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Yang G, Wijma HJ, Rozeboom HJ, Mascotti ML, Fraaije MW. Identification and characterization of archaeal and bacterial F 420 -dependent thioredoxin reductases. FEBS J 2023; 290:4777-4791. [PMID: 37403630 DOI: 10.1111/febs.16896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
The thioredoxin pathway is an antioxidant system present in most organisms. Electrons flow from a thioredoxin reductase to thioredoxin at the expense of a specific electron donor. Most known thioredoxin reductases rely on NADPH as a reducing cofactor. Yet, in 2016, a new type of thioredoxin reductase was discovered in Archaea which utilize instead a reduced deazaflavin cofactor (F420 H2 ). For this reason, the respective enzyme was named deazaflavin-dependent flavin-containing thioredoxin reductase (DFTR). To have a broader understanding of the biochemistry of DFTRs, we identified and characterized two other archaeal representatives. A detailed kinetic study, which included pre-steady state kinetic analyses, revealed that these two DFTRs are highly specific for F420 H2 while displaying marginal activity with NADPH. Nevertheless, they share mechanistic features with the canonical thioredoxin reductases that are dependent on NADPH (NTRs). A detailed structural analysis led to the identification of two key residues that tune cofactor specificity of DFTRs. This allowed us to propose a DFTR-specific sequence motif that enabled for the first time the identification and experimental characterization of a bacterial DFTR.
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Affiliation(s)
- Guang Yang
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | - Hein J Wijma
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | | | - Maria Laura Mascotti
- Molecular Enzymology Group, University of Groningen, The Netherlands
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Argentina
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, The Netherlands
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2
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Kang SW, Antoney J, Lupton DW, Speight R, Scott C, Jackson CJ. Asymmetric Ene-Reduction by F 420 -Dependent Oxidoreductases B (FDOR-B) from Mycobacterium smegmatis. Chembiochem 2023; 24:e202200797. [PMID: 36716144 DOI: 10.1002/cbic.202200797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 01/31/2023]
Abstract
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.
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Affiliation(s)
- Suk Woo Kang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,Natural Products Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451 (Republic of, Korea
| | - James Antoney
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - David W Lupton
- School of Chemistry, Monash University, Melbourne, Victoria, 3800, Australia
| | - Robert Speight
- School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Colin Scott
- Environment, Commonwealth Scientific and Industrial Research Organization, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
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3
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
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.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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4
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Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions. Microbiol Mol Biol Rev 2016; 80:451-93. [PMID: 27122598 DOI: 10.1128/mmbr.00070-15] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
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.
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5
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Mao T, Show KY. Influence of ultrasonication on anaerobic bioconversion of sludge. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2007; 79:436-41. [PMID: 17489279 DOI: 10.2175/106143006x123049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The influence of ultrasonication on hydrolysis, acidogenesis, and methanogenesis in anaerobic decomposition of sludge was investigated. The sonicated sludge exhibited prehydrolysis and preacidogenesis effects in the anaerobic decomposition process. First-order hydrolysis rates increased from 0.0384 day(-1) in the control digester to 0.0672 day(-1) in the digester fed, with sludge sonicated at 0.52 W/mL. The sonication appeared to be ineffective in relation to acidogenesis reaction rates, but it provided a better buffering capacity to diminish the adverse effect of acidification. Digesters fed with sonicated sludge demonstrated enhanced methanogenesis over the control unit. Determination by coenzyme F420 verified that sonication is able to promote the growth of methanogenic biomass and facilitate a positive methanogenic microbial development in suppressing the initial methanogenesis limitation. The results suggest that ultrasonication could enhance anaerobic decomposition of sludge, resulting in an accelerated bioconversion, improved organics degradation, improved biogas production, and increased methane content.
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Affiliation(s)
- Taohong Mao
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
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6
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Kamagata Y, Mikami E. Some characteristics of two morphotypes of Methanothrix soehngenii from mesophilic anaerobic digesters. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/0922-338x(90)90062-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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7
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8
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Peck MW. Changes in concentrations of coenzyme F420 analogs during batch growth of Methanosarcina barkeri and Methanosarcina mazei. Appl Environ Microbiol 1989; 55:940-5. [PMID: 2729992 PMCID: PMC184228 DOI: 10.1128/aem.55.4.940-945.1989] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
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.
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Affiliation(s)
- M W Peck
- Institute of Food Research, Norwich Laboratory, United Kingdom
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9
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Schulze D, Menkhaus M, Fiebig R, Dellweg H. Anaerobic treatment of protein-containing waste waters: correlation between coenzyme F420 and methane production. Appl Microbiol Biotechnol 1988. [DOI: 10.1007/bf00269077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Gorris LG, van der Drift C, Vogels GD. Separation and quantification of cofactors from methanogenic bacteria by high-performance liquid chromatography: optimum and routine analyses. J Microbiol Methods 1988. [DOI: 10.1016/0167-7012(88)90018-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Gorris LG, de Kok TM, Kroon BM, van der Drift C, Vogels GD. Relationship between Methanogenic Cofactor Content and Maximum Specific Methanogenic Activity of Anaerobic Granular Sludges. Appl Environ Microbiol 1988; 54:1126-30. [PMID: 16347625 PMCID: PMC202615 DOI: 10.1128/aem.54.5.1126-1130.1988] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study we investigated whether a relationship exists between the methanogenic activity and the content of specific methanogenic cofactors of granular sludges cultured on different combinations of volatile fatty acids in upflow anaerobic sludge blanket or fluidized-bed reactors. Significant correlations were measured in both cases between the contents of coenzyme F
420
−2 or methanopterin and the maximum specific methanogenic activities on propionate, butyrate, and hydrogen, but not acetate. For both sludges the content of sarcinapterin appeared to be correlated with methanogenic activities on propionate, butyrate, and acetate, but not hydrogen. Similar correlations were measured with regard to the total content of coenzyme F
420
−4 and F
420
−5 in sludges from fluidized-bed reactors. The results indicate that the contents of specific methanogenic cofactors measured in anaerobic granular sludges can be used to estimate the hydrogenotrophic or acetotrophic methanogenic potential of these sludges.
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Affiliation(s)
- L G Gorris
- Department of Microbiology, Faculty of Science, University of Nijmegen, NL-6525 ED Nijmegen, The Netherlands
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12
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Kemp HA, Archer DB, Morgan MR. Enzyme-Linked Immunosorbent Assays for the Specific and Sensitive Quantification of
Methanosarcina mazei
and
Methanobacterium bryantii. Appl Environ Microbiol 1988; 54:1003-8. [PMID: 16347594 PMCID: PMC202587 DOI: 10.1128/aem.54.4.1003-1008.1988] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three microtitration plate enzyme-linked immunosorbent assays (ELISAs) have been developed: a competitive ELISA and a two-site (or indirect sandwich) ELISA for
Methanosarcina mazei
S6 and a two-site ELISA for
Methanobacterium bryantii
FR-2. The assays were sensitive, with limits of cell protein detection of 3 ng ml
−1
, 5 ng ml
−1
, and 50 ng ml
−1
, respectively, and showed good precision. The
M. mazei
assays used monoclonal antibodies and were entirely species specific, showing no cross-reaction with methanogens of other genera or with other species of the same genus. The
Methanobacterium bryantii
assay, which used two polyclonal antisera, showed only a slight cross-reaction with one other
Methanobacterium
species but no cross-reaction with methanogens of other genera. The use of the ELISAs for quantitative analysis of mixed cultures and of sewage sludge samples was investigated. Sludge diluted at 1:10
3
or more caused no significant interference in any of the three ELISAs. Various cultures of bacteria, methanogens, and nonmethanogens at a protein concentration of 50 μg ml
−1
showed no significant interference in the
M. mazei
competitive assay and the
Methanobacterium bryantii
two-site assay, although they did cause falsely low results in the
M. mazei
two-site assay.
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Affiliation(s)
- H A Kemp
- AFRC Institute of Food Research, Norwich Laboratory, Colney Lane, Norwich NR4 7UA, United Kingdom
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13
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Heine-Dobbernack E, Schoberth SM, Sahm H. Relationship of Intracellular Coenzyme F
420
Content to Growth and Metabolic Activity of
Methanobacterium bryantii
and
Methanosarcina barkeri. Appl Environ Microbiol 1988; 54:454-9. [PMID: 16347558 PMCID: PMC202472 DOI: 10.1128/aem.54.2.454-459.1988] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
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Affiliation(s)
- E Heine-Dobbernack
- Institut für Biotechnologie der Kernforschungsanlage Jülich, Postfach 1913, D-5170 Jülich 1, and Institut für Technologie der Bundesforschungsanstalt für Landwirtschaft, D-3300 Braunschweig, Federal Republic of Germany
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14
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Reynolds P, Colleran E. Evaluation and improvement of methods for coenzyme F420 analysis in anaerobic sludges. J Microbiol Methods 1987. [DOI: 10.1016/0167-7012(87)90032-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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16
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STAFFORD DAVIDA. Industrial Application and Commercialization of Anaerobic Digestion. Poult Sci 1987. [DOI: 10.3382/ps.0660934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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17
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Gorris L, Kemp H, Archer D. Quantification of methanogenic biomass by enzyme-linked immunosorbent assay and by analysis of specific methanogenic cofactors. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0144-4565(87)90047-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Estimation of microbial mass concentration based on fluorometric measurement of cell protein. ACTA ACUST UNITED AC 1986. [DOI: 10.1016/0385-6380(86)90028-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Whitmore T, Etheridge S, Stafford D, Leroff U, Hughes D. The evaluation of anaerobic digester performance by coenzyme F420 analysis. ACTA ACUST UNITED AC 1986. [DOI: 10.1016/0144-4565(86)90010-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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van Bruggen JJA, Zwart KB, van Assema RM, Stumm CK, Vogels GG. Methanobacterium formicicum, an endosymbiont of the anaerobic ciliateMetopus striatus McMurrich. Arch Microbiol 1984. [DOI: 10.1007/bf00692703] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Schneckenburger H, Reuter B, Schoberth S. Time-resolved microfluorescence for measuring coenzyme F420inMethanobacterium thermoautotrophicum. FEMS Microbiol Lett 1984. [DOI: 10.1111/j.1574-6968.1984.tb00727.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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22
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Time-resolved fluorescence microscopy for measuring specific coenzymes in methanogenic bacteria. Anal Chim Acta 1984. [DOI: 10.1016/s0003-2670(00)81514-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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