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

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.

[1]  J. Heider,et al.  Characterization of 2-ketoisovalerate ferredoxin oxidoreductase, a new and reversible coenzyme A-dependent enzyme involved in peptide fermentation by hyperthermophilic archaea , 1996, Journal of bacteriology.

[2]  B. Guigliarelli,et al.  Isolation and characterization of the pyruvate-ferredoxin oxidoreductase from the sulfate-reducing bacterium Desulfovibrio africanus. , 1995, Biochimica et biophysica acta.

[3]  C. Clayton,et al.  Identification of carboxylation enzymes and characterization of a novel four-subunit pyruvate:flavodoxin oxidoreductase from Helicobacter pylori , 1995, Journal of bacteriology.

[4]  Z. Krozowski.  The short-chain alcohol dehydrogenase superfamily: Variations on a common theme , 1994, The Journal of Steroid Biochemistry and Molecular Biology.

[5]  M. Adams,et al.  Biochemical diversity among sulfur-dependent, hyperthermophilic microorganisms. , 1994, FEMS microbiology reviews.

[6]  M. Adams,et al.  Indolepyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. A new enzyme involved in peptide fermentation. , 1994, The Journal of biological chemistry.

[7]  M. Adams,et al.  Characterization of an ancestral type of pyruvate ferredoxin oxidoreductase from the hyperthermophilic bacterium, Thermotoga maritima. , 1994, Biochemistry.

[8]  M. Adams,et al.  Pyruvate ferredoxin oxidoreductases of the hyperthermophilic archaeon, Pyrococcus furiosus, and the hyperthermophilic bacterium, Thermotoga maritima, have different catalytic mechanisms. , 1994, Biochemistry.

[9]  G. Schneider,et al.  A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase, pyruvate oxidase and pyruvate decarboxylase. , 1993, Structure.

[10]  R. Haselkorn,et al.  Growth of the cyanobacterium Anabaena on molecular nitrogen: NifJ is required when iron is limited. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J. Strauss,et al.  Chicken sterol carrier protein 2/sterol carrier protein x: cDNA cloning reveals evolutionary conservation of structure and regulated expression. , 1993, Archives of biochemistry and biophysics.

[12]  M. Adams,et al.  Purification and characterization of pyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. , 1993, Biochimica et biophysica acta.

[13]  G. Schneider,et al.  Thiamin diphosphate dependent enzymes: transketolase, pyruvate oxidase and pyruvate decarboxylase , 1993 .

[14]  M. Adams.  Enzymes and proteins from organisms that grow near and above 100 degrees C. , 1993, Annual review of microbiology.

[15]  E. Schwartz,et al.  Molecular biology of hydrogen utilization in aerobic chemolithotrophs. , 1993, Annual review of microbiology.

[16]  W. Zillig,et al.  Elements of an archaeal promoter defined by mutational analysis. , 1992, Nucleic acids research.

[17]  A. Kletzin.  Molecular characterisation of a DNA ligase gene of the extremely thermophilic archaeon Desulfurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases. , 1992, Nucleic acids research.

[18]  M. Surette,et al.  Signal transduction in bacterial chemotaxis , 1992, The Journal of biological chemistry.

[19]  D. Oesterhelt,et al.  Improved purification, crystallization and primary structure of pyruvate:ferredoxin oxidoreductase from Halobacterium halobium. , 1992, European journal of biochemistry.

[20]  S. Nordlund,et al.  Purification and partial characterization of a pyruvate oxidoreductase from the photosynthetic bacterium Rhodospirillum rubrum grown under nitrogen-fixing conditions. , 1991, The Biochemical journal.

[21]  M. Adams,et al.  The extremely thermophilic eubacterium, Thermotoga maritima, contains a novel iron-hydrogenase whose cellular activity is dependent upon tungsten. , 1991, The Journal of biological chemistry.

[22]  W. Klingmüller,et al.  Cotranscription of the electron transport protein genes nifJ and nifF in Enterobacter agglomerans 333 , 1991, Journal of bacteriology.

[23]  C. Walsh,et al.  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. , 1990, Biochemistry.

[24]  R. Perham,et al.  A common structural motif in thiamin pyrophosphate‐binding enzymes , 1989, FEBS letters.

[25]  J. Beynon,et al.  The nucleotide sequence of the nifJ gene of Klebsiella pneumoniae. , 1988, Nucleic acids research.

[26]  A. Rump,et al.  Nucleotide sequence of a 24,206-base-pair DNA fragment carrying the entire nitrogen fixation gene cluster of Klebsiella pneumoniae. , 1988, Journal of molecular biology.

[27]  W. Zillig,et al.  Transcription termination in the archaebacterium Sulfolobus: signal structures and linkage to transcription initiation. , 1988, Nucleic acids research.

[28]  R. Mason,et al.  Free radical intermediates in the reaction of pyruvate:ferredoxin oxidoreductase in Tritrichomonas foetus hydrogenosomes. , 1987, The Journal of biological chemistry.

[29]  P. Leadlay,et al.  Purification and characterization of pyruvate: ferredoxin oxidoreductase from the anaerobic protozoon Trichomonas vaginalis. , 1987, The Biochemical journal.

[30]  W. Orme-Johnson,et al.  Clostridial pyruvate oxidoreductase and the pyruvate-oxidizing enzyme specific to nitrogen fixation in Klebsiella pneumoniae are similar enzymes. , 1987, The Journal of biological chemistry.

[31]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[32]  O. Wieland.  The mammalian pyruvate dehydrogenase complex: structure and regulation. , 1983, Reviews of physiology, biochemistry and pharmacology.

[33]  D. Oesterhelt,et al.  The catalytic mechanism of 2-oxoacid:ferredoxin oxidoreductases from Halobacterium halobium. One-electron transfer at two distinct steps of the catalytic cycle. , 1981, European journal of biochemistry.

[34]  D. Oesterhelt,et al.  Purification and properties of two 2-oxoacid:ferredoxin oxidoreductases from Halobacterium halobium. , 1981, European journal of biochemistry.

[35]  K. Uyeda,et al.  Pyruvate-ferredoxin oxidoreductase. 3. Purification and properties of the enzyme. , 1971, The Journal of biological chemistry.