Flavin Mononucleotide-Binding Flavoprotein Family in the Domain
            <i>Archaea</i>

Ding, Yan; Ferry, James G.

doi:10.1128/jb.186.1.90-97.2004

Cited by 19 publications

(38 citation statements)

References 34 publications

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“…afpA appears to encode a novel dihydromethanopterin reductase. Ding and Ferry have recently purified an AfpA homolog from A. fulgidus and demonstrated that it is an FMN-binding electron carrier protein (8). These authors also analyzed the distribution of AfpAs in prokaryotes based on the genomic sequences available at the time and concluded that these were restricted to methanogenic archaea.…”

Section: Discussionmentioning

confidence: 99%

“…However, one additional gene is present upstream of orf20, having homologs in Archaea, encoding a conserved archaeal flavoprotein (afpA) (8). In addition to the two gene islands, three other archaeal gene homologs were found in the genome.…”

Section: Gene Islands Encoding H 4 Mpt-linked C 1 Transfer Reactions mentioning

confidence: 99%

“…Two novel genes were found conserved in a number of proteobacterial gene clusters that were not identifiable in the genome of M. extorquens (3) but have homologs in Archaea: orf1 and afpA. No function has been proposed for homologs of orf1 in Archaea; however, AfpA in Archaeoglobus fulgidus has been proposed to be involved in electron transfer between ferredoxin and the CO dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) complex (8). The possible involvement of orf1 and afpA in the C 1 transfer pathway was tested via mutagenesis in M. flagellatus.…”

Section: Gene Islands Encoding H 4 Mpt-linked C 1 Transfer Reactions mentioning

confidence: 99%

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Analysis of Gene Islands Involved in Methanopterin-Linked C ₁ Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Kalyuzhnaya¹,

Korotkova²,

Crowther³

et al. 2005

J Bacteriol

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In this study, the occurrence and chromosomal clustering of genes encoding C 1 transfer reactions linked to tetrahydromethanopterin (H 4 MPT) were analyzed in a variety of proteobacteria and in representatives of the Planctomycetes via genomic analysis or via partial sequencing by cosmid walking. Although a tendency for clustering was found common for the genes of interest, significant variations in gene order and the degree of clustering were uncovered both between and within different groups of Proteobacteria and between Proteobacteria and Planctomycetes. Phylogenetic analyses suggested that the evolution of genes encoding H 4 MPT-linked reactions in Proteobacteria involved lateral transfers within Proteobacteria and possibly between Proteobacteria and other phyla. Gene cluster comparisons revealed a number of novel genes potentially involved in the C 1 transfer reactions, and these were analyzed by mutation and expression analyses. Four genes, a homolog of pabB, and three genes conserved between methanogenic Archaea and Bacteria possessing H 4 MPT-linked functions, orfY, orf1, and afpA were shown to be involved in formaldehyde oxidation/detoxification, as judged by specific mutant phenotypes. In particular, pabB contributes to the biosynthesis of para-aminobenzoic acid, a precursor of both tetrahydrofolate and H 4 MPT, and afpA apparently encodes a novel dihydromethanopterin reductase, based on mutant complementation experiments.One of the major breakthroughs in the understanding of methylotrophy in Bacteria during the recent decade, the recognition of the tetrahydromethanopterin (H 4 MPT)-linked pathway for formaldehyde oxidation as a major C 1 oxidation pathway, was due to a serendipitous discovery of a cluster of genes in Methylobacterium extorquens AM1 that are homologous to the genes involved in methanogenesis in Archaea (7). It has since been demonstrated that this pathway is nearly ubiquitous in gram-negative methylotrophs (26). More recently, the pathway's presence has been expanded beyond methylotrophs (20), and even beyond Proteobacteria into the Planctomycetes (5, 10). Although phylogenetic analysis has argued against recent lateral transfer of the genes in question between methanogenic Archaea and Proteobacteria (5), the history of these genes in Bacteria remains poorly understood. Although some congruence has been observed between the phylogenetic positions of the respective species within Proteobacteria and phylogenies of genes involved in H 4 MPT-linked reactions (13, 15), the relationships of the latter are not always well resolved and sometimes are complicated by the presence of multiple gene copies. In the present study we attempted a more comprehensive analysis of gene islands in Bacteria involved in H 4 MPTlinked C 1 transfers via analysis of available genomic sequences, via expanding gene databases by cosmid walking, and via mutagenesis and phylogenetic analysis. The following major objectives were pursued: (i) to determine whether gene clustering patterns are conserved within specific gr...

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Section: Discussionmentioning

confidence: 99%

Section: Gene Islands Encoding H 4 Mpt-linked C 1 Transfer Reactions mentioning

confidence: 99%

Section: Gene Islands Encoding H 4 Mpt-linked C 1 Transfer Reactions mentioning

confidence: 99%

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Analysis of Gene Islands Involved in Methanopterin-Linked C ₁ Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Kalyuzhnaya¹,

Korotkova²,

Crowther³

et al. 2005

J Bacteriol

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“…In contrast to M. barkeri, Methanosarcina acetivorans lacks the Ech hydrogenase (11). It can nevertheless grow on acetate, which is why another complex present in this organism, the Rnf complex, is thought to be involved in the aceticlastic pathway of methanogenesis as an acceptor for Fd red (8,10,17). The Methanosarcina mazei genome, however, contains genes coding for the Ech hydrogenase, but this species lacks the Rnf complex (5).…”

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confidence: 99%

Function of Ech Hydrogenase in Ferredoxin-Dependent, Membrane-Bound Electron Transport in Methanosarcina mazei

et al. 2010

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Reduced ferredoxin is an intermediate in the methylotrophic and aceticlastic pathway of methanogenesis and donates electrons to membrane-integral proteins, which transfer electrons to the heterodisulfide reductase. A ferredoxin interaction has been observed previously for the Ech hydrogenase. Here we present a detailed analysis of a Methanosarcina mazei ⌬ech mutant which shows decreased ferredoxin-dependent membranebound electron transport activity, a lower growth rate, and faster substrate consumption. Evidence is presented that a second protein whose identity is unknown oxidizes reduced ferredoxin, indicating an involvement in methanogenesis from methylated C 1 compounds.The aceticlastic pathway of methanogenesis creates approximately 70% (10) of the biologically produced methane and is of great ecological importance, as methane is a potent greenhouse gas. Organisms using this pathway to convert acetate to methane belong exclusively to the genera Methanosarcina and Methanosaeta. The two carbon atoms of acetate have different fates in the pathway. The methyl moiety is converted to methane, whereas the carbonyl moiety is further oxidized to CO 2 and the electrons derived from this oxidation step are used to reduce ferredoxin (Fd) (6). During methanogenesis from methylated C 1 compounds (methanol and methylamines), onequarter of the methyl groups are oxidized to obtain electrons for the reduction of heterodisulfide (27). A key enzyme in the oxidative part of methylotrophic methanogenesis is the formylmethanofuran dehydrogenase, which oxidizes the intermediate formylmethanofuran to CO 2 (7). The electrons are transferred to Fd. It has been suggested that reduced ferredoxin (Fd red ) donates electrons to the respiratory chain with the heterodisulfide (coenzyme M [CoM]-S-S-CoB) as the terminal electron acceptor and that the reaction is catalyzed by the Fd red :CoM-S-S-CoB oxidoreductase system (7, 24). The direct membranebound electron acceptor for Fd red is still a matter of debate; for the Ech hydrogenase, a reduced ferredoxin-accepting, H 2 -evolving activity has been observed for Methanosarcina barkeri (20), which implies that the H 2 :CoM-S-S-CoB oxidoreductase system is involved in electron transport (13). Direct electron flow from the Ech hydrogenase to the heterodisulfide reductase has not been shown to date (20,21). In contrast to M. barkeri, Methanosarcina acetivorans lacks the Ech hydrogenase (11). It can nevertheless grow on acetate, which is why another complex present in this organism, the Rnf complex, is thought to be involved in the aceticlastic pathway of methanogenesis as an acceptor for Fd red (8,10,17). The Methanosarcina mazei genome, however, contains genes coding for the Ech hydrogenase, but this species lacks the Rnf complex (5).To investigate whether the Ech hydrogenase is the only means by which M. mazei channels electrons from Fd red into the respiratory chain, a mutant lacking the Ech hydrogenase (M. mazei ⌬ech mutant) was constructed. Electron transport experiments using Fd red as the el...

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“…Genome sequencing has revealed that some betaproteobacteria also lack the dmrA gene but contain instead an additional gene (afpA) coding for an archaealflavoprotein-like flavoprotein (AfpA) of undetermined function (22,23). The bacterial AfpA homolog contains a predicted flavin mononucleotide (FMN)-binding site but lacks a recognizable binding site for other cofactors.…”

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confidence: 99%

Discovery and Characterization of the First Archaeal Dihydromethanopterin Reductase, an Iron-Sulfur Flavoprotein from Methanosarcina mazei

Wang

Tiongson

Rasche

2013

Journal of Bacteriology

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The microbial production of methane by methanogenic archaea is dependent on the synthesis of the pterin-containing cofactor tetrahydromethanopterin (H 4 MPT). The enzyme catalyzing the last step of H 4 MPT biosynthesis (dihydromethanopterin reductase) has not previously been identified in methane-producing microorganisms. Previous complementation studies with the methylotrophic bacterium Methylobacterium extorquens have indicated that an uncharacterized archaeal-flavoprotein-like flavoprotein (AfpA) from Methylobacillus flagellatus or Burkholderia xenovorans can replace the activity of a phylogenetically unrelated bacterial dihydromethanopterin reductase (DmrA). We propose that MM1854, a homolog of AfpA from Methanosarcina mazei, catalyzes the last step of H 4 MPT biosynthesis in methane-producing microorganisms. To test this hypothesis, a six-histidine (His 6 )-tagged version of MM1854 was produced. Bioinformatic analysis revealed the presence of one flavin mononucleotide (FMN)-binding site and two iron-sulfur cluster sites, consistent with an oxidoreductase enzyme. Purified His 6 -MM1854 occurred as a homodimer of 29-kDa subunits, and the UV-visible spectrum of the purified protein showed absorbance peaks at 380 and 460 nm, characteristic of oxidized FMN. NAD(P)H was incapable of directly reducing the flavin cofactor, but dithionite eliminated the FMN peaks, indicating successful electron transfer to MM1854. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin could also reduce the FMN peaks. A newly developed assay indicated that dithiothreitol-reduced MM1854 could transfer electrons to dihydromethanopterin. This assay was also effective with a heatstable DmrX analog from Methanocaldococcus jannaschii (MJ0208). These results provide the first biochemical evidence that MM1854 and MJ0208 function as archaeal dihydromethanopterin reductases (DmrX) and that ferredoxin may serve as an electron donor.

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Flavin Mononucleotide-Binding Flavoprotein Family in the Domain Archaea

Cited by 19 publications

References 34 publications

Analysis of Gene Islands Involved in Methanopterin-Linked C ₁ Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Analysis of Gene Islands Involved in Methanopterin-Linked C ₁ Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Function of Ech Hydrogenase in Ferredoxin-Dependent, Membrane-Bound Electron Transport in Methanosarcina mazei

Discovery and Characterization of the First Archaeal Dihydromethanopterin Reductase, an Iron-Sulfur Flavoprotein from Methanosarcina mazei

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Flavin Mononucleotide-Binding Flavoprotein Family in the Domain Archaea

Cited by 19 publications

References 34 publications

Analysis of Gene Islands Involved in Methanopterin-Linked C 1 Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Analysis of Gene Islands Involved in Methanopterin-Linked C 1 Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Function of Ech Hydrogenase in Ferredoxin-Dependent, Membrane-Bound Electron Transport in Methanosarcina mazei

Discovery and Characterization of the First Archaeal Dihydromethanopterin Reductase, an Iron-Sulfur Flavoprotein from Methanosarcina mazei

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Analysis of Gene Islands Involved in Methanopterin-Linked C ₁ Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Analysis of Gene Islands Involved in Methanopterin-Linked C ₁ Transfer Reactions Reveals New Functions and Provides Evolutionary Insights