FEMS MicrobiologyReviews87 (1990)377-382 Publishedby Elsevier 377 FEMSRE00176 Formate dehydrogenase James G. Ferry Department of Anaerobic Microbiology, VirginiaPolytechnicInstitute and State University, 81acksbur~ U.S.A. Key words: Aerobic microbiology; Anaerobic microbiology; Energy-conservingpathways; Biochemistry; Molybdenum; Selenium; Molecular genetics; Molecular regulation I. SUMMARY 2. INTRODUCTION Formate is a substrate, or product, of diverse reactions catalyzed by eukaryotic organisms, eubacteria, and archaebacteria. A survey of metabolic groups reveals that forraate is a common growth substrate, especially among the anaerobic eubacteria and archaebacteria. Formate also functions as an accessory reductant for the utilization of more complex substrates, and an intermediate in energy-conserving pathways. The diversity of reactions involving formate dehydrogenases is apparent in the structures of electron acceptors which include pyridine nucleotides, 5deazaflavin, quinones, and ferredoxin. This diversity of electron acceptors is reflected in the composition of formate dehydrogenase. Studies on these enzymes have contributed to the biochemical and genetic understanding of selenium, molybdenum, tungsten, and iron in biology. The regulation of formate dehydrogenase synthesis serves as a model for understanding, general principles of regulation in anaerobic organisms. A diversity of microorganisms produce or consume formate in a variety of metabolic pathways. These include aerobic and anaerobic organisms from among the eubacteria, archaebacteria and eukaryotic yeasts. All contain the enzyme formate dehydrogenase which catalyzes the reversible two-electron oxidation of formate (HCOO- = CO2 + H++ 2e-). Among the aerobes, formate supports the growth of several facultative, chemolithotrophic eubacteria [1-3]. Methylotrophic organisms, without the ribulose-5-phosphate cycle for carbon assimilation, convert methanol to formate which is further oxidized to carbon dioxide. Methylotrophic aerobes also utilize formate as a sole source of energy. Recently, an electron transfer system that transports electrons from formate to nitrogenase was reported in extracts of the obligate methanotroph Methylosinus trichosporum . In addition to formate, Pseudomonas oxalaticus grows with oxalate as the .sole energy source, and formate produced in this reaction is further oxidized to carbon dioxide . A greater diversity of anaerobic bacteria is able to metabolize formate. The acid is produced during the fermentation of sugars catalyzed by pyrurate formate-lyase or by the reduction of carbon dioxide . Formate is also a product of the Correspondence to: J.G. Ferry, Departmentof AnaerobicMicrobiology,VirginiaPolytechnicInstituteand State University. Blacksbur8, VA 24061, U.S.A. 0168-6445/90/$03.50© 1990Federationof EuropeanMicrobiologicalSocieties 378 fermentation of aromatic compounds , L-( + )tartaric acid  and oxalate . A recent report suggests that the inward transport of divalent oxalate is coupled to the outward movement of the monovalent formate anion, and that this electrogenic antiport is the basis for energy coupling in Oxalobacterformigenes . Formate is an intermediate in nonsaccharolytic fermentations; it is produced from formyltetrahydrofolate in the fermentation of purines and by reduction of carbon dioxide during fermentation of hypoxanthine . In the Wood pathway for the synthesis of acetate , the methyl group is synthesized by reduction of CO2 to formate followed by the formation of formyltetrahydrofolate and reduction to methyltetrahydrofolate. The methyl group of methyltetrahydrofolate is transferred to a site on carbon monoxide dehydrogenase where it condenses with a carbonyl group (originating from CO2, CO or the carboxyl group of pyruvate) and CoASH to form acetyi-CoA. Many facultative and strictly anaerobic bacteria obtain energy for growth by electron transport phosphorylation coupled to the oxidation of formate and reduction of exogenous electron acceptors including nitrate and fumarate . Several anaerobic bacteria also contain a formic hydrogenlyase system, but only a small amount of energy is available from the conversion of formate to H 2 plus CO2, and it is unlikely that cells benefit. The sulfate-reducing bacteria are strict anaerobes which obtain energy for growth by the dis'~.nilatory reduction of sulfate to sulfide . The electron donors are diverse and include H 2 and formate. In addition to sulfate, several strictly anaerobic bacteria have been isolated that reduce elemental sulfur, or oxides of sulfur, but not sulfate. The strictly anaerobic methane-producing archaebacteria obtain energy for growth by the cleavage of acetate or the reduction of carbon dioxide . The eight electrons required for the reduction of carbon dioxide originate from H2 or formate. The first one-carbon derivative in the pathway is formylmethanofuran but free formate is not an intermediate. The Methanobacterium formicicum formate dehydrogenase also participates in a coenzyme F42o-mediatedformic hydrogenlyase system . Some homoacetogenic bacteria utilize formate as a sole electron donor. Recently, it was reported that Aiteromonas putrefaciens obtains energy for growth by the oxidation of formate and reduction of Mn(IV) or Fe(III) . In addition to anaerobic respirations, organisms are described that require H2 or formate as an accessory reductant for the fermentation of some organic substrates [17,18]. The conversion of complex organic matter to methane in anaerobic freshwater habitats involves microbial food chains comprised of interacting metabolic groups (consortia) of organisms. The fermentative bacteria degrade polymers to H 2, formate, acetate, higher volatile fatty acids, and other fermentation products. The H 2, formate, and acetate are further degraded by the methaneproducing bacteria, terminal organisms of the consortia. The higher fatty acids, and other fermentation products, are cor~verted to methanogenic substrates by ~he acetog-~is. The acetogens rely on the methanogens to lower the concentration of highly reduced prt~duc~s, s~a'zethe oxidations are thermodynamically unfavo.rable. For historical reasons this syntrophy is referred to as 'interspecies H 2 transfer" but recently a major involvement of formate in int~rspecies electron transfer was proposed [1~,19]. 3. BIOCHEMISTRY OF FORMAIE DEHYDROGENASES Table 1 lists the properties of formate dehydrogenases extensively purified from aerobic organisms. All of these enzymes have a high K m for formate, reduce NAD +, and are inhibited by azide. The enzyme from P. oxalaticus is distinct from all others in that it is a heterodimeric, oxygen-sensitive, iron-sulfur, flavoprotein ; all others are homodimeric with no known metals or cofactors. The flavin dissociates from the P. oxalaticus enzyme under reducing conditions yielding an inactive deflavoprotein. Flavins are generally required by dehydrogenases to transfer electrons from one-electron centers to the obligate two-electron accepting pyridine nucleotide. Thus, the requirement for FMN implies that electrons may be transferred from the iron-sulfur center to 379 Table 1 Properties of formate dehydrogenases extensivelypurified from aerobic eubacteria and yeasts Organism Pseudomonas oxalaticus Native Subunit molecular molecular weight weight Km Referformate ences (mM) (M,) (M,) 315000 a 2 (100000) 13.5 112(59000)  Achromobacter parvulu~ 80000 a 2 (46000) 15 121] Moraxena 98000 a (48000) 13  Pichia pastoris 94000 a 2 (47000~ 16  Candida methylica 70000 a 2 (46000) 13  Candida methanolica 8284000 a 2 (43000) attain C-I 3.0  the flavin which d o n a t e s an electron pair to N A D +. Table 2 lists the properties of f o r m a t e dehydrogenuses purified from anaerobic archaebacteria and eubacteria. All are extremely sensitive to oxygen. Azide is a p o t e n t inhibitor, the only exception being the formate d e h y d r o g e n a s e f r o m M e t h a n o c o c c u s vannieiii . T h e enzymes c o n t a i n a complex inventory of redox centers a n d reduce a diversity of physiological electron acceptors, a striking d e p a r t u r e f r o m the e n z y m e s o f aerobic eubacteria a n d eukaryctes (Table 1). M a n y of the purified enzymes contain a cofactor similar to the 6-substituted pterin ( m o l y b d o p t e r i n ) p r e s e n t in all m o l y b d c e n z y m e s other t h a n nitrogenase . T h e cofactor f r o m the methanogenic a r c h a e b a c t e r i u m M e t h a n o b a c t e r i u m f o r m i c i c u m is a 6-substituted pterin, b u t apparentiy the structure of the side chain is different f r o m the p r o p o s e d structure o f the eukaryotic cofactor . Interestingly, the side Table 2 Properties of formate dehydrogenases extensively purified from anaerobic archaebacteria and eubacteria Native molecular weight (Mr) 105000 Subunit molecular weight (M,) N.D." Metals and cofactors (mol/mol native) Electron acceptor Km formate (mM) Refer~nces 1 Mo, 4.8-10.1 Fe 10-20 S F420b N.D.  Methanobacterium formieicum 177000 aj (85000) BI (53000) 1 FAD, plcr~n 1 Mo, 2 Zn, 21-24 Fe, 25-29 S F420 0.6  Escherichia c coli 590000 u4 (110000) ~4 (32000) Y4(20000) 4 cytochrome b 4 Mo, 4 Se, 56 Fe. 52 S quinone 0.03  Clostridium thermoaceticum 340000 a 2 (96000) ~z (76000) pterin 2 W, 2 Se, 36 Fe. 50 S NADP 0.2  Clostridium d pasteurianum 118000 a I (76000) /~l (34000) pterin, 2 Mo, 24 Fe, 28 S ferredoxin 1.7  Vibrio c succinogenes 263000 a 2 (110000) 1 Mo, 19 Fe, 18 S quinone 1.5  Organism Methanococcu.v vannielii ND, not determined, b F420, 5-deazaflavin; ~ formate dehydrogenase coupled to nitrate reduction; d formate dehydrogenase coupled to carbon dioxide reduction; e formate dehydrogenase coupled to fumarate reductase. " 380 chain of the eubacterial molybdopterin (bactopterin) from the carbon monoxide dehydrogenase of the aerobe Pseudomonas carboxydoflava is structurally distinct from the eukaryotic cofactor . The F420-reducing formate deh~drogenase from M. formicicum is the only one reported to contain flavin. Coenzyme F420 is an o01igate t~voelectron acceptor; thus, FAD is postulated to shuttle electrons between one-electron centers and 1:42o . In low-salt buffer FAD dissociates from the enzyme under reducing conditions, or during turnover, with loss of ability to reduce F420. The presence of flavins has not been reported for either the F420- or NADP-reducing enzymes from M. vannielii or CIostridium thermoaceticum. Selenium is a c o , n o n , but not essential, componew. of formate dehydrogenases from anaerobic organism.% The metal is present in a selenocysteine residue of the largest subunit of the formic hydrogeniyase-linked formate dehydrogenase from E. coli ~35]. Comparison of the deduced amino acid sequences of the large subunits from the selenium-dependent formate dehydrogenase from E. coli and the selenium-independent enzyme from M. formicicum reveals high overall identity [36,37]. The methanogen enzyme shares striking identity with the E. coli enzyme in the regions flanking the selenocysteine; interestingly, the methanogen enzyme contains cysteine in the position corresponding to selenocysteine in the E. coli enzyme. The conservation of this sequence in both enzymes implies that it supports a common function. 4. GENETICS Relatively little is known of the genetics of formate dehydrogenases from aerobic organisms. Conversely, the regulation of anaerobic metabolism (including the synthesis of the formic hydrogenlyase-linked formate dehydrogenase-H) has been extensively studied in E. coll. An active fnr gene product is required for expression of anaerobically inducible genes which encode pyruvate formate-lyase and enzymes catalyzing the formate-dependent reduction of fumarate, trimethylamine-N-oxide, or nitrate . Anoxic growth in the presence of these electron aeceptors repre.~ses synthesis of the formic hydrogenlyase system in order to direct electron flow from formate t~.~rds reduction of the electron acceptors. During fermentative metabolism (in the absence of exogenous electron acceptors), formate is required for expression of the formic hydrogenlyase system. A mutant, defective in pyruvate formatelyase, requires exogenously supplied formate for transcription of at least two genes involved in the synthesis of formic hydrogenlyase : the fdhF gene encoding the M r = 80000 subunit of formate dehydrogenase-H, and hyd-17 required for hydrogenase-3 expression. Anaerobic expression and induction of formate dehydrogenase-H by formate depends on a region of 185 nucleotidcs upstream of the translational start of the fdhF gene [39,40]. The fnr gene product does not interact with the regulatory sequence; instead, a sigma factor is involved in the regulation of transcription. Recently, mutations in trans were reported which affect the anaerobic expression of the fdhF gene . Molybdate is required for transcription of fdhF ; however, mutations blocking the synthesis of functional molybdopterin cofactor have no influence on the transcription of fdhF and hyd-17, indicating that the cofactor is not involved in regulation [39,42]. Recently, it was reported that the hark gene product is involved in nitrate repression of fdhF and hyd-17 . Incorporation of selenocysteine into the formate dehydrogenase-H of E. coli is through cotranslational insertion directed by an in-frame UGA stop codon . Translation of the UGA codon requires a functional pathway for incorporation of selenocysteine. Four genes have been identified: the selA and selB genes with unknown function, the seIC gene coding for the functional tRNA which inserts selenocysteine into protein , and seiD which is involved in selenium incorporation into protein or tRNA. The genetics of formate dehydrogenase-N (linked to the reduction of nitrate) of E. coli have been studied in parallel with nitrate reductase. Genes involved in the synthesis of active molybdopterin for both enzymes are designated chlA, chlB, chlD, chiE. Mutations in the chl genes also effect the synthesis of an active formate dehydrogenase-N and formate dehydrogenase-H [45-47]. 381 T h e chIB gene p r o d u c t ( F A factor) facilitates ass e m b l y of active nitrate reductase which implies a similar function for the formate dehydrogenase, possibly m o l y b d o p t e r i n insertion into apoenzymes. 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