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J Bacteriol. Jan 1996; 178(1): 248–257.
PMCID: PMC177646

Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Thermotoga maritima.

Abstract

Previous studies have shown that the hyperthermophilic archaeon Pyrococcus furiosus contains four distinct cytoplasmic 2-ketoacid oxidoreductases (ORs) which differ in their substrate specificities, while the hyperthermophilic bacterium Thermotoga maritima contains only one, pyruvate ferredoxin oxidoreductase (POR). These enzymes catalyze the synthesis of the acyl (or aryl) coenzyme A derivative in a thiamine PPi-dependent oxidative decarboxylation reaction with reduction of ferredoxin. We report here on the molecular analysis of the POR (por) and 2-ketoisovalerate ferredoxin oxidoreductase (vor) genes from P. furiosus and of the POR gene from T. maritima, all of which comprise four different subunits. The operon organization for P. furiosus POR and VOR was porG-vorDAB-porDAB, wherein the gamma subunit is shared by the two enzymes. The operon organization for T. maritima POR was porGDAB. The three enzymes were 46 to 53% identical at the amino acid level. Their delta subunits each contained two ferredoxin-type [4Fe-4S] cluster binding motifs (CXXCXXCXXXCP), while their beta subunits each contained four conserved cysteines in addition to a thiamine PPi-binding domain. Amino-terminal sequence comparisons show that POR, VOR, indolepyruvate OR, and 2-ketoglutarate OR of P. furiosus all belong to a phylogenetically homologous OR family. Moreover, the single-subunit pyruvate ORs from mesophilic and moderately thermophilic bacteria and from an amitochondriate eucaryote each contain four domains which are phylogenetically homologous to the four subunits of the hyperthermophilic ORs (27% sequence identity). Three of these subunits are also homologous to the dimeric POR from a mesophilic archaeon, Halobacterium halobium (21% identity). A model is proposed to account for the observed phenotypes based on genomic rearrangements of four ancestral OR subunits.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Adams MW. Enzymes and proteins from organisms that grow near and above 100 degrees C. Annu Rev Microbiol. 1993;47:627–658. [PubMed]
  • Adams MW. Biochemical diversity among sulfur-dependent, hyperthermophilic microorganisms. FEMS Microbiol Rev. 1994 Oct;15(2-3):261–277. [PubMed]
  • Alex LA, Reeve JN, Orme-Johnson WH, Walsh CT. Cloning, sequence determination, and expression of the genes encoding the subunits of the nickel-containing 8-hydroxy-5-deazaflavin reducing hydrogenase from Methanobacterium thermoautotrophicum delta H. Biochemistry. 1990 Aug 7;29(31):7237–7244. [PubMed]
  • Arnold W, Rump A, Klipp W, Priefer UB, Pühler A. Nucleotide sequence of a 24,206-base-pair DNA fragment carrying the entire nitrogen fixation gene cluster of Klebsiella pneumoniae. J Mol Biol. 1988 Oct 5;203(3):715–738. [PubMed]
  • Bauer CC, Scappino L, Haselkorn R. Growth of the cyanobacterium Anabaena on molecular nitrogen: NifJ is required when iron is limited. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):8812–8816. [PMC free article] [PubMed]
  • Blamey JM, Adams MW. Purification and characterization of pyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. Biochim Biophys Acta. 1993 Jan 15;1161(1):19–27. [PubMed]
  • Blamey JM, Adams MW. Characterization of an ancestral type of pyruvate ferredoxin oxidoreductase from the hyperthermophilic bacterium, Thermotoga maritima. Biochemistry. 1994 Feb 1;33(4):1000–1007. [PubMed]
  • Brostedt E, Nordlund S. Purification and partial characterization of a pyruvate oxidoreductase from the photosynthetic bacterium Rhodospirillum rubrum grown under nitrogen-fixing conditions. Biochem J. 1991 Oct 1;279(Pt 1):155–158. [PMC free article] [PubMed]
  • Cannon M, Cannon F, Buchanan-Wollaston V, Ally D, Ally A, Beynon J. The nucleotide sequence of the nifJ gene of Klebsiella pneumoniae. Nucleic Acids Res. 1988 Dec 9;16(23):11379–11379. [PMC free article] [PubMed]
  • Docampo R, Moreno SN, Mason RP. Free radical intermediates in the reaction of pyruvate:ferredoxin oxidoreductase in Tritrichomonas foetus hydrogenosomes. J Biol Chem. 1987 Sep 15;262(26):12417–12420. [PubMed]
  • Friedrich B, Schwartz E. Molecular biology of hydrogen utilization in aerobic chemolithotrophs. Annu Rev Microbiol. 1993;47:351–383. [PubMed]
  • Hain J, Reiter WD, Hüdepohl U, Zillig W. Elements of an archaeal promoter defined by mutational analysis. Nucleic Acids Res. 1992 Oct 25;20(20):5423–5428. [PMC free article] [PubMed]
  • Halboth S, Klein A. Methanococcus voltae harbors four gene clusters potentially encoding two [NiFe] and two [NiFeSe] hydrogenases, each of the cofactor F420-reducing or F420-non-reducing types. Mol Gen Genet. 1992 May;233(1-2):217–224. [PubMed]
  • Hawkins CF, Borges A, Perham RN. A common structural motif in thiamin pyrophosphate-binding enzymes. FEBS Lett. 1989 Sep 11;255(1):77–82. [PubMed]
  • Hrdý I, Müller M. Primary structure and eubacterial relationships of the pyruvate:ferredoxin oxidoreductase of the amitochondriate eukaryote Trichomonas vaginalis. J Mol Evol. 1995 Sep;41(3):388–396. [PubMed]
  • Hughes NJ, Chalk PA, Clayton CL, Kelly DJ. Identification of carboxylation enzymes and characterization of a novel four-subunit pyruvate:flavodoxin oxidoreductase from Helicobacter pylori. J Bacteriol. 1995 Jul;177(14):3953–3959. [PMC free article] [PubMed]
  • Juszczak A, Aono S, Adams MW. The extremely thermophilic eubacterium, Thermotoga maritima, contains a novel iron-hydrogenase whose cellular activity is dependent upon tungsten. J Biol Chem. 1991 Jul 25;266(21):13834–13841. [PubMed]
  • Kelly RM, Adams MW. Metabolism in hyperthermophilic microorganisms. Antonie Van Leeuwenhoek. 1994;66(1-3):247–270. [PubMed]
  • Kerscher L, Oesterhelt D. Purification and properties of two 2-oxoacid:ferredoxin oxidoreductases from Halobacterium halobium. Eur J Biochem. 1981 Jun 1;116(3):587–594. [PubMed]
  • Kerscher L, Oesterhelt D. The catalytic mechanism of 2-oxoacid:ferredoxin oxidoreductases from Halobacterium halobium. One-electron transfer at two distinct steps of the catalytic cycle. Eur J Biochem. 1981 Jun 1;116(3):595–600. [PubMed]
  • Kletzin A. Molecular characterisation of a DNA ligase gene of the extremely thermophilic archaeon Desulfurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases. Nucleic Acids Res. 1992 Oct 25;20(20):5389–5396. [PMC free article] [PubMed]
  • Krozowski Z. The short-chain alcohol dehydrogenase superfamily: variations on a common theme. J Steroid Biochem Mol Biol. 1994 Nov;51(3-4):125–130. [PubMed]
  • Kunow J, Linder D, Thauer RK. Pyruvate: ferredoxin oxidoreductase from the sulfate-reducing Archaeoglobus fulgidus: molecular composition, catalytic properties, and sequence alignments. Arch Microbiol. 1995 Jan;163(1):21–28. [PubMed]
  • Lechner K, Heller G, Böck A. Organization and nucleotide sequence of a transcriptional unit of Methanococcus vannielii comprising genes for protein synthesis elongation factors and ribosomal proteins. J Mol Evol. 1989 Jul;29(1):20–27. [PubMed]
  • Mai X, Adams MW. Indolepyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. A new enzyme involved in peptide fermentation. J Biol Chem. 1994 Jun 17;269(24):16726–16732. [PubMed]
  • Meinecke B, Bertram J, Gottschalk G. Purification and characterization of the pyruvate-ferredoxin oxidoreductase from Clostridium acetobutylicum. Arch Microbiol. 1989;152(3):244–250. [PubMed]
  • Muller YA, Lindqvist Y, Furey W, Schulz GE, Jordan F, Schneider G. A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase, pyruvate oxidase and pyruvate decarboxylase. Structure. 1993 Oct 15;1(2):95–103. [PubMed]
  • Pfeifer SM, Sakuragi N, Ryan A, Johnson AL, Deeley RG, Billheimer JT, Baker ME, Strauss JF., 3rd Chicken sterol carrier protein 2/sterol carrier protein x: cDNA cloning reveals evolutionary conservation of structure and regulated expression. Arch Biochem Biophys. 1993 Jul;304(1):287–293. [PubMed]
  • Pieulle L, Guigliarelli B, Asso M, Dole F, Bernadac A, Hatchikian EC. Isolation and characterization of the pyruvate-ferredoxin oxidoreductase from the sulfate-reducing bacterium Desulfovibrio africanus. Biochim Biophys Acta. 1995 Jul 3;1250(1):49–59. [PubMed]
  • Plaga W, Lottspeich F, Oesterhelt D. Improved purification, crystallization and primary structure of pyruvate:ferredoxin oxidoreductase from Halobacterium halobium. Eur J Biochem. 1992 Apr 1;205(1):391–397. [PubMed]
  • Reiter WD, Palm P, Zillig W. Transcription termination in the archaebacterium Sulfolobus: signal structures and linkage to transcription initiation. Nucleic Acids Res. 1988 Mar 25;16(6):2445–2459. [PMC free article] [PubMed]
  • Smith ET, Blamey JM, Adams MW. Pyruvate ferredoxin oxidoreductases of the hyperthermophilic archaeon, Pyrococcus furiosus, and the hyperthermophilic bacterium, Thermotoga maritima, have different catalytic mechanisms. Biochemistry. 1994 Feb 1;33(4):1008–1016. [PubMed]
  • Stock JB, Surette MG, McCleary WR, Stock AM. Signal transduction in bacterial chemotaxis. J Biol Chem. 1992 Oct 5;267(28):19753–19756. [PubMed]
  • Uyeda K, Rabinowitz JC. Pyruvate-ferredoxin oxidoreductase. 3. Purification and properties of the enzyme. J Biol Chem. 1971 May 25;246(10):3111–3119. [PubMed]
  • Wahl RC, Orme-Johnson WH. Clostridial pyruvate oxidoreductase and the pyruvate-oxidizing enzyme specific to nitrogen fixation in Klebsiella pneumoniae are similar enzymes. J Biol Chem. 1987 Aug 5;262(22):10489–10496. [PubMed]
  • Wieland OH. The mammalian pyruvate dehydrogenase complex: structure and regulation. Rev Physiol Biochem Pharmacol. 1983;96:123–170. [PubMed]
  • Williams K, Lowe PN, Leadlay PF. Purification and characterization of pyruvate: ferredoxin oxidoreductase from the anaerobic protozoon Trichomonas vaginalis. Biochem J. 1987 Sep 1;246(2):529–536. [PMC free article] [PubMed]
  • Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576–4579. [PMC free article] [PubMed]

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