Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid

Buchenau, Bärbel; Thauer, Rudolf K.

doi:10.1007/s00203-004-0714-0

Cited by 35 publications

(50 citation statements)

References 60 publications

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“…The genome also does not contain gene homologues for PurN and PurH, which could catalyze the transfer of the formyl group of N 10 -formyltetrahydrofolate to positions 2 and 8 of purines. This is in agreement with the findings that M. stadtmanae does not contain tetrahydrofolate and that for thermodynamic reasons N 5 -formyl-H 4 MPT cannot substitute for N 10 -formyltetrahydrofolate in the two formyltransferase reactions (8). The genome contains a CDS for a molybdopterindependent formate dehydrogenase.…”

Section: Resultssupporting

confidence: 91%

The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H ₂ for Methane Formation and ATP Synthesis

Seedorf²,

et al. 2006

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Methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic archaea. This human intestinal inhabitant can generate methane only by reduction of methanol with H 2 and is dependent on acetate as a carbon source. We report here the genome sequence of M. stadtmanae, which was found to be composed of 1,767,403 bp with an average G؉C content of 28% and to harbor only 1,534 protein-encoding sequences (CDS). The genome lacks 37 CDS present in the genomes of all other methanogens. Among these are the CDS for synthesis of molybdopterin and for synthesis of the carbon monoxide dehydrogenase/acetylcoenzyme A synthase complex, which explains why M. stadtmanae cannot reduce CO 2 to methane or oxidize methanol to CO 2 and why this archaeon is dependent on acetate for biosynthesis of cell components. Four sets of mtaABC genes coding for methanol:coenzyme M methyltransferases were found in the genome of M. stadtmanae. These genes exhibit homology to mta genes previously identified in Methanosarcina species. The M. stadtmanae genome also contains at least 323 CDS not present in the genomes of all other archaea. Seventythree of these CDS exhibit high levels of homology to CDS in genomes of bacteria and eukaryotes. These 73 CDS include 12 CDS which are unusually long (>2,400 bp) with conspicuous repetitive sequence elements, 13 CDS which exhibit sequence similarity on the protein level to CDS encoding enzymes involved in the biosynthesis of cell surface antigens in bacteria, and 5 CDS which exhibit sequence similarity to the subunits of bacterial type I and III restriction-modification systems.There are two types of methanogenic archaea, those belonging to the order Methanosarcinales, which contain cytochromes and which can use methanol, methyl amines, acetate, and/or CO 2 plus H 2 as methanogenic substrates, and those belonging to the orders Methanobacteriales, Methanomicrobiales, Methanococcales, and Methanopyrales, which are devoid of cytochromes and which can use CO 2 plus H 2 and/or formate only to fuel anaerobic growth (95, 102). The energy metabolism of both types of methanogens has been investigated in detail (17). However, there are still a few pertinent questions. For example, why is the growth yield on H 2 and CO 2 of methanogens lacking cytochromes considerably lower (Ͻ50%) than that of cytochrome-containing methanogens? The growth yield on H 2 and CO 2 of Methanobrevibacter arboriphilus is 1.3 g/mol methane, whereas that of Methanosarcina barkeri is 7.3 g/mol (101). Could the reason for this be that in cytochrome-containing methanogens two steps in the reduction of CO 2 to methane, methyl transfer from methyl-tetrahydromethanopterin (methyl-H 4 MPT) to coenzyme M and reduction of the heterodisulfide coenzyme M-S-S-coenzyme B (CoM-S-S-CoB) with H 2 , are coupled with energy conservation, whereas in methanogens without cytochromes only one step, the methyltransfer reaction, is coupled? Indeed, methanogens with cytochromes contain a heterodisulfide reductase (HdrDE) that is anchored via a cytoc...

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Section: Resultssupporting

confidence: 91%

The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H ₂ for Methane Formation and ATP Synthesis

Seedorf²,

et al. 2006

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“…Generally, methanogenic archaea use tetrahydromethanopterin (H 4 MPT) for all C 1 metabolism, while methylotrophic bacteria contain an H 4 MPTrelated carrier for their C 1 energy metabolism and H 4 folate presumably for biosynthetic purposes (3). The one known exception to this is Methanosarcina species, which use both folate and MPT (6). Despite the similarities between MPT and folate, most of the enzymes that employ each respective coenzyme (7) and the enzymes involved in their biosynthesis (27) are not homologous, indicating that these C 1 carriers evolved independently.…”

Section: Ethanopterin (Mpt) (mentioning

confidence: 99%

Identification of a Unique Radical S -Adenosylmethionine Methylase Likely Involved in Methanopterin Biosynthesis in Methanocaldococcus jannaschii

Allen

White

2014

J Bacteriol

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Methanopterin (MPT) and its analogs are coenzymes required for methanogenesis and methylotrophy in specialized microorganisms. The methyl groups at C-7 and C-9 of the pterin ring distinguish MPT from all other pterin-containing natural products. However, the enzyme(s) responsible for the addition of these methyl groups has yet to be identified. Here we demonstrate that a putative radical S-adenosyl-L-methionine (SAM) enzyme superfamily member encoded by the MJ0619 gene in the methanogen Methanocaldococcus jannaschii is likely this missing methylase. When MJ0619 was heterologously expressed in Escherichia coli, various methylated pterins were detected, consistent with MJ0619 catalyzing methylation at C-7 and C-9 of 7,8-dihydro-6-hydroxymethylpterin, a common intermediate in both folate and MPT biosynthesis. Site-directed mutagenesis of Cys77 present in the first of two canonical radical SAM CX 3 CX 2 C motifs present in MJ0619 did not inhibit C-7 methylation, while mutation of Cys102, found in the other radical SAM amino acid motif, resulted in the loss of C-7 methylation, suggesting that the first motif could be involved in C-9 methylation, while the second motif is required for C-7 methylation. Further experiments demonstrated that the C-7 methyl group is not derived from methionine and that methylation does not require cobalamin. When E. coli cells expressing MJ0619 were grown with deuterium-labeled acetate as the sole carbon source, the resulting methyl group on the pterin was predominantly labeled with three deuteriums. Based on these results, we propose that this archaeal radical SAM methylase employs a previously uncharacterized mechanism for methylation, using methylenetetrahydrofolate as a methyl group donor.

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“…1). The enzymes that catalyze interconversions of the pathway intermediates are highly conserved across the three domains of life (1)(2)(3)(4)(5)(6). Serine hydroxymethyltransferase (GlyA) catalyzes the reversible reaction of conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylene-tetrahydrofolate (5,10-CH 2 -THF) (7).…”

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One-Carbon Metabolic Pathway Rewiring in Escherichia coli Reveals an Evolutionary Advantage of 10-Formyltetrahydrofolate Synthetase (Fhs) in Survival under Hypoxia

et al. 2015

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bIn cells, N 10 -formyltetrahydrofolate (N 10 -fTHF) is required for formylation of eubacterial/organellar initiator tRNA and purine nucleotide biosynthesis. Biosynthesis of N 10 -fTHF is catalyzed by 5,10-methylene-tetrahydrofolate dehydrogenase/cyclohydrolase (FolD) and/or 10-formyltetrahydrofolate synthetase (Fhs). All eubacteria possess FolD, but some possess both FolD and Fhs. However, the reasons for possessing Fhs in addition to FolD have remained unclear. We used Escherichia coli, which naturally lacks fhs, as our model. We show that in E. coli, the essential function of folD could be replaced by Clostridium perfringens fhs when it was provided on a medium-copy-number plasmid or integrated as a single-copy gene in the chromosome. The fhs-supported folD deletion (⌬folD) strains grow well in a complex medium. However, these strains require purines and glycine as supplements for growth in M9 minimal medium. The in vivo levels of N 10 -fTHF in the ⌬folD strain (supported by plasmid-borne fhs) were limiting despite the high capacity of the available Fhs to synthesize N 10 -fTHF in vitro. Auxotrophy for purines could be alleviated by supplementing formate to the medium, and that for glycine was alleviated by engineering THF import into the cells. The ⌬folD strain (harboring fhs on the chromosome) showed a high NADP ؉ -to-NADPH ratio and hypersensitivity to trimethoprim. The presence of fhs in E. coli was disadvantageous for its aerobic growth. However, under hypoxia, E. coli strains harboring fhs outcompeted those lacking it. The computational analysis revealed a predominant natural occurrence of fhs in anaerobic and facultative anaerobic bacteria.T he pathway of one-carbon metabolism is central to the synthesis of purine nucleotides, thymidylate, glycine, and methionine (Fig. 1). The enzymes that catalyze interconversions of the pathway intermediates are highly conserved across the three domains of life (1-6). Serine hydroxymethyltransferase (GlyA) catalyzes the reversible reaction of conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylene-tetrahydrofolate (5,10-CH 2 -THF) (7). FolD, a bifunctional enzyme, carries out sequential steps of reversible conversions of 5,10-CH 2 -THF to 5,10-methenyltetrahydrofolate (5,10-CH ϩ -THF), followed by the conversion of the latter to N 10 -formyltetrahydrofolate (N 10 -fTHF) by its dehydrogenase and cyclohydrolase activities, respectively (8). Availability of N 10 -fTHF is crucial for the de novo pathway of purine nucleotide biosynthesis and formylation of the initiator tRNA (tRNA fMet ) to initiate protein synthesis in eubacteria and eukaryotic organelles (9). N 10 -fTHF can also be synthesized by formyltetrahydrofolate synthetase, Fhs (also known as formate-tetrahydrofolate ligase), by utilizing THF, formate, and ATP (Fig. 1). The dual scheme of N 10 -fTHF synthesis is conserved in eukaryotes and some archaea (6). Many eukaryotic organisms possess FolD with trifunctional activities of dehydrogenase-cyclohydrolase-synthetase (10, 11). Among eubacter...

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Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid

Cited by 35 publications

References 60 publications

The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H ₂ for Methane Formation and ATP Synthesis

The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H ₂ for Methane Formation and ATP Synthesis

Identification of a Unique Radical S -Adenosylmethionine Methylase Likely Involved in Methanopterin Biosynthesis in Methanocaldococcus jannaschii

One-Carbon Metabolic Pathway Rewiring in Escherichia coli Reveals an Evolutionary Advantage of 10-Formyltetrahydrofolate Synthetase (Fhs) in Survival under Hypoxia

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Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid

Cited by 35 publications

References 60 publications

The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H 2 for Methane Formation and ATP Synthesis

The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H 2 for Methane Formation and ATP Synthesis

Identification of a Unique Radical S -Adenosylmethionine Methylase Likely Involved in Methanopterin Biosynthesis in Methanocaldococcus jannaschii

One-Carbon Metabolic Pathway Rewiring in Escherichia coli Reveals an Evolutionary Advantage of 10-Formyltetrahydrofolate Synthetase (Fhs) in Survival under Hypoxia

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The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H ₂ for Methane Formation and ATP Synthesis

The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H ₂ for Methane Formation and ATP Synthesis