Open access peer-reviewed chapter

Searching for Metabolic Pathways of Anaerobic Digestion: A Useful List of the Key Enzymes

Written By

Anna Sikora, Anna Detman, Damian Mielecki, Aleksandra Chojnacka and Mieczysław Błaszczyk

Submitted: May 29th, 2018 Reviewed: September 1st, 2018 Published: November 5th, 2018

DOI: 10.5772/intechopen.81256

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Abstract

The general scheme of anaerobic digestion is well known. It is a complex process promoted by the interaction of many groups of microorganisms and has four major steps: hydrolysis, acidogenesis, acetogenesis, and methanogenesis. The aim of the study was to prepare a systematized list of the selected enzymes responsible for the key pathways of anaerobic digestion based on the Kyoto Encyclopedia of Genes and Genomes database resource. The list contains (i) key groups of hydrolases involved in the process of degradation of organic matter; (ii) the enzymes catalyzing reactions leading to pyruvate formation; (iii) the enzymes of metabolic pathways of further pyruvate transformations; (iv) the enzymes of glycerol transformations; (v) the enzymes involved in transformation of gaseous or nongaseous products of acidic fermentations resulting from nonsyntrophic nutritional interactions between microbes; (vi) the enzymes of amino acid fermentations; (vii) the enzymes involved in acetogenesis; and (viii) the enzymes of the recognized pathways of methanogenesis. Searching for the presence and activity of the enzymes as well as linking structure and function of microbial communities allows to develop a fundamental understanding of the processes, leading to methane production. In this contribution, the present study is believed to be a piece to the enzymatic road map of anaerobic digestion research.

Keywords

  • anaerobic digestion
  • enzymes
  • hydrolysis
  • acidogenesis
  • acetogenesis
  • methanogenesis
  • syntrophy
  • metabolic pathways

1. Introduction

Anaerobic digestion (AD), whose final products are methane and carbon dioxide, is a common process in natural anoxic environments such as water sediments, wetlands, or marshlands. The environments have to be rich in organic matter and poor with other electron acceptors such as nitrate, compounds containing oxidized forms of metals, and sulfate. AD is also common in landfills and wastewater treatment plants and was used by man to produce biogas from waste biomass as an alternative energy source.

AD is a complex process that requires the metabolic interaction of many groups of microorganisms responsible for four closely related major steps. The first one is hydrolysis of complex organic polymers (e.g., polysaccharides, lipids, proteins) to monomers (sugars, fatty acids, amino acids). The second step is acidogenesis that results in formation of hydrogen and carbon dioxide as well as nongaseous fermentation products, that is, low-molecular-weight organic acids and alcohols. These products are further oxidized to hydrogen, carbon dioxide, and acetate in acetogenic step that involves mainly syntrophic degradation of nongaseous fermentation products. The fourth step is methanogenesis. Three groups of substrates for methane production and three types of methanogenic pathways are known: splitting of acetate (aceticlastic/acetotrophic methanogenesis); reduction of CO2 with H2 or formate and rarely ethanol or secondary alcohols as electron donors (hydrogenotrophic methanogenesis); and reduction of methyl groups of methylated compounds such as methanol, methylated amines, or methylated sulfides (hydrogen-dependent and hydrogen-independent methylotrophic methanogenesis). The two last steps, acetogenesis and methanogenesis, are closely related and involve syntrophic associations between hydrogen-producing acetogenic bacteria and hydrogenotrophic methanogens (Figure 1) [1, 2, 3, 4, 5].

Figure 1.

A scheme of anaerobic digestion of organic matter. Enzymes catalysing specific reactions of AD are presented in Tables 14. Thus in Figure 1 there are the links to Tables 14. Furthermore, background colours in the Figure correspond to the background colours of the title rows in the Tables 14: hydrolysis is indicated in green, acidogenesis in orange, acetogenesis in blue and methanogenesis in yellow. A, B, C, D, E refer to the title rows in Table 2; F, G refer to the title rows in Table 3.

Recently, there has been a rapid development in culture-independent techniques (meta-omics approaches such as metagenomics, metatranscriptomics, metaproteomics, metabolomics) for exploring microbial communities, which have led to a new insight into their structure and function in both natural environments and anaerobic digesters. The current trends involve the combined use of meta-omic approaches and detailed reactor performance data as well as isotope labeling techniques that allow us to develop a fundamental understanding of the processes occurring in AD. Those activities are aimed to improve biogas production and increase the share of renewable energy in total energy consumption [6, 7, 8, 9].

Analysis of many studies on metagenomes of microbial communities from anaerobic digesters shows that (i) contribution of methanogens in the methane-yielding microbial communities is relatively small, below 20%; (ii) the most abundant phyla of bacteria are usually Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria; (iii) methanogenic archaea are dominated by acetotrophs or hydrogenotrophs with a certain contribution of methylotrophs; (iv) substrate, operational conditions such as temperature, pH, ammonia concentration, etc. shape the structure, percentage distribution of specific taxons, and functioning of the community of microorganisms; (v) it is important to describe interactions within microbial communities and assign functions in AD steps to specific groups of microbes; and (vi) the majority of sequences are not classified at the genus level confirming that most of the microorganisms are still unrecognized [6, 10, 11, 12, 13, 14, 15].

In this contribution, the purpose of the study was to prepare a list of the selected enzymes and their catalyzed reactions, being a specific enzymatic road map of AD metabolic pathways, useful in molecular studies. The available metabolic pathway databases such as KEGG PATHWAY Database [16, 17, 18], MetaCyc Metabolic Pathway Database, BioCyc Database Collection [19], and BRENDA—The Comprehensive Enzyme Information System [20] were used to select metabolic pathways dedicated only to AD from hydrolysis to methanogenic steps exerted by microbes.

Hydrolytic enzyme Reaction/process EC number
Esterases Acting on ester bonds EC 3.1
Glycosidases Acting on glycoside bonds EC 3.2
Acting on cellulose
Cellulase; endo-1,4-beta-d-glucanase Endohydrolysis of (1 → 4)-beta-d-glucosidic linkages in cellulose, lichenin, and cereal beta-d-glucans EC 3.2.1.4
Cellulose 1,4-beta-cellobiosidase (nonreducing end) Hydrolysis of (1 → 4)-beta-d-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the nonreducing ends of the chains EC 3.2.1.91
Beta-glucosidase Hydrolysis of terminal, nonreducing beta-d-glucosyl residues with release of beta-d-glucose EC 3.2.1.21
Acting on hemicellulose
Endo-1,4-beta-xylanase Endohydrolysis of (1 → 4)-beta-d-xylosidic linkages in xylans EC 3.2.1.8
Xylan 1,4-beta-xylosidase Hydrolysis of (1 → 4)-beta-d-xylans, to remove successive D-xylose residues from the nonreducing termini EC 3.2.1.37
Mannan endo-1,4-beta-mannosidase Random hydrolysis of (1 → 4)-beta-d-mannosidic linkages in mannans, galactomannans, and glucomannans EC 3.2.1.78
Beta-mannosidase Hydrolysis of terminal, nonreducing beta-d-mannose residues in beta-d-mannosides EC 3.2.1.25
Alpha-galactosidase Hydrolysis of terminal, nonreducing alpha-d-galactose residues in alpha-d-galactosides, including galactose oligosaccharides, galactomannans,and galactolipids EC 3.2.1.22
Alpha-glucuronidase An alpha-d-glucuronoside + H2O → an alcohol + d-glucuronate EC 3.2.1.139
Peptidases Acting on peptide bonds EC 3.4
Other hydrolases
Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds EC 3.5
Hydrolases acting on ether bonds EC 3.3
Hydrolases acting on carbon-carbon bonds EC 3.7
Hydrolases acting on halide bonds EC 3.8
Hydrolases acting on phosphorus-nitrogen bonds EC 3.9
Hydrolases acting on sulfur-nitrogen bonds EC 3.10
Hydrolases acting on carbon-phosphorus bonds EC 3.11
Hydrolases acting on sulfur-sulfur bonds EC 3.12
Hydrolases acting on carbon-sulfur bonds EC 3.13
Hydrolases acting on acid anhydrides EC 3.6

Table 1.

The selected enzymes of hydrolytic step of anaerobic digestion [21, 22].

Enzyme Reaction/process EC number
A. Pyruvate formation from carbohydrates [23]
Glycolysis (the Embden-Meyerhof-Parnas pathway)
Hexose kinase D-Glucose + ATP ↔ D-glucose-6-phosphate + ADP EC 2.7.1.1
Phosphoglucose isomerase D-Glucose 6-phosphate ↔ D-fructose 6-phosphate EC 5.3.1.9
Phosphofructose kinase ATP + D-fructose 6-phosphate ↔ ADP + D-fructose 1,6-bisphosphate EC 2.7.1.11
Fructose-bisphosphate aldolase Fructose-1,6-bisphosphate ↔ dihydroxyacetone phosphate + glyceraldehyde-3-phosphate EC 4.1.2.13
Triose phosphate isomerase Glyceraldehyde 3-phosphate ↔ dihydroxyacetone phosphate EC 5.3.1.1
Glyceraldehyde-3-phosphate dehydrogenase D-Glyceraldehyde 3-phosphate + phosphate + NAD+ ↔ 1,3-bisphosphoglycerate + NADH + H+ EC 1.2.1.12
Phosphoglycerate kinase 1,3-Bisphosphoglycerate + ADP ↔ 3-phosphoglycerate + ATP EC 2.7.2.3
Phosphoglycerate mutase 3-Phosphoglycerate ↔ 2-phosphoglycerate EC 5.4.2.1
Enolase 2-Phospho-D-glycerate ↔ phosphoenolpyruvate + H2O EC 4.2.1.11
Pyruvate kinase Phosphoenolpyruvate + ADP ↔ pyruvate + ATP EC 2.7.1.40
2-Keto-3-deoxy-6-phosphogluconate (the Entner-Doudoroff pathway)
Glucose-6-phosphate dehydrogenase D-glucose 6-phosphate + NADP+ ↔ 6-phospho-D-glucono-1,5-lactone + NADPH + H+ EC 1.1.1.49
Phosphogluconate dehydrogenase 6-Phospho-D-gluconate + NAD(P)+ ↔ 6-phospho-2-dehydro-D-gluconate + NAD(P)H + H+ EC 1.1.1.43
2-Keto-3-deoxy-6-phosphogluconate aldolase 2-Dehydro-3-deoxy-6-phospho-D-gluconate ↔ pyruvate + D-glyceraldehyde 3-phosphate EC 4.1.2.14
B. Further transformations of pyruvate—glycolytic fermentations [2327]
Lactate dehydrogenase Pyruvate + NADH ↔ lactate + NAD+ EC 1.1.1.27
Pyruvate:ferredoxin oxidoreductase, PFOR Pyruvate + CoA + oxidized Fd ↔ acetyl-CoA + reduced Fd + CO2 + H+ EC 1.2.7.1
NADH:ferredoxin oxidoreductase, NFOR Oxidized Fd + NADH ↔ reduced Fd + NAD+ + H+ EC 1.18.1.3
Ferredoxin hydrogenase 2 reduced ferredoxin + 2 H+ ↔ H2 + 2 oxidized ferredoxin EC 1.12.7.2
Phosphotransacetylase CoA + acetyl phosphate ↔ acetyl-CoA + phosphate EC 2.3.1.8
Acetate kinase ATP + acetate ↔ ADP + acetyl phosphate EC 2.7.2.1
NAD+-dependent ethanol dehydrogenase Acetaldehyde + NADH + H+ ↔ ethanol + NAD+
An aldehyde + NADH + H+ ↔ a primary alcohol + NAD+
EC 1.1.1.1
Acetaldehyde dehydrogenase Acetaldehyde + CoA + NAD+ ↔ acetyl-CoA + NADH + H+ EC 1.2.1.10
Acetyl-CoA acetyltransferase 2-acetyl-CoA ↔ CoA + acetoacetyl-CoA EC 2.3.1.9
3-Hydroxybutyryl-CoA dehydrogenase 3-Acetoacetyl-CoA + NADPH + H+ ↔ 3-hydroxybutanoyl-CoA + NADP+ EC 1.1.1.157
Crotonase
3-OH-butyryl-CoA dehydratase
3-Hydroxybutanoyl-CoA ↔ crotonoyl-CoA + H2O EC 4.2.1.55
2NADH+ oxidized Fd + crotonyl-CoA → 2 NAD+ reduced Fd + butyryl-CoA catalyzed by butyryl CoA dehydrogenase/electron-transfer flavoprotein complex
Butyryl-CoA dehydrogenase A short-chain acyl-CoA + electron-transfer flavoprotein ↔ a short-chain trans-2,3-dehydroacyl-CoA + reduced electron-transfer flavoprotein EC 1.3.8.1
Butyryl-CoA dehydrogenase/Etf complex Butanoyl-CoA + 2 NAD+ + 2 reduced Fd ↔ Crotonoyl-CoA + 2 NADH + 2 oxidized Fd EC 1.3.1.109
Phosphotransbutyrylase Butanoyl-CoA + phosphate ↔ CoA + butanoyl phosphate EC 2.3.1.19
Butyrate kinase Butanoyl phosphate + ADP ↔ butanoate + ATP EC 2.7.2.7
PFL—pyruvate formate lyase Pyruvate + CoA ↔ acetyl-CoA + formate EC 2.3.1.54
FHL—formate hydrogen lyase Formate → H2 + CO2 EC 1.17.99.7
Pyruvate carboxylase ATP + pyruvate + HCO3 ↔ ADP + phosphate + oxaloacetate EC 6.4.1.1
Malate dehydrogenase Malate + NAD+ ↔ oxaloacetate + NADH + H+ EC 1.1.1.37
Fumarate hydratase Malate ↔ fumarate + H2O EC 4.2.1.2
Fumarate reductase Fumarate + a quinol ↔ succinate + a quinone EC 1.3.5.4
Fumarate + NADH ↔ succinate + NAD+ EC 1.3.1.6
Succinyl-CoA synthetase GTP + succinate + CoA = GDP + phosphate + succinyl-CoA EC 6.2.1.4
Methylmalonyl CoA mutase Succinyl-CoA ↔ (R)-methylmalonyl-CoA EC 5.4.99.2
Methylmalonyl CoA epimerase (R)-methylmalonyl-CoA ↔ (S)-methylmalonyl-CoA EC 5.1.99.1
Methylmalonyl-CoA decarboxylase (S)-methylmalonyl-CoA ↔ propanoyl-CoA + CO2 EC 4.1.1.41
Propionate-CoA transferase Acetate + propanoyl-CoA ↔ acetyl-CoA + propanoate EC 2.8.3.1
C. Transformation of gaseous and nongaseous products of acidic fermentations (the selected examples)
Transformation of lactate and acetate to butyrate, hydrogen, and carbon dioxide ([28] and cited therein)
Lactate dehydrogenases (S)-lactate + NAD+ ↔ pyruvate + NADH + H+ EC 1.1.1.27
(R)-lactate + NAD+ ↔ pyruvate + NADH + H+ EC 1.1.1.28
Lactate + 2 NAD+ + 2 reduced Fd ↔ pyruvate + 2 NADH + 2 oxidized Fd
See Table 3
EC 1.3.1.110
Pyruvate is oxidized to acetyl coenzyme A, which is further routed to acetate and butyrate with hydrogen release. See Part B: Further transformations of pyruvate—glycolytic fermentations
Transformation of ethanol and acetate to butyrate and hydrogen in Clostridium kluyveri [29]
Acetate kinase See Part B. Further transformations of pyruvate—glycolytic fermentations EC 2.7.2.1
Acetyl-CoA acetyltransferase EC 2.3.1.9
3-Hydroxybutyryl-CoA dehydrogenase EC 1.1.1.157
3-Hydroxyacyl-CoA dehydratase EC 4.2.1.55
Butyryl-CoA dehydrogenase/Etf complex EC 1.3.1.109
Acetate CoA-transferase Acyl-CoA + acetate ↔ a fatty acid anion + acetyl-CoA EC 2.8.3.8
Reductive carbon monoxide dehydrogenase/acetyl-CoA synthase pathway (reductive CODH/ACS) [30]
NADP-dependent formate dehydrogenase CO2 + NADPH ↔ formate + NADP+ EC 1.17.1.10
Formyltetrahydrofolate synthetase ATP + formate + tetrahydrofolate ↔ ADP + phosphate + 10-formyltetrahydrofolate EC 6.3.4.3
Methenyltetrahydrofolate cyclohydrolase 10-Formyltetrahydrofolate ↔ 5,10-methenyltetrahydrofolate + H2O EC 3.5.4.9
NADP-dependent methylenetetrahydrofolate dehydrogenase 5,10-Methenyltetrahydrofolate + NADPH + H+ ↔ 5,10-Methylenetetrahydrofolate + NADP+ EC 1.5.1.5
Ferredoxin-dependent methylenetetrahydrofolate reductase 5,10-Methylenetetrahydrofolate + 2 reduced Fd + 2 H+ ↔ 5-methyltetrahydrofolate + 2 oxidized Fd EC 1.5.7.1
5,10-Methylenetetrahydrofolate reductase 5,10-Methylenetetrahydrofolate + NAD(P)H + H+ ↔ 5-methyltetrahydrofolate + NAD(P)+ EC 1.5.1.20
5-Methyltetrahydrofolate:corrinoid/iron–sulfur protein Co-methyltransferase [Co(I) corrinoid Fe-S protein] + 5-methyltetrahydrofolate ↔ [methyl-Co(III) corrinoid Fe-S protein] + tetrahydrofolate EC 2.1.1.258
Carbon monoxide dehydrogenase CO2 + 2 reduced Fd + 2 H+ ↔ CO + H2O + 2 oxidized Fd EC 1.2.7.4
CO-methylating acetyl-CoA synthase CO + CoA + [methyl-Co(III) corrinoid Fe-S protein] ↔ acetyl-CoA + [Co(I) corrinoid Fe-S protein] EC 2.3.1.169
D. Glycerol transformations [31, 32]
Oxidative pathway
Glycerol dehydrogenase Glycerol + NAD+ ↔ glycerone (dihydroxyacetone) + NADH + H+ EC 1.1.1.6
Dihydroxyacetone kinase ATP + glycerone ↔ ADP + glycerone phosphate EC 2.7.1.29
For further reactions, see Part A: Pyruvate formation
Reductive pathway
Glycerol dehydratase Glycerol ↔ 3-hydroxypropionaldehyde + H2O EC 4.2.1.30
1,3-Propanediol dehydrogenase 3-Hydroxypropionaldehyde + NADH + H+ ↔ 1,3-propanediol + NAD+ EC 1.1.1.202
E. Amino acids fermentations [3337]
Syntrophy with H2-scavenging microorganism: amino acid degradation involves NAD(P)- or FAD-dependent deamination of amino acids to the corresponding α-keto acids by amino acid dehydrogenases (EC 1.4.1.X): RCH(NH4+)COO + H2O → RCOCOO + NH4+ + H2 and further conversion of α-keto acids via oxidative decarboxylation to fatty acids: RCOCOO + H2O → RCOO + CO2 + H2 [33]
Without syntrophy with H2-scavenging microorganism: Stickland Reaction—coupled oxidation-reduction reactions between suitable amino acids (coupled deamination of amino acids); one member of the pair is oxidized (dehydrogenated) and the other is reduced (hydrogenated) [34], for example,
Alanine and glycine: alanine + 2 glycine + 3H2O → 3 acetate + 3NH4+ + HCO3 + H+
Valine and glycine: valine + 2 glycine + 3H2O → isobutyrate + 2 acetate + 3NH4+ + HCO3 + H+
Leucine and glycine: leucine + 2 glycine + 3H2O → isovalerate + 2 acetate + 3NH4+ + HCO3 + H+
Examples of amino acid dehydrogenases catalyzing deamination of amino acids to the corresponding α-keto acids [33]
Aspartate dehydrogenase L-aspartate + H2O + NAD(P)+ ↔ oxaloacetate + NH3 + NAD(P)H + H+ EC 1.4.1.21
Valine dehydrogenase L-valine + H2O + NADP+ ↔ 3-methyl-2-oxobutanoate + NH3 + NADPH + H+ EC 1.4.1.8
Alanine dehydrogenase L-alanine + H2O + NAD+ ↔ pyruvate + NH3 + NADH + H+ EC 1.4.1.1
Leucine dehydrogenase L-leucine + H2O + NAD+ ↔ 4-methyl-2-oxopentanoate + NH3 + NADH + H+ EC 1.4.1.9
Key enzymes of Stickland reaction [3436]
Glycine reductase GR pathway (grd operon)
Glycine reductase Glycine + phosphate + reduced thioredoxin + H+ ↔ acetyl phosphate + NH3 + oxidized thioredoxin + H2O EC 1.21.4.2
Acetate kinase Acetyl phosphate + ADP ↔ acetate + ATP EC 2.7.2.1
Proline reductase PR pathway (prd operon)
D-proline reductase (dithiol) D-proline + dihydrolipoate ↔5-aminopentanoate (5-aminovalerate) + lipoate EC 1.21.4.1
Others examples [33]
Serine dehydratase L-serine ↔ pyruvate + NH3 (overall reaction)
(1a) L-serine ↔ 2-aminoprop-2-enoate + H2O
(1b) 2-Aminoprop-2-enoate ↔ 2-iminopropanoate (spontaneous)
(1c) 2-Iminopropanoate + H2O ↔ pyruvate + NH3 (spontaneous)
EC 4.3.1.17
Threonine dehydratase L-threonine ↔ 2-oxobutanoate + NH3 (overall reaction)
(1a) L-threonine ↔ 2-aminobut-2-enoate + H2O;
(1b) 2-Aminobut-2-enoate ↔ 2-iminobutanoate (spontaneous)
(1c) 2-Iminobutanoate + H2O ↔ 2-oxobutanoate + NH3 (spontaneous)
EC 4.3.1.19
Detailed pathways of glutamate fermentation via 3-methylaspartate [37]
Glutamate mutase (methylaspartate mutase) L-glutamate ↔ L-threo-3-methylaspartate EC 5.4.99.1
Methyl aspartase L-threo-3-methylaspartate mesaconate (2-methylfumarate) + NH3 EC 4.3.1.2
Mesaconase (2-methylmalate dehydratase) 2-Methylfumarate + H2O (S)-2-methylmalate 4.2.1.34
Citramalate lyase (2S)-2-hydroxy-2-methylbutanedioate acetate + pyruvate
(S)-2-methylmalate = 2-hydroxy-2-methylbutanedioate
4.1.3.22
For further transformations of pyruvate to acetate and butyrate, see Part B.
For further transformations of pyruvate to propionate, see Part B.
Detailed pathway of glutamate fermentation via 2-hydroxyglutarate [37]
Glutamate dehydrogenase L-glutamate + H2O + NAD+ ↔ 2-oxoglutarate + NH3 + NADH + H+ 1.4.1.2
2-Hydroxyglutarate dehydrogenase (S)-2-hydroxyglutarate + acceptor ↔ 2-oxoglutarate + reduced acceptor 1.1.99.2
Glutaconate (2-hydroxyglutarate) CoA-transferase Acetyl-CoA + (E)-glutaconate ↔ acetate + glutaconyl-1-CoA 2.8.3.12
2-Hydroxyglutaryl-CoA dehydratase (R)-2-hydroxyglutaryl-CoA ↔ (E)-glutaconyl-CoA + H2O EC 4.2.1.167
Glutaconyl-CoA decarboxylase 4-Carboxybut-2-enoyl-CoA ↔ but-2-enoyl-CoA + CO2 4.1.1.70

Table 2.

The selected enzymes of acidogenic step of anaerobic digestion. A, B, C, D, and E refer to the processes indicated in Figure 1.

Enzyme Reaction/process EC number
F. Acetogenesis dependent on syntrophic relations between microorganisms
Acetate oxidation by, for example, Clostridium ultunense—oxidative carbon monoxide dehydrogenase/acetyl-CoA synthase pathway (oxidative CODH/ACS):
Acetate + 4H2O → 2 HCO3 + 4H2 + H+, ΔG0’ = + 104.6 kJ/mol, with the H2 consuming methanogen, ΔG0’ = −31.0 kJ/mol [38]
NADP-dependent formate dehydrogenase See Table 2, Part C
Formyltetrahydrofolate synthetase
Methenyltetrahydrofolate cyclohydrolase
NADP-dependent methylenetetrahydrofolate dehydrogenase
Ferredoxin-dependent methylenetetrahydrofolate reductase
5,10-Methylenetetrahydrofolate reductase
5-Methyltetrahydrofolate:corrinoid/iron-sulfur protein Co-methyltransferase
Carbon monoxide dehydrogenase
CO-methylating acetyl-CoA synthase
Reverse electron transfer during acetate oxidation has yet to be confirmed. Direct interspecies electron transfer (DIET) is not excluded (Westerholm et al., 2016)
Acetate oxidation by Geobacter sulfurreducens:
Acetate oxidation coupled to reduction of fumarate to succinate (∆G°′ = −249 kJ per mol acetate), acetate metabolism proceeds via reactions of the citric acid cycle [39]
Acetate kinase See Table 2, Part B
Phosphotransacetylase
Citric acid cycle
Citrate synthase Acetyl-CoA + H2O + oxaloacetate ↔ citrate + CoA EC 2.3.3.1
Aconitase Citrate ↔ isocitrate (overall reaction) EC 4.2.1.3
Isocitrate dehydrogenase (NADP+-dependent) Isocitrate + NADP+ ↔ 2-oxoglutarate + CO2 + NADPH + H+ EC1.1.1.42
2-Oxoglutarate:ferredoxin oxidoreductase 2-Oxoglutarate + CoA + 2 oxidized Fd = succinyl-CoA + CO2 + 2 reduced Fd + 2 H+ EC 1.2.7.3
Succinyl-CoA:acetate CoA-transferase Succinyl-CoA + acetate ↔ acetyl-CoA + succinate EC 2.8.3.18
Succinate dehydrogenase succinate + a quinone ↔ fumarate + a quinol EC 1.3.5.1
Fumarate hydratase (S)-malate ↔ fumarate + H2O EC 4.2.1.2
Malate dehydrogenase (S)-malate + NAD+ ↔ oxaloacetate + NADH + H+ EC 1.1.1.37
Butyrate oxidation by Syntrophomonas wolfei:
Butyrate + 2H2O → 2 acetate + 2H+ + 2H2, ΔG0’ = + 48.3 kJ/mol, with the H2 consuming methanogen, ΔG0’ = −17.3 kJ/mol [4]
CoA transferase Butyrate + acetyl-CoA ↔ butyryl-CoA + acetate EC 2.8.3.9
Butyryl-CoA dehydrogenase See Table 2, Part B
Crotonase-3-OH-butyryl-CoA dehydratase
3-Acetyl-CoA acetyltransferase
Hydroxybutyryl-CoA dehydrogenase
Phosphotransacetylase
Acetate kinase
Butyrate oxidation coupled with a reverse electron transfer that involves electron transfer flavoprotein EtfAB, membrane-anchored electron carrier DUF224 protein, the menaquinone pool in the membrane, a membrane-bound cytochrome, NADH:hydrogenase/formate-dehydrogenase complex (NDH/HYD1/FDH-1 complex), Rnf (proton-translocating ferredoxin:NAD+ oxidoreductase) [40]
Propionate oxidation by Syntrophobacter wolinii:
Propionate + 3H2O → acetate + HCO3 + H+ + 3H2, ΔG0’ = + 76.0 kJ/mol, with the H2 consuming methanogen, ΔG0’ = −22.4 kJ/mol [4]
Pyruvate carboxylase See Table 2, Part B
Malate dehydrogenase
Fumarate hydratase
Fumarate reductase
Succinate dehydrogenase Succinate + a quinone ↔ fumarate + a quinol EC 1.3.5.1
Succinyl-CoA synthetase See Table 2, Part B
Methylmalonyl CoA mutase
Methylmalonyl CoA epimerase
Methylmalonyl-CoA decarboxylase
Propionate-CoA transferase
Propionate oxidation coupled with a reverse electron transfer that involves menaquinone, proteins encoded by cytochrome c homologous genes, cytochrome b:quinone oxidoreductases, formate dehydrogenases, hydrogenases including confurcating [FeFe]-hydrogenases [41]
Six syntrophy-specific functional domains found in the genomes of the butyrate- or propionate-oxidizing syntrophs [42] InterPro number
Extra-cytoplasmic formate dehydrogenase (FDH) alpha subunit, EC 1.17.1.9 IPR006443
FdhE-like protein—tightly connected with FDH IPR024064
FDH accessory protein—tightly connected with FDH IPR006452
CapA—a membrane-bound complex, a protein involved in capsule or biofilm formation that may facilitate syntrophic growth (also present in acetate-oxidizers) IPR019079
FtsW, RodA, SpoVE—membrane-integrated proteins involved in membrane integration, cell division, sporulation, and shape determination IPR018365
Ribonuclease P involved in tRNA maturation IPR020539
Functional domains involved in electron transfer identified by [42] InterPro number
Cytoplasmic FDH IPR027467, IPR006655, IPR006478, IPR019575, IPR001949
Extracytoplasmic FDH IPR006443
Formate transporter IPR000292, IPR024002
Fe-Fe hydrogenase IPR004108, IPR009016, IPR003149, IPR013352
NiFe hydrogenase IPR001501, IPR018194
Rnf complex: 2 reduced Fd + NAD+ + H+ + Na+ ↔ 2 oxidized Fd + NADH + Na+ (EC 1.18.1.8) IPR007202, IPR010207, IPR026902, IPR010208, IPR004338, IPR011303, IPR007329
Ech complex: 2 reduced Fd + NADP+ + H+ ↔ 2 oxidized Fd + NADPH (EC 1.18.1.2) IPR001750, IPR001516, IPR001694, IPR006137, IPR001268, IPR012179, IPR001135
Etf alpha, Etf beta, Bcd (Butyryl-CoA dehydrogenase): see Table 2, Part B (EC 1.3.1.109) IPR014731, IPR012255, IPR006089, IPR009075, IPR006092, IPR006091, IPR013786, IPR009100
Cytochromes:
c
cIII
b561
b5
IPR023155, IPR024673
IPR020942, IPR002322
IPR016174, IPR000516
IPR001199
DUF224 protein complex IPR003816, IPR004017, IPR023234
Lactate oxidation by Desulfovibrio vulgaris:
Lactate + H2O → acetate + CO2 + 4 H2, ΔG0’ = −8.8 kJ/mol with the H2 consuming methanogen, ΔG0’ = −74.2 kJ/mol [43]
Lactate dehydrogenase See Table 2, Part B
Pyruvate:ferredoxin oxidoreductase
Phosphate acetyltransferase
Acetate kinase
Alcohol dehydrogenase
Lactate oxidation coupled with a reverse electron transfer that involves the membrane-bound Qmo complex, cytochromes, hydrogenases (Coo, Hyn, Hyd, Hys), formate dehydrogenases, menaquinone, membrane-bound Qrc complex [43, 44]
Ethanol oxidation by Pelobacter carbinolicus
Ethanol + H2O → acetate + H+ + 2H2, ΔG0’ = + 9.6 kJ/mol with the H2 consuming methanogen, ΔG0’ = − 56 kJ/mol [4]
NAD+-dependent ethanol dehydrogenase See Table 2, Part B
Acetaldehyde dehydrogenase (acetylating)
Nonacetylating acetaldehyde dehydrogenase An aldehyde + NAD+ + H2O ↔ a carboxylate + NADH + H+ EC 1.2.1.3
Phosphotransacetylase See Table 2, Part B
Acetate kinase
Ethanol oxidation coupled with a reverse electron transfer that involves membrane-bound ion-translocating ferredoxin:NAD+ oxidoreductase, formate dehydrogenases, and confurcating hydrogenases [1, 45]
G. Acetogenesis independent on syntrophic relations between microorganisms
Ethanol oxidation by Acetobacterium woodii: 2 ethanol + 2 CO2 → 3 acetate—75.4 kJ/mol [46]
Bifunctional acetaldehyde-CoA/alcohol dehydrogenase Ethanol + NAD+ → acetaldehyde + NADH + H+
acetaldehyde + NAD+ + CoA → acetyl-CoA + 2 NADH + H+
Ethanol is oxidized to acetyl-CoA in a two-step reaction by a bifunctional acetylating ethanol/aldehyde dehydrogenase
[EC:1.2.1.10 1.1.1.1]
Acetyl-CoA is transformed to acetate with the release of ATP See Table 2, Part B
Reduction of ferredoxin by NADH by reverse electron flow in a reaction catalyzed by Rnf complex See Part F
Carbon dioxide is reduced to acetate via the Wood-Ljungdahl pathway See Table 2, Part C
Lactate oxidation by Acetobacterium woodii: 2 lactate → 3 acetate—61 kJ/mol [47]
Lactate dehydrogenase Lactate + 2 NAD+ + 2 reduced Fd ↔ pyruvate + 2 NADH + 2 oxidized Fd
The enzyme uses flavin-based electron confurcation to drive endergonic lactate oxidation with NAD+ as oxidant at the expense of simultaneous exergonic electron flow from reduced ferredoxin to NAD+
EC 1.3.1.110
Pyruvate is transformed to acetyl-CoA and further to acetate with the release of ATP See Table 2, Part B
Reduction of ferredoxin by NADH by reverse electron flow in a reaction catalyzed by Rnf complex See Part F
Carbon dioxide is reduced to acetate via the Wood-Ljungdahl pathway See Table 2, Part C

Table 3.

The selected enzymes of acetogenic step of anaerobic digestion. F and G refer to the processes indicated in Figure 1.

Enzyme Reaction/process EC number
MFR—methanofuran, H-S-CoM—coenzyme M, H-S-CoB—coenzyme B, H4MPT—tetrahydromethanopterin, F420—5’deazaflavin, H4SPT—tetrahydrosarcinapterin
Hydrogenotrophic pathway
Formylmethanofuran dehydrogenase CO2 + MFR + 2 reduced Fd + 2H+ ↔ formyl-MFR + H2O + 2 oxidized Fd EC 1.2.7.12
Formylmethanofuran-H4MPT formyltransferase Formyl-MFR + H4MPT ↔ MFR + formyl-H4MPT EC 2.3.1.101
Methenyl-H4MPT cyclohydrolase Formyl-H4MPT + H+ ↔ methenyl-H4MPT + H2O EC 3.5.4.27
F420-dependent methylene-H4MPT dehydrogenase Methenyl-H4MPT + reduced F420 ↔ methylene-H4MPT + oxidized F420 EC 1.5.98.1
H2-forming methylene-H4MPT dehydrogenase Methenyl-H4MPT + H2 ↔ methylene-H4MPT + H+ EC 1.12.98.2
F420-dependent methylene-H4MPT reductase Methylene-H4MPT + reduced F420 ↔ CH3-H4MPT + oxidized F420 EC 1.5.98.2
Methyl-H4MPT:coenzyme M methyl-transferase Coenzyme M + methyl-H4MPT + 2 Na+/in ↔ 2-methyl-coenzyme M + 2 Na+/out + H4MPT EC 2.1.1.86
Methyl-CoM reductase CH3-S-CoM + H-S-CoB ↔ CoM-S-S-CoB + CH4 EC 2.8.4.1
Heterodisulfide reductase CoM-S-S-CoB + dihydromethanophenazine ↔ CoB + CoM + methanophenazine EC 1.8.98.1
Acetotrophic pathway
Acetate kinase-phosphotransacetylase system in Methanosarcina; acetate thiokinase in Methanosaeta Acetate + CoA ↔ acetyl-CoA + H2O EC 2.7.2.1
EC 2.3.1.8
EC 6.2.1.1
CO-methylating acetyl-CoA synthase Acetyl-CoA + a [Co(I) corrinoid Fe-S protein] ↔ CO + CoA + [methyl-Co(III) corrinoid Fe-S protein] EC 2.3.1.169
5-Methyltetrahydrosarcinapterin:corrinoid/iron-sulfur protein Co-methyltransferase [Methyl-Co(III) corrinoid Fe-S protein] + tetrahydrosarcinapterin ↔ a [Co(I) corrinoid Fe-S protein] + 5-methyltetrahydrosarcinapterin EC 2.1.1.245
Anaerobic carbon monoxide dehydrogenase CO + H2O + 2 oxidized Fd ↔ CO2 + 2 reduced Fd + 2 H+ EC 1.2.7.4
Methyl H4SPT: coenzyme M methyltransferase CH3 H4SPT + H-S-CoM ↔ CH3-S-CoM + H4SPT EC 2.1.1.-
Methyl-CoM reductase CH3-S-CoM + H-S-CoB ↔ CoM-S-S-CoB + CH4 EC 2.8.4.1
Heterodisulfide reductase CoM-S-S-CoB + dihydromethanophenazine ↔ CoB + CoM + methanophenazine EC 1.8.98.1
Methylotrophic pathway
Methanol:corrinoid protein Co-methyltransferase Methanol + Co(I) corrinoid protein ↔ Methyl-Co(III) corrinoid protein + H2O EC 2.1.1.90
[Methyl-Co(III) corrinoid protein]:coenzyme M methyltransferase Coenzyme M + Methyl-Co(III) corrinoid protein ↔ 2-(methylthio)ethanesulfonate + Co(I) corrinoid protein EC 2.1.1.246
Methylamine:corrinoid protein Co-methyltransferase Methylamine + [Co(I) methylamine-specific corrinoid protein] ↔ a [methyl-Co(III) methylamine-specific corrinoid protein] + NH3 EC 2.1.1.248
Dimethylamine:corrinoid protein Co-methyltransferase Dimethylamine + [Co(I) dimethylamine-specific corrinoid protein] ↔ a [methyl-Co(III) dimethylamine-specific corrinoid protein] + methylamine EC 2.1.1.249
Trimethylamine:corrinoid protein Co-methyltransferase Trimethylamine + a [Co(I) trimethylamine-specific corrinoid protein] ↔ a [methyl-Co(III) trimethylamine-specific corrinoid protein] + dimethylamine EC 2.1.1.249
[Methyl-Co(III) methylamine-specific corrinoid protein]:coenzyme M methyltransferase [Methyl-Co(III) methylamine-specific corrinoid protein] + CoM ↔ methyl-CoM + a [Co(I) methylamine-specific corrinoid protein] EC 2.1.1.247
Methyl-CoM reductase CH3-S-CoM + H-S-CoB ↔ CoM-S-S-CoB + CH4 EC 2.8.4.1
Heterodisulfide reductase CoM-S-S-CoB + dihydromethanophenazine ↔ CoB + CoM + methanophenazine EC 1.8.98.1

Table 4.

The selected enzymes of methanogenic step of anaerobic digestion [48, 49].

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2. Selected enzymes of anaerobic digestion

Figure 1 shows a scheme of AD and Tables 14 present a summary of the selected enzymes and enzymatic reactions involved in decomposition of organic matter to methane and carbon dioxide. Tables 14 are an extension of Figure 1, and in Figure 1, there are the links to Tables 14.

The key groups of hydrolases involved in the process of degradation of organic matter are esterases, glycosidases, and peptidases, which catalyze the cleavage of ester bonds, glycoside bonds, and peptide bonds, respectively (Table 1). Table 1 also includes other classes of hydrolases such as acting on carbon-nitrogen bonds, other than peptide bonds.

In the acidogenic stage of AD, the key step is pyruvate formation from carbohydrates (Table 2, Part A) or other compounds and further pyruvate transformations toward short-chain fatty acids and ethanol (Table 2, Part B). The Part C of the Table 2 also considers transformation of gaseous and nongaseous products of acidic fermentations, resulting from nonsyntrophic nutritional interaction between bacteria. The Parts D and E present the enzymes of glycerol and amino acid transformations, respectively. The latter requires syntrophic cooperation between microorganisms.

The enzymes catalyzing oxidation of nongaseous products of acidogenesis mainly butyrate, propionate, acetate, lactate, ethanol including the enzymes of reverse electron transfer (process responsible for energy conservation in syntrophically growing acetogens) are shown in Table 3.

The enzymes of the three recognized pathways of methanogenesis such as acetotrophic, hydrogenotrophic, and methylotrophic are listed in Table 4.

The data were prepared on the basis of detailed analysis of AD research. The enzyme nomenclature comes from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database resource.

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3. Conclusion

Biomass conversion to methane and carbon dioxide is the effect of complex interactions between microorganisms. These processes occur due to the microbial enzymatic machinery involved in specific metabolic pathways. Meta-omic analyses of microbial communities involved in AD reveal (i) dependence of microbial communities on the type of feedstock and operational conditions and (ii) describe interactions within microbial communities and ecophysiological functions of the specific taxa. Searching for the gene presence, gene expression, and protein expression, as well as linking structure and function of microbial communities, allows to develop a fundamental understanding of AD. This chapter is believed to contribute to the studies on the enzymatic road map of anaerobic digestion. However, it is only the tip of the iceberg of processes occurring in the microbial cells/microbial communities.

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Acknowledgments

We acknowledge the support of The National Science Centre, Poland, through grant UMO-2015/17/B/NZ9/01718 and The National Centre for Research and Development, Poland, through grant BIOSTRATEG2/297310/13/NCBiR/2016.

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Conflict of interest

The authors declare that there are no conflicts of interest.

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Written By

Anna Sikora, Anna Detman, Damian Mielecki, Aleksandra Chojnacka and Mieczysław Błaszczyk

Submitted: May 29th, 2018 Reviewed: September 1st, 2018 Published: November 5th, 2018