Growth- and substrate-dependent transcription of the formate dehydrogenase (fdhCAB) operon in Methanobacterium thermoformicicum Z-245

Abstract

The formate dehydrogenase-encoding fdhCAB operon and flanking genes have been cloned and sequenced from Methanobacterium thermoformicicum Z-245. fdh transcription was shown to be initiated 21 bp upstream from fdhC, although most fdh transcripts terminated or were processed between fdhC and fdhA. The resulting fdhC, fdhAB, and fdhCAB transcripts were present at all growth stages in cells growing on formate but were barely detectable during early exponential growth on H 2 plus CO 2 . The levels of the fdh transcripts did, however, increase dramatically in cells growing on H 2 plus CO 2 , coincident with the decrease in the growth rate and the onset of constant methanogenesis that occurred when culture densities reached an optical density at 600 nm of ϳ0.5. The mth transcript that encodes the H 2 -dependent methenyl-H 4 MPT reductase (MTH) and the frh and mvh transcripts that encode the coenzyme F 420 -reducing (FRH) and nonreducing (MVH) hydrogenases, respectively, were also present in cells growing on formate, consistent with the synthesis of three hydrogenases, MTH, FRH, and MVH, in the absence of exogenously supplied H 2 . Reducing the H 2 supply to M. thermoformicicum cells growing on H 2 plus CO 2 reduced the growth rate and CH 4 production but increased frh and fdh transcription and also increased transcription of the mtd, mer, and mcr genes that encode enzymes that catalyze steps 4, 5, and 7, respectively, in the pathway of CO 2 reduction to CH 4 . Reducing the H 2 supply to a level insufficient for growth resulted in the disappearance of all methane gene transcripts except the mcr transcript, which increased. Regions flanking the fdhCAB operon in M. thermoformicicum Z-245 were used as probes to clone the homologous region from the Methanobacterium thermoautotrophicum ⌬H genome. Sequencing revealed the presence of very similar genes except that the genome of M. thermoautotrophicum, a methanogen incapable of growth on formate, lacked the fdhCAB operon.Methanobacterium thermoautotrophicum ⌬H and Methanobacterium thermoformicicum Z-245 are very closely related, thermophilic methanogens that could be considered members of the same species (16,23,41). However, M. thermoautotrophicum grows only by the H 2 -dependent reduction of CO 2 to CH 4 (9, 39), whereas M. thermoformicicum is more metabolically versatile and can also catabolize formate to CH 4 and therefore can grow in the absence of exogenously supplied H 2 . The availability of H 2 determines which of two intersecting pathways of CO 2 reduction to CH 4 is employed by M. thermoautotrophicum (20, 39). When excess H 2 is available, the mth and mrt genes are transcribed, resulting in the synthesis of the H 2 -dependent N 5 ,N 10 -methenyltetrahydromethanopterin (methenyl-H 4 MPT) reductase (MTH) and methyl coenzyme M reductase (MR) II, respectively, that catalyze steps 4 and 7 in the seven-step pathway of CO 2 reduction to CH 4 (5, 25, 27, 49). However, under H 2 -limited growth conditions, these steps are catalyzed by the reduced coenzyme F 420 -dependent N 5...

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

“…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.…”

“…The smaller mRNAs could be formed by termination or processing between fdhC and fdhA, although a separate initiation of transcription in this region could not be ruled out. In M. thermoautotrophicus Z-245 the levels of fdh mRNA increased when the availability of hydrogen was decreased (15).…”

“…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.…”

“…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.…”

“…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).…”