Dissimilatory sulfite reductase from Archaeoglobus profundus and Desulfotomaculum thermocisternum: Phylogenetic and structural implications from gene sequences

Extremophiles

Volumn 3, Issue 1, 1999, Pages 63-70

  Larsen, Øivind ^a   Lien, Torleiv ^a   Birkeland, Nils Kåre ^a  

^a UNIVERSITY OF BERGEN   (Norway)

Author keywords

Archaeoglobus profundus; Desulfotomaculum thermocisternum; Dissimilatory sulfite reductase; Phylogenetic analysis; Sequence analysis

Indexed keywords

AMINO ACID ANALYSIS; ARCHAEOGLOBUS FULGIDUS; BACTERIAL GENETICS; CLONED GENE; DISSIMILATORY SULFITE REDUCTASE; ENZYMIC REDUCTION; ESCHERICHIA COLI; GENE SEQUENCE; PHYLOGENY;

AMINO ACID SEQUENCE; ARCHAEA; BASE SEQUENCE; CHROMOSOME MAPPING; CLONING, MOLECULAR; DNA, ARCHAEAL; GENES, ARCHAEAL; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES ACTING ON SULFUR GROUP DONORS; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY, AMINO ACID;

ARCHAEA; ARCHAEOGLOBUS FULGIDUS; ARCHAEOGLOBUS PROFUNDUS; BACTERIA (MICROORGANISMS); DESULFOTOMACULUM THERMOCISTERNUM; DESULFOVIBRIO VULGARIS; ESCHERICHIA COLI; POSIBACTERIA;

EID: 0033021380     PISSN: 14310651     EISSN: None     Source Type: Journal    
DOI: 10.1007/s007920050100     Document Type: Article

References (32)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidmar JG, Smith JA, Struhl K (1992) Short protocols in molecular biology, 2nd edn. Greene Publishing and Wiley, New York
3. Beeder J, Torsvik T, Lien T (1995) Thermodesulforhabdus norvegicus gen. nov., sp. nov., a novel thermophilic sulfate-reducing bacterium from oil field waler. Arch Microbiol 164:331-336
4. Bruschi M, Hatch kian C, Le Gall J, Moura JJ, Xavier AV (1976) Purification, characterization and biological activity of three forms of ferredoxin from the sulfate-reducing bacterium Desulfovibrio gigas. Biochim Biophys Acta 449:275-284
5. Burggraf S, Jannasch HW, Nicolaus B, Stetter KO (1990) Archaeoglobus profundus sp. nov., represents a new species within the sulfate-reducing Archaebacteria. Syst Appl Microbiol 13:24-28
6. Chen L, Liu MY, LeGall J (1991) Calcium is required for the reduction of sulfite from hydrogen in a reconstituted electron transfer chain from the sulfate reducing bacterium. Desulfovibrio gigas. Biochem Biophys Res Commun 180:238-242
7. Crane BR, Siegel LM, Getzoff ED (1995) Sulfite reductase structure at 1.6 Å: evolution and catalysis for reduction of inorganic anions. Science 270:59-67
8. Crane BR, Getzoff ED (1996 The relationship between structure and function for the sulfite reductases. Curr Opin Struct Biol 6:744-756
9. Dahl C, Kredich NM, Deutzmann R, Trüper HG (1993) Dissimilatory sulphite reductase from Archaeoglobus fulgidus: physico-chemical properties of the enzyme and cloning, sequencing and analysis of the reductase genes. J Gen Microbiol 139:1817-1828
10. Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein sequence and structure. National Biochemical Research Foundation, Washington, DC
11. Devereux R, Delaney M, Widdel F, Stahl DA (1989) Natural relationships among sulfate-reducing eubacteria. J Bacteriol 171:6689-6695
12. Diaz-Lazcoz Y, Henaut A, Vigier P, Risler J-L (1995) Differential codon usage for conserved amino acids: evidence that the serine codons TCN were primordial. J Mol Biol 250:123-127
13. Fauque G, Lino AR, Czechowski M, Kang L, DerVartanian DV, Moura JJ, LeGall J, Moura I (1990) Purification and characterization of bisulfite reductase (desulfofuscidin) from Desulfovibrio thermophilus and its complexes with exogenous ligands. Biochim Biophys Acta 1040:112-118
14. Forterre P (1997) Protein versus rRNA: problems in rooting the universal tree of life. ASM News 63:89-95
15. Graves MC, Rabinowitz JC (1986) In vivo and in vitro transcription of the Clostridium pasteurianum ferredoxin gene. Evidence for "extended" promoter elements in gram-positive organisms. J Biol Chem 261:11409-11415
16. Henry EA, Devereux R, Maki JS, Gilmour CC, Woese CR, Mandelco L, Schaunder R, Remsen CC, Mitchell R (1994) Characterization of a new thermophilic sulfate-reducing bacterium -Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov. - its phylogenetic relationship to thermodesulfobacterium commune and their origins deep within the bacterial domain. Arch Microbiol 161:62-69
17. Hipp WM, Pott AS, Thum-Schmitz N, Faath I, Dahl C, Trüper HG (1997) Towards the phytogeny of APS reductases and sirohaem sulfite reductases in sulfate-reducing and sulfur-oxidizing prokaryotes. Microbiology 143:2891-2902
18. Huang CJ, Barrett EL (1991) Sequence analysis and expression of the Salmonella typhimurium asr operon encoding production of hydrogen sulfide from sulfite. J Bacteriol 173:1544-1553
19. Karkhoff-Schweizer RR, Huber DP, Voordouw G (1995) Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR. Appl Environ Microbiol 61:290-296
20. Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou LX, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature (Lond) 390:364-370
21. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessières P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Cummings NJ, Daniel RA, Denizot F, Devine KM, Düsterhöft A, Ehrlich SD, Emmerson PT, Entian KD, Errington J, Fabret C, Ferrari E, Foulger D, Fritz C, Fujita M, Fujita Y, Fuma S, Galizzi A, Galleron N, Ghim SY, Glaser P, Goffeau A, Golightly EJ, Grandi G, Guiseppi G, Guy BJ, Haga K, Haiech J, Harwood CR, Hénaut A, Hubert H, Holsappel S, Hosono S, Hullo MF, Itaya M, Jones L, Joris B, Karamata D, Kasahara Y, Klaerr-Blanchard M, Klein C, Kobayashi Y, Koetter P, Koningstein G, Krogh S, Kumano M, Kurita K, Lapidus A, Lardinois S, Lauber J, Lazarevic V, Lee SM, Levine A, Liu H, Masuda S, Mauël C, Médigue C, Medina N, Mellado RP, Mizuno M, Moestl D, Nakai S, Noback M, Noone D, O'Reilly M, Ogawa K, Ogiwara A, Oudega B, Park SH, Parro V, Pohl TM, Portetelle D, Porwollik S, Prescott AM, Presecan E, Pujic P, Purnelle B, Rapoport G, Rey M, Reynolds S, Rieger M, Rivolta C, Rocha E, Roche B, Rose M, Sadaie Y, Sato T, Scanlan E, Schleich S, Schroeter R, Scoffone F, Sekiguchi J, Sekowska A, Seror SJ, Serror P, Shin BS, Soldo B, Sorokin A, Tacconi E, Takagi T, Takahashi H, Takemaru K, Takeuchi M, Tamakoshi A, Tanaka T, Terpstra P, Tognoni A, Tosato V, Uchiyama S, Vandenbol M, Vannier F, Vassarotti A, Viari A, Wambutt R, Wedler E, Wedler H, Weitzenegger T, Winters P, Wipat A, Yamamoto H, Yamane K, Yasumoto K, Yata K, Yoshida K, Yoshikawa HF, Zumstein E, Yoshikawa H, Danchin A (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature (Lond) 390:249-256
22. Molitor M, Dahl C, Molitor I, Schafer U, Speich N, Huber R, Deutzmann R, Trüper HG (1998) A dissimilatory sirohaem-sulfite-reductase-type protein from the hyperthermophilic archaeon Pyrobaculum islandicum. Microbiology 144:529-541
23. 420, in Archaeoglobus fulgidus. Arch Microbiol 152:362-368
24. Nilsen RK, Torsvik T, Lien T (1996) Desulfotomaculum thermocisternum sp. nov., a sulfate reducer isolated from a hot North Sea oil reservoir. Int J Syst Bacteriol 46:397-402
25. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358
26. Peck HPJ, Lissolo T (1987) Assimilatory and dissimilatory sulphate reduction: enzymology and bioenergetics. In: Cole JA, Ferguson S (eds) The nitrogen and sulphur cycles. Cambridge University Press, Cambridge, p. 42
27. Sambrook JE, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Habor Laboratory, Cold Spring Harbor, New York
28. Stackebrandt E, Sproer C, Rainey FA, Burghardt J, Pauker O, Hippe H (1997) Phylogenetic analysis of the genus Desulfotomaculum: evidence for the misclassification of Desulfotomaculum guttoideum and description of Desulfotomaculum orientis as Desulfosporosinus orientis gen. nov., comb. nov. Int J Syst Bacteriol 47:1134-1139
29. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
30. Widdel F, Bak F (1992) Gram-negative sulfate-reducing bacteria. In: Barlows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryots: a handbook on the biology of bacteria; ecology, physiology, identification, applications, 2nd edn, vol 4. Springer, New York
31. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
32. Woese CR, Achenbach L, Rouviere P, Mandelco L (1991) Archaeal phylogeny: reexaminination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst Appl Microbiol 14:364-371