Function and Regulation of the Formate Dehydrogenase Genes of the Methanogenic ArchaeonMethanococcus maripaludis

Abstract

Methanococcus maripaludis is a mesophilic species of Archaea capable of producing methane from two substrates: hydrogen plus carbon dioxide and formate. To study the latter, we identified the formate dehydrogenase genes of M. maripaludis and found that the genome contains two gene clusters important for formate utilization. Phylogenetic analysis suggested that the two formate dehydrogenase gene sets arose from duplication events within the methanococcal lineage. The first gene cluster encodes homologs of formate dehydrogenase ␣ (FdhA) and ␤ (FdhB) subunits and a putative formate transporter (FdhC) as well as a carbonic anhydrase analog. The second gene cluster encodes only FdhA and FdhB homologs. Mutants lacking either fdhA gene exhibited a partial growth defect on formate, whereas a double mutant was completely unable to grow on formate as a sole methanogenic substrate. Investigation of fdh gene expression revealed that transcription of both gene clusters is controlled by the presence of H 2 and not by the presence of formate.Hydrogen and carbon dioxide are common substrates for methanogenic Archaea. Many species of hydrogenotrophic methanogens can use formate in place of H 2 , while others cannot. The ability to use formate can be attributed to the enzyme formate dehydrogenase, which in methanogens catalyzes the reaction that produces reduced coenzyme F 420 from the oxidation of formate (9, 10, 18). The enzyme consists of two protein subunits (17), ␣ and ␤, encoded by fdhA and fdhB, respectively (15,19).The presence or absence of formate dehydrogenase genes does not predict the ability to grow on formate. Species known to contain contiguously encoded homologs of fdhA and fdhB include Methanococcus maripaludis, Methanococcus voltae, Methanobacterium formicicum, Methanococcus jannaschii, and Methanopyrus kandleri. Of these species, only the first three can use formate (4). In the species Methanothermobacter thermautotrophicus, strain Z-245 can use formate but strain ⌬H cannot. This difference is attributed to the presence in the former strain of fdh genes that are absent from the same genomic context in the latter (15). Nevertheless, fdhA and fdhB homologs are present in the genome of strain ⌬H, albeit not closely related to those known in strain Z-245. Furthermore, at least one species that is unable to grow on formate, M. jannaschii, possesses formate dehydrogenase enzyme activity (11).The organization and regulation of formate dehydrogenase genes have been studied in M. formicicum (23) and M. thermoautotrophicus strain Z-245 (15), both of which use formate. In each species a gene designated fdhC precedes fdhA and fdhB. FdhC contains several potential membrane-spanning regions (23) and may encode a formate transporter. Northern blots in both species indicated the presence of three mRNA types, one containing fdhC, fdhA, and fdhB, another containing fdhC alone, and the third containing fdhA and fdhB. An apparent transcription start site was identified upstream of fdhC in both species. The smaller mRNAs could be ...

Effects of H 2 and Formate on Growth Yield and Regulation of Methanogenesis in Methanococcus maripaludis

“…In a previous study by Wood et al, our lab reported that either Fdh was sufficient for growth on formate, whereas a later study by Lupa et al reported that only Fdh1 supported growth on formate unless a ⌬fdh1 mutant was incubated for prolonged periods, ϳ70 h (15,35). This suggests that enrichment of a suppressor mutation may have accounted for the initial observations of Wood et al; the data in our present study agree with this interpretation.…”

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

“…maripaludis are selenoproteins (266); hence, the organism requires the presence of selenium to grow on formate (267,268). Genetic dissection has demonstrated that each homolog confers a competitive growth advantage, with single mutants impaired and double mutants unviable for formatotrophic growth (242). Interestingly, while some Methanosarcina species carry genes that encode Ffd homologs (269), methanogens with cytochromes cannot sustain formate-dependent growth.…”

“…This process is especially ecologically significant, given that formate produced by fermentative bacteria can be consumed by methanogens through interspecies transfer (244). It is well established that formatotrophic growth is linked to F 420 metabolism (17) and that it depends on F 420 -reducing formate dehydrogenases (called Ffd or Fdh) (242). Although Ffd has not been structurally characterized, biochemical studies on the enzyme from Methanobacterium formicicum (Mb.…”

“…Many hydrogenotrophic methanogens can also grow using formate as the sole electron donor, including species from the genera Methanococcus (241,242), Methanobacterium (243), and Methanospirillum (184). This process is especially ecologically significant, given that formate produced by fermentative bacteria can be consumed by methanogens through interspecies transfer (244).…”

Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea

“…A second Fdh (Fdh2; Mmp0138 -0139) was similarly regulated although not as markedly. The Fdhs reduce F 420 when formate instead of H 2 is the electron donor (12). The remaining genes that were markedly regulated by H 2 were those encoding F 420 -dependent methylenetetrahydromethanopterin dehydrogenase (Mtd; Mmp0372) and F 420 -dependent methylenetetrahydromethanopterin reductase (Mmp0058), central steps in methanogenesis.…”