the chromophore. Three crystal structures of photolyases from Escherichia coli (Ec-photolyase), Anacystis nidulans (An-photolyase), and Thermus thermophilus (Tt-photolyase) have been determined; however, no archaeal photolyase structure is available. A similarity search of archaeal genomic data indicated the presence of a homologous gene, ST0889, on Sulfolobus tokodaii strain7. An enzymatic assay reveals that ST0889 encodes photolyase from S. tokodaii (St-photolyase). We have determined the crystal structure of the St-photolyase protein to confirm its structural features and to investigate the mechanism of the archaeal DNA repair system with light energy. The crystal structure of the St-photolyase is superimposed very well on the three known photolyases including the catalytic cofactor FAD. Surprisingly, another FAD molecule is found at the position of the light-harvesting cofactor. This second FAD molecule is well accommodated in the crystal structure, suggesting that FAD works as a novel light-harvesting cofactor of photolyase. In addition, two of the four CPD recognition residues in the crystal structure of An-photolyase are not found in St-photolyase, which might utilize a different mechanism to recognize the CPD from that of An-photolyase.

Quantification of methanogens by fluorescence in situ hybridization with oligonucleotide probe

To monitor anaerobic environmental engineering system, new method of quantification for methanogens was tested. It is based on the measurement of specific binding (hybridization) of 16S rRNA-targeted oligonucleotide probe Arc915, performed by fluorescence in situ hybridization (FISH) and quantified by fluorescence spectrometry. Average specific binding of Arc915 probe was 13.4+/-0.5 amol/cell of autofluorescent methanogens. It was 14.3, 13.3, and 12.9 amol/cell at the log phase, at stationary phase and at the period of cell lysis of batch culture, respectively. Specific binding of Arc915 probe per 1 ml of microbial sludge suspension from anaerobic digester linearly correlated with concentration of autofluorescent cells of methanogens. Coefficient of correlation was 0.95. Specific binding of oligonucleotide probe Arc915 can be used for the comparative estimation of methanogens during anaerobic digestion of organic waste. Specific binding of Arc915 probe was linear function of anaerobic sludge concentration when it was between 1.4 and 14.0 mg/ml. Accuracy of the measurements in this region was from 5 to 12%.

Microorganisms metabolizing on clay grains in 3-km-deep Greenland basal ice

We have discovered > 10(8) microbial cells/cm3 attached to clay grains in the bottom 13 m of the GISP2 (Greenland Ice Sheet Project) ice core. Their concentration correlates with huge excesses of CO2 and CH4. We show that Fe-reducing bacteria produce most of the excess CO2 and methanogenic archaea produce the excess CH4. The number of attached cells per clay grain is proportional to grain perimeter rather than to area, which implies that nutrients are accessed at grain edges. We conclude that Fe-reducing microbes immobilized on clay surfaces metabolize via "shuttle" molecules that transport electrons to grain edges, where they reduce Fe(III) ions at edges to Fe(II) while organic acid ions are oxidized to CO2. Driven by the concentration gradient, electrons on Fe(II) ions at grain edges "hop" to Fe(III) ions inward in the same edges and oxidize them. The original Fe(III) ions can then attach new electrons from shuttle molecules at the edges. Our mechanism explains how Fe-reducers can reduce essentially all Fe(III) in clay minerals. We estimate that the Fe(III) in clay grains in the GISP2 silty ice can sustain Fe-reducing bacteria at the ambient temperature of -9 degrees C for approximately 10(6) years. F420 autofluorescence imaging shows that > 2.4% of the cells are methanogens, which account for the excess methane.

Microbial origin of excess methane in glacial ice and implications for life on Mars

Methane trapped in the 3,053-m-deep Greenland Ice Sheet Project 2 ice core provides an important record of millennial-scale climate change over the last 110,000 yr. However, at several depths in the lowest 90 m of the ice core, the methane concentration is up to an order of magnitude higher than at other depths. At those depths we have discovered methanogenic archaea, the in situ metabolism of which accounts for the excess methane. The total concentration of all types of microbes we measured with direct counts of Syto-23-stained cells tracks the excess of methanogens that we identified by their F420 autofluorescence and provides independent evidence for anomalous layers. The metabolic rate we estimated for microbes at those depths is consistent with the Arrhenius relation for rates found earlier for microbes imprisoned in rock, sediment, and ice. It is roughly the same as the rate of spontaneous macromolecular damage inferred from laboratory data, suggesting that microbes imprisoned in ice expend metabolic energy mainly to repair damage to DNA and amino acids rather than to grow. Equating the loss rate of methane recently discovered in the Martian atmosphere to the production rate by possible methanogens, we estimate that a possible Martian habitat would be at a temperature of approximately 0 degrees C and that the concentration, if uniformly distributed in a 10-m-thick layer, would be approximately 1 cell per ml.

Methanococcus jannaschii coenzyme F420 analogs contain a terminal alpha-linked glutamate

Analyses of the F(420)s present in Methanococcus jannaschii have shown that these cells contain a series of gamma-glutamyl-linked F(420)s capped with a single, terminal alpha-linked L-glutamate. The predominant form of F(420) was designated as alpha-F(420)-3 and represented 86% of the F(420)s in these cells. Analyses of Methanosarcina thermophila, Methanosarcina barkeri, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Mycobacterium smegmatis showed that they contained only gamma-glutamyl-linked F(420)s.

Large-scale production of coenzyme F420-5,6 by using Mycobacterium smegmatis

Production of coenzyme F420 and its biosynthetic precursor FO was examined with a variety of aerobic actinomycetes to identify an improved source for these materials. Based on fermentation costs, safety, and ease of growth, Mycobacterium smegmatis was the best source for F420-5,6. M. smegmatis produced 1 to 3 micromol of intracellular F420 per liter of culture, which was more than the 0.85 to 1.0 micromol of F420-2 per liter usually obtained with Methanobacterium thermoautotrophicum and approximately 10-fold higher than what was previously reported for the best aerobic actinomycetes. An improved chromatography system using rapidly flowing quaternary aminoethyl ion-exchange material and Florisil was used to more quickly and easily purify F420 than with previous methods.

Demonstration that fbiC is required by Mycobacterium bovis BCG for coenzyme F(420) and FO biosynthesis

Using the nitroimidazopyran-based antituberculosis drug PA-824 as a selective agent, transposon-generated Mycobacterium bovis strain BCG (M. bovis) mutants that could not make coenzyme F(420) were identified. Four independent mutants that could not make F(420) or the biosynthesis intermediate FO were examined more closely. These mutants contained transposons inserted in the M. bovis homologue of the Mycobacterium tuberculosis gene Rv1173, which we have named fbiC. Complementation of an M. bovis FbiC(-) mutant with fbiC restored the F(420) phenotype. These data demonstrate that fbiC is essential for F(420) production and that FbiC participates in a portion of the F(420) biosynthetic pathway between pyrimidinedione and FO. Homologues of fbiC were found in all 11 microorganisms that have been fully sequenced and that are known to make F(420). Four of these homologues (all from members of the aerobic actinomycetes) coded for proteins homologous over the entire length of the M. bovis FbiC, but in seven microorganisms two separate genes were found to code for proteins homologous with either the N-terminal or C-terminal portions of the M. bovis FbiC. Histidine-tagged FbiC overexpressed in Escherichia coli produced a fusion protein of the molecular mass predicted from the M. bovis BCG sequence (approximately 95,000 Da), as well as three other histidine-tagged proteins of significantly smaller size, which are thought to be proteolysis products of the FbiC fusion protein.

Identification of an archaeal 2-hydroxy acid dehydrogenase catalyzing reactions involved in coenzyme biosynthesis in methanoarchaea

Two putative malate dehydrogenase genes, MJ1425 and MJ0490, from Methanococcus jannaschii and one from Methanothermus fervidus were cloned and overexpressed in Escherichia coli, and their gene products were tested for the ability to catalyze pyridine nucleotide-dependent oxidation and reduction reactions of the following alpha-hydroxy-alpha-keto acid pairs: (S)-sulfolactic acid and sulfopyruvic acid; (S)-alpha-hydroxyglutaric acid and alpha-ketoglutaric acid; (S)-lactic acid and pyruvic acid; and 1-hydroxy-1,3,4,6-hexanetetracarboxylic acid and 1-oxo-1,3,4, 6-hexanetetracarboxylic acid. Each of these reactions is involved in the formation of coenzyme M, methanopterin, coenzyme F(420), and methanofuran, respectively. Both the MJ1425-encoded enzyme and the MJ0490-encoded enzyme were found to function to different degrees as malate dehydrogenases, reducing oxalacetate to (S)-malate using either NADH or NADPH as a reductant. Both enzymes were found to use either NADH or NADPH to reduce sulfopyruvate to (S)-sulfolactate, but the V(max)/K(m) value for the reduction of sulfopyruvate by NADH using the MJ1425-encoded enzyme was 20 times greater than any other combination of enzymes and pyridine nucleotides. Both the M. fervidus and the MJ1425-encoded enzyme catalyzed the NAD(+)-dependent oxidation of (S)-sulfolactate to sulfopyruvate. The MJ1425-encoded enzyme also catalyzed the NADH-dependent reduction of alpha-ketoglutaric acid to (S)-hydroxyglutaric acid, a component of methanopterin. Neither of the enzymes reduced pyruvate to (S)-lactate, a component of coenzyme F(420). Only the MJ1425-encoded enzyme was found to reduce 1-oxo-1,3,4,6-hexanetetracarboxylic acid, and this reduction occurred only to a small extent and produced an isomer of 1-hydroxy-1,3,4,6-hexanetetracarboxylic acid that is not involved in the biosynthesis of methanofuran c. We conclude that the MJ1425-encoded enzyme is likely to be involved in the biosynthesis of both coenzyme M and methanopterin.

Estimation of methanogen biomass by quantitation of coenzyme M

Determination of the role of methanogenic bacteria in an anaerobic ecosystem often requires quantitation of the organisms. Because of the extreme oxygen sensitivity of these organisms and the inherent limitations of cultural techniques, an accurate biomass value is very difficult to obtain. We standardized a simple method for estimating methanogen biomass in a variety of environmental matrices. In this procedure we used the thiol biomarker coenzyme M (CoM) (2-mercaptoethanesulfonic acid), which is known to be present in all methanogenic bacteria. A high-performance liquid chromatography-based method for detecting thiols in pore water (A. Vairavamurthy and M. Mopper, Anal. Chim. Acta 78:363-370, 1990) was modified in order to quantify CoM in pure cultures, sediments, and sewage water samples. The identity of the CoM derivative was verified by using liquid chromatography-mass spectroscopy. The assay was linear for CoM amounts ranging from 2 to 2,000 pmol, and the detection limit was 2 pmol of CoM/ml of sample. CoM was not adsorbed to sediments. The methanogens tested contained an average of 19.5 nmol of CoM/mg of protein and 0.39 +/- 0.07 fmol of CoM/cell. Environmental samples contained an average of 0.41 +/- 0.17 fmol/cell based on most-probable-number estimates. CoM was extracted by using 1% tri-(N)-butylphosphine in isopropanol. More than 90% of the CoM was recovered from pure cultures and environmental samples. We observed no interference from sediments in the CoM recovery process, and the method could be completed aerobically within 3 h. Freezing sediment samples resulted in 46 to 83% decreases in the amounts of detectable CoM, whereas freezing had no effect on the amounts of CoM determined in pure cultures. The method described here provides a quick and relatively simple way to estimate methanogenic biomass.

Function of coenzyme F420 in aerobic catabolism of 2,4, 6-trinitrophenol and 2,4-dinitrophenol by Nocardioides simplex FJ2-1A

2,4,6-Trinitrophenol (picric acid) and 2,4-dinitrophenol were readily biodegraded by the strain Nocardioides simplex FJ2-1A. Aerobic bacterial degradation of these pi-electron-deficient aromatic compounds is initiated by hydrogenation at the aromatic ring. A two-component enzyme system was identified which catalyzes hydride transfer to picric acid and 2,4-dinitrophenol. Enzymatic activity was dependent on NADPH and coenzyme F420. The latter could be replaced by an authentic preparation of coenzyme F420 from Methanobacterium thermoautotrophicum. One of the protein components functions as a NADPH-dependent F420 reductase. A second component is a hydride transferase which transfers hydride from reduced coenzyme F420 to the aromatic system of the nitrophenols. The N-terminal sequence of the F420 reductase showed high homology with an F420-dependent NADP reductase found in archaea. In contrast, no N-terminal similarity to any known protein was found for the hydride-transferring enzyme.

Molecular analysis of the gene encoding F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis

The gene fgd, which codes for F420-dependent glucose-6-phosphate dehydrogenase (FGD), was cloned from Mycobacterium smegmatis, and its sequence was determined and analyzed. A homolog of FGD which has a very high similarity to the M. smegmatis FGD-derived amino acid sequence was identified in Mycobacterium tuberculosis. FGD showed significant homology with F420-dependent N5,N10-methylene-tetrahydromethanopterin reductase (MER) from methanogenic archaea and with several hypothetical proteins from M. tuberculosis and Archaeoglobus fulgidus, but FGD showed no significant homology with NADP-dependent glucose-6-phosphate dehydrogenases. Multiple alignment of FGD and MER proteins revealed four conserved consensus sequences. Multiple alignment of FGD with the hypothetical proteins also revealed portions of the same conserved sequences. Moderately high levels of FGD were expressed in Escherichia coli BL21(DE3) carrying fgd in pBluescript.

Si-face stereospecificity at C5 of coenzyme F420 for F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis and F420-dependent alcohol dehydrogenase from Methanoculleus thermophilicus

Coenzyme F420 is a 5-deazaflavin. Upon reduction, 1,5-dihydro-coenzyme F420 is formed with a prochiral center at C5. In this study we report that the F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis and the F420-dependent alcohol dehydrogenase from Methanoculleus thermophilicus are Si-face stereospecific with respect to C5 of the 5-deazaflavin. These results were obtained by following the stereochemical course of the reversible incorporation of 3H into F420 from tritium-labeled substrates. Our findings bring to eight the number of coenzyme-F420-dependent enzymes shown to be Si-face stereospecific. No F420-dependent enzyme with Re-face stereospecificity is known. This is noteworthy since coenzyme F420 is functionally similar to pyridine nucleotides for which both Si-face and Re-face specific enzymes have been found.

Si-face stereospecificity at C5 of coenzyme F420 for F420-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase, F420-dependent N5,N10-methylenetetrahydromethanopterin reductase and F420H2:dimethylnaphthoquinone oxidoreductase

Coenzyme F420-dependent enzymes catalyze the reversible reduction of F420 by stereospecific hydride transfer to C5 of 5-deazaflavin. Two F420-dependent enzymes have been investigated with respect to the stereochemistry of hydride transfer, the F420-dependent NADP reductase and the F420-reducing hydrogenase. Both enzymes were found to be Si-face specific. In this study we report that three additional F420-dependent enzymes are also Si-face specific: N5,N10-methylenetetrahydromethanopterin dehydrogenase, N5,N10-methylenetetrahydromethanopterin reductase and coenzyme F420H2: dimethylnaphthoquinone oxidoreductase (F420H2 dehydrogenase). Thus, all five characterized F420-dependent enzymes are Si-face specific, which is noteworthy since coenzyme F420 is functionally similar to pyridine nucleotides and both Si-face specific and Re-face specific pyridine-nucleotide-dependent enzymes exist.

Effect of temperature on the spectral properties of coenzyme F420 and related compounds

The uv-visible spectra of 7,8-didemethyl-8-hydroxy-5-deazaflavin-5'-phosphoryllactyl glutamate (coenzyme F420), a naturally occurring 5-deazaflavin derivative, in three different buffers changed with a rise in temperature; the effect on the extinction coefficient at 420 nm (epsilon 420) was as follows: In phosphate-buffered solutions at pH less than 7.5, the epsilon 420 increased (at pH 5.0 for a temperature shift from 15 to 60 degrees C, delta epsilon 420 was +87%), but between pH 7.5 and 8, epsilon 420 changed very little. At pH greater than 8.0 in phosphate- or borate-buffered solutions, epsilon 420 decreased slightly. In morpholineethanesulfonic acid (Mes)-buffered F420 solutions at pH 5 and 5.5, epsilon 420 changed very little, whereas at pH 6-8, the epsilon 420 decreased. Absorbance of F420 at 401 nm in phosphate buffer at pH 5 to 9 was not significantly affected by temperature. Changes in epsilon 420 due to temperature change corresponded to changes in the pKa of 8-OH of the deazaflavin molecule; studies with adenylated F420 showed that the 8-OH of F420 was responsible for these changes.(ABSTRACT TRUNCATED AT 250 WORDS)

Biosynthetic precursors of deazaflavins

The incorporation of 13C- and 14C-labeled precursors into 5-deaza-7,8-didemethyl-8-hydroxyriboflavin (factor F0) was studied with growing cells of Methanobacterium thermoautotrophicum. 5-Amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione was incorporated into the deazaflavin and into riboflavin without dilution. Tyrosine and 4-hydroxyphenylpyruvate were incorporated into the deazaflavin and into cellular protein. 4-Hydroxybenzaldehyde was not incorporated. A reaction mechanism is proposed for the formation of the deazaflavin chromophore from 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione and tyrosine or 4-hydroxyphenylpyruvate.

Methyl-coenzyme M reductase and other enzymes involved in methanogenesis from CO2 and H2 in the extreme thermophile Methanopyrus kandleri

Methanopyrus kandleri belongs to a novel group of abyssal methanogenic archaebacteria that can grow at 110 degrees C on H2 and CO2 and that shows no close phylogenetic relationship to any methanogen known so far. Methyl-coenzyme M reductase, the enzyme catalyzing the methane forming step in the energy metabolism of methanogens, was purified from this hyperthermophile. The yellow protein with an absorption maximum at 425 nm was found to be similar to the methyl-coenzyme M reductase from other methanogenic bacteria in that it was composed each of two alpha-, beta- and gamma-subunits and that it contained the nickel porphinoid coenzyme F430 as prosthetic group. The purified reductase was inactive. The N-terminal amino acid sequence of the gamma-subunit was determined. A comparison with the N-terminal sequences of the gamma-subunit of methyl-coenzyme M reductases from other methanogenic bacteria revealed a high degree of similarity. Besides methyl-coenzyme M reductase cell extracts of M. kandleri were shown to contain the following enzyme activities involved in methanogenesis from CO2 (apparent Vmax at 65 degrees C): formylmethanofuran dehydrogenase, 0.3 U/mg protein; formyl-methanofuran:tetrahydro-methanopterin formyltransferase, 13 U/mg; N5,N10-methylenetetrahydromethanopterin cyclohydrolase, 14U/mg; N5,N10-methenyltetrahydromethanopterin dehydrogenase (H2-forming), 33 U/mg; N5,N10-methylenetetrahydromethanopterin reductase (coenzyme F420 dependent), 4 U/mg; heterodisulfide reductase, 2 U/mg; coenzyme F420-reducing hydrogenase, 0.01 U/mg; and methylviologen-reducing hydrogenase, 2.5 U/mg. Apparent Km values for these enzymes and the effect of salts on their activities were determined. The coenzyme F420 present in M. kandleri was identified as coenzyme F420-2 with 2-gamma-glutamyl residues.

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.

Characterization of an 8-hydroxy-5-deazaflavin:NADPH oxidoreductase from Streptomyces griseus

An 8-hydroxy-5-deazaflavin-dependent oxidoreductase was isolated from the actinomycete Streptomyces griseus and purified 590-fold with 72% overall yield. The enzyme catalyzes electron transfer between 8-hydroxy-5-deazaflavins and NADPH. It seems to be more specific than methanogenic oxidoreductase as it has an absolute requirement for both the 5-deazaflavin structure and the presence of an 8-hydroxy group in the substrate. A molecular weight of 42,000 was found with gel permeation chromatography, while SDS gel electrophoresis indicated the presence of two identical subunits. Maximal enzymatic activity was found at 0.32 M NaCl and pH 5.9 for reduction of 8-hydroxy-5-deazaflavin and pH 7.9 for the reverse reaction. From the kinetic constants it was estimated that the main function of this oxidoreductase is probably to provide cells with reduced 8-hydroxy-5-deazaflavin to be used in specific reduction reactions. These results indicate the occurrence of 8-hydroxy-5-deazaflavin-dependent electron transfer in microorganisms not belonging to the archaebacteria.

Structural diversity among methanofurans from different methanogenic bacteria

An examination of the methanofurans isolated from a wide range of methanogenic bacteria and from Archaeoglobus fulgidus has revealed at least five chromatographically distinct methanofurans. Bacteria from each major genus of methanogenic bacteria have been found to contain a chemically different methanofuran. The nature of the differences in the methanofurans appears to lie in the modification of the side chain attached to the basic core structure of 4-[N-(gamma-L-glutamyl-gamma-L-glutamyl)-p-(beta-aminoethyl)phenoxyme thy l]-2-(amino-methyl)furan. This was supported by the structural elucidation of the methanofuran isolated from Methanobrevibacter smithii, designated methanofuran-c, which was the same as the originally characterized methanofuran except for a hydroxy group at the 2 position of the 4,5-dicarboxyoctanedioic acid moiety of the molecule.

Folic acid and pteroylpolyglutamate contents of archaebacteria

Cell extracts of methanogens and the thermoacidophile Sulfolobus solfataricus contained little or no folic acid (pteroylglutamate) or pteroylpolyglutamate activity (less than 0.1 nmol/g [dry weight]). However, the halophile Halobacterium salinarum contained pteroylmono- or pteroyldiglutamates, and Halobacterium volcanii and Halobacterium halobium contained pteroyltriglutamates at levels equivalent to those in eubacteria (greater than 1 nmol/g [dry weight]).

Vitamin contents of archaebacteria

The levels of six water-soluble vitamins of seven archaebacterial species were determined and compared with the levels found in a eubacterium, Escherichia coli. Biotin, riboflavin, pantothenic acid, nicotinic acid, pyridoxine, and lipoic acid contents of Halobacterium volcanii, Methanobacterium thermoautotrophicum delta H, "Archaeoglobus fulgidus" VC-16, Thermococcus celer, Pyrodictium occultum, Thermoproteus tenax, and Sulfolobus solfataricus were measured by using bioassays. The archaebacteria examined were found to contain these vitamins at levels similar to or significantly below the levels found in in E. coli. Riboflavin was found at levels comparable to those in E. coli. Pyridoxine was as abundant among the archaebacteria of the methanogenhalophile branch as in E. coli. It was only one-half as abundant in the sulfur-metabolizing branch. "A. fulgidus," however, contained only 4% as much pyridoxine as E. coli. Nicotinic and pantothenic acids were approximately 10-fold less abundant (except for a 200-fold-lower nicotinic acid level in "A. fulgidus"). Nicotinic acid may be replaced by an 8-hydroxy-5-deazaflavin coenzyme (factor F420) in some archaebacteria (such as "A. fulgidus"). Compared with the level in E. coli, biotin was equally as abundant in Thermococcus celer and Methanobacterium thermoautotrophicum, about one-fourth less abundant in P. occultum and "A. fulgidus," and 25 to over 100 times less abundant in the others. The level of lipoic acid was up to 20 times lower in H. volcanii, Methanobacterium thermoautotrophicum, and Thermococcus celer. It was over two orders of magnitude lower among the remaining organisms. With the exception of "A. fulgidus," lipoic acid, pantothenic acid, and pyridoxine were more abundant in the members of the methanogen-halophile branch of the archaebacteria than in the sulfur-metabolizing branch.

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.