Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans

Journal of Bacteriology

Volumn 178, Issue 2, 1996, Pages 347-356

  Hernandez, Julia M ^a   Baker, Stefanie H ^b   Lorbach, Stanley C ^b   Shively, Jessup M ^b   Tabita, F Robert ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b CLEMSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBULOSEBISPHOSPHATE CARBOXYLASE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; CONTROLLED STUDY; ENZYME ASSAY; ENZYME MECHANISM; NONHUMAN; PRIORITY JOURNAL; THIOBACILLUS;

AMINO ACID SEQUENCE; BASE SEQUENCE; ENZYME ACTIVATION; GENES, BACTERIAL; KINETICS; MOLECULAR SEQUENCE DATA; RHODOBACTER SPHAEROIDES; RIBULOSE-BISPHOSPHATE CARBOXYLASE; RIBULOSEPHOSPHATES; SEQUENCE ANALYSIS, DNA; SUBSTRATE SPECIFICITY; THIOBACILLUS;

BACTERIA (MICROORGANISMS); PROTEOBACTERIA; RHODOBACTER SPHAEROIDES; THIOBACILLUS DENITRIFICANS;

EID: 0030033929     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.178.2.347-356.1996     Document Type: Article

References (62)

1. Andrews, T. J., and B. Ballment. 1984. Active-site carbamate formation and reaction-intermediate-analog binding by ribulosebisphosphate carboxylase/oxygenase in the absence of its small subunits. Proc Natl. Acad. Sci USA 81:3660-3664.
2. Birnboim, H. C., and J. Doly. 1979 A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7:1513-1523
3. 2 RubisCO from a marine obligately autotrophic hydrogen-oxidizing bacterium. Hydrogenovibrio marinus strain MH-110. FEMS Microbiol. Lett 109:49-53.
4. Codd, G. A. 1988. Carboxysomes and ribulose bisphosphate carboxylase/oxygenase. Adv. Microb Physiol. 29:115-164.
5. Edmondson, D. L., H. J. Kane, and T. J. Andrews. 1990. Substrate isomerization inhibits ribulosebisphosphate carboxylase-oxygenase during catalysis. FEBS Lett. 260:62-66.
6. English, R. S., C. A. Williams, S. C. Lorbach, and J. M. Shively. 1992. Two forms of ribulose-1,5-bisphosphate carboxylase/oxygenase from Thiobacillus denitrificans. FEMS Microbiol. Lett 94:111-120
7. Falcone, D. L., and F. R. Tabita. 1991. Expression of endogenous and foreign ribulose 1,5-bisphosphate carboxylase-oxygenase (RubisCO) genes in a RubisCO deletion mutant of Rhodobacter sphaeroides. J. Bacteriol. 173:2099-2108
8. 2 fixation genes in a photosynthetic bacterial host. J. Bacteriol. 175:866-869.
9. Gibson, J. L. 1980. Different molecular forms of ribulose 1,5-bisphosphate carboxylase from Rhodopseudomonas sphaeroides Ph.D thesis. University of Texas, Austin.
10. 2 fixation, p. 1107-1124. In R E. Blankenship, M. T. Madigan, and C. E. Bauer (ed ), Anoxygenic photosynthetic bacteria Kluwer Academic Publishers. Dordrecht, The Netherlands.
11. 2 fixation operon of Rhodobacter sphaeroides J. Biol. Chem. 266:14646-14653.
12. Gibson, J. L., and F. R. Tabita. 1977. Different molecular forms of D-ribulose-1.5-bisphosphate carboxylase from Rhodopseudomonas sphaeroides. J. Biol Chem. 252:943-949.
13. Gibson, J. L., and F. R. Tabita. 1979 Activation of ribulose-r,5-bisphosphate carboxylase from Rhodopseudomonas sphaeroides: probable role of the small subunit. J Bacteriol. 140:1023-1027.
14. Gibson, J. L., and F. R. Tabita. 1985. Structural differences in the catalytic subunits of form I and form II ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodopseudomonas sphaeroides. J. Bacteriol. 164:1188-1193.
15. Hartman, F. C., and M. R. Harpel. 1993. Chemical and genetic piobes of the active site of D-ribulose-1,5-bisphosphate carboxylase/oxygenase: a retrospective based on the three-dimensional structure. Adv. Enzymol. Relat. Areas Mol. Biol. 67:1-75
16. Hartman, F. C., and M. R. Harpel. 1994. Structure, function, regulation, and assembly of D-ribulose-1,5-bisphosphate carboxylase/oxygenase. Annu. Rev. Biochem. 63:197-234
17. 2 fixation by mineral-leaching bacteria: characteristics of the ribulose bisphosphate carboxylase-oxygenase of Thiobacillus ferrooxidans. Biotechnol. Appl. Biochem 9:497-505
18. Jordan, D. B., and W. L. Ogren. 1981. Species variation in the specificity of ribulose bisphosphate carboxylase/oxygenase Nature (London) 291:513-515.
19. Jordan, D. B., and W. L. Ogren. 1981. A sensitive assay procedure for simultaneous determination of ribulose-1,5-bisphosphate carboxylase and oxygenase activities. Plant Physiol (Bethesda) 67:237-245.
20. Jouanneau, Y., and F. R. Tabita. 1986 Independent regulation of synthesis of form 1 and form II ribulose bisphosphate carboxylase/oxygenase in Rhodopseudomonas sphaeroides. J. Bacteriol 165:620-624.
21. Keen, N. T., S. Tamaki, D. Kobayashi, and D. Trollinger. 1988 Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria Gene 70:191-197
22. Kobayashi, H., A. M. Viale, T. Takabe, T. Akazawa, K. Wada, K. Shinozaki, K. Kobayashi, and M. Sugiura. 1991. Sequence and expression of genes encoding the large and small subunits of ribulose 1,5-bisphosphate carboxylase'oxygenase from Chromatium vinosum. Gene 97:55-62
23. Kusano, T., T. Takeshima, C. Inoue, and K. Sugawara. 1991 Evidence for two sets of structural genes coding for ribulose bisphosphate carboxylase in Thiobacillus ferrooxidans. J Bacteriol. 173:7313-7323
24. Laing, W. A., and J. T. Christeller. 1976. A model for the kinetics of activation and catalysis of ribulose-1,5-bisphosphate carboxylase. Biochem J. 159:563-570.
25. Larimer, F. W., M. R. Harpel, and F. C. Hartman. 1994. β-Elimination of phosphate from reaction intermediates by site-directed mutants of ribulose-bisphosphate carboxylase/oxygenase. J. Biol Chem. 269:11114-11120.
26. Larimer, F. W., and T. S. Soper. 1993. Overproduction of Anabaena 7120 ribulose-bisphosphate carboxylase/oxygenase in Escherichia coli. Gene 126:85-92.
27. Lee, B., B. A. Read, and F. R. Tabita. 1991 Catalytic properties of recombinant octameric, hexadecameric, and heterologous cyanobacterial/bacterial ribulose-1,5-bisphosphate carboxylase/oxygenase. Arch. Biochem Biophys 291:1-7.
28. Lee, E. H., M. R. Harpel, Y. R. Chen, and F. C. Hartman. 1993. Perturbation of reaction-intermediate partitioning by a site-directed mutant of ribulose-bisphosphate carboxylase/oxygenase. J. Biol. Chem. 268:26583-26591.
29. Li, L. A. 1994. Molecular and biochemical studies of RubisCO activation in Anabaena species. Ph.D. thesis. The Ohio State University, Columbus.
30. Lorimer, G. H., Y. R. Chen, and F. C. Hartman. 1993. A role for the ε-amino group of lysine-334 of ribulose-1,5-bisphosphate carboxylase in the addition of carbon dioxide to the 2,3-enediol(ate) of ribulose-1,5-bisphosphate. Biochemistry 32:9018-9024.
31. Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning: a laboratory manual, p. 166-167. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
32. McFadden, B. A., and A. R. Denend. 1972. Ribulose diphosphate carboxylase from autotrophic microorganisms. J. Bacteriol. 110:633-642
33. Morse, D., P. Salois, P. Markovic, and J. W. Hastings. 1995. A nuclear-encoded form II RubisCO in dinoflagellates. Science 268:1622-1624.
34. Muller, E. D., J. Chory, and S. Kaplan. 1985. Cloning and characterization of the gene product of the form II ribulose-1,5-bisphosphate carboxylase gene of Rhodopseudomonas sphaeroides. J. Bacteriol. 161:469-472.
35. Nargang, F., L. McIntosh, and C. Somerville. 1984. Nucleotide sequence of the ribulosebisphosphate carboxylase gene from Rhodospirillum rubrum Mol. Gen. Genet. 193:220-224.
36. Newman, J., and S. Gutteridge. 1993. The X-ray structure of Synechococcus ribulose-bisphosphate carboxylase/oxygenase-activated complex at 2.2 Å. J Biol. Chem. 268:25876-25886.
37. Ormerod, J. G., K. S. Ormerod, and H. Gest. 1961. Light-dependent utilization of organic compounds and photoproduction of molecular hydrogen by photosynthetic bacteria; relationships with nitrogen metabolism. Arch. Biochem. Biophys. 94:449-463.
38. Pierce, J., G. H. Lorimer, and G. S. Reddy. 1986. Kinetic mechanism of ribulosebisphosphate carboxylase: evidence of an ordered, sequential reaction. Biochemistry 25:1636-1644.
39. Purohoit, K., B. A. McFadden, and A. L. Cohen. 1976. Purification, quaternary structure, composition, and properties of D-ribulose-1,5-bisphosphate carboxylase from Thiobacillus intermedius. J. Bacteriol. 127:505-515.
40. Quivey, R. G., and F. R. Tabita. 1984. Cloning and expression in Escherichia coli of the form II ribulose-1,5-bisphosphate carboxylase/oxygenase gene from Rhodopseudomonas sphaeroides Gene 31:91-101.
41. Read, B. A., and F. R. Tabita. 1992 Amino acid substitutions in the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase that influence catalytic activity of the holoenzyme. Biochemistry 31:519-525.
42. Read, B. A., and F. R. Tabita. 1994. High substrate specificity factor for ribulose bisphosphate carboxylase/oxygenase from eukaryotic marine algae and properties of recombinant cyanobacterial RubisCO containing "algal" residue modifications. Arch. Biochem. Biophys. 312:210-218.
43. Schloss, J. V., E. F. Phares, M. V. Long, I. L. Norton, C. D. Stringer, and F. C. Hartman. 1979. Isolation, characterization, and crystallization of ribulosebisphosphate carboxylase from autotrophically grown Rhodospirillum rubrum. J. Bacteriol 137:490-501
44. Schneider, G., Y. Lindqvist, and T. Lindqvist. 1990 Cristallographic refine-ment and structure of ribulose-1,5-bisphosphate carboxylase from Rhodespirillum rubrum at 1.7 Å resolution. J. Mol. Biol. 211:989-1008.
45. Simon, R., U. Priefer, and A. Pühler. 1983. A broad-host-range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria Bio/Technology 1:784-791.
46. Snead, R. M., and J. M. Shively. 1978. D-Ribulose-1,5-bisphosphate carboxylase from Thiobacillus neapolitanus Curr Microbiol. 1:309-314.
47. Spreitzer, R. J., D. B. Jordan, and W. L. Ogren. 1982. Biochemical and genetic analysis of an RuBP carboxylase/oxygenase-deficient mutant and revertants of Chlamydomonas reinhardii. FEBS Lett. 148:117-121.
48. Stein, J. L., M. Haywood, and H. Felbeck. 1990. Nucleotide sequence and expression of a deep-sea ribulose-1,5-bisphosphate carboxylase gene cloned from a chemoautotrophic bacterial endosymbiont. Proc. Natl. Acad. Sci USA 87:8850-8854.
49. Stoner, M. T., and J. M. Shively. 1993. Cloning and expression of the D-ribulose-1,5-bisphosphate carboxylase/oxygenase form II gene from Thiobacillus intermedius in Escherichia coli. FEMS Microbiol. Lett. 107:287-292
50. Tabita, F. R. 1988. Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms. Microbiol. Rev 52:155-189.
51. 2 fixation in purple bacteria, p. 895-914. In R. E Blankenship, M. T. Madigan, and C. E Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
52. Tabita, F. R., J. L. Gibson, W. J. Mandy, and R. G. Quivey, Jr. 1986. Synthesis and assembly of a novel recombinant ribulose 1,5-bisphosphate carboxylase/oxygenase. Bio/Technology 4:138-141.
53. Tabita, F. R., and B. A. McFadden. 1972. Regulation of ribulose-1,5-diphosphate carboxylase by 6-phospho-D-gluconate. Biochem. Biophys. Res. Commun. 48:1153-1159.
54. Tabita, F. R., and B. A. McFadden. 1974. D-Ribulose 1,5-diphosphate carboxylase from Rhodospirillum rubrum. I. Levels, purification, and effects of metallic ions. J. Biol. Chem. 249:3453-3458.
55. Tabita, F. R., and B. A. McFadden. 1974. D-Ribulose 1,5-diphosphate carboxylase from Rhodospirillum rubrum II. Quaternary structure, composition, catalytic, and immunological properties. J. Biol. Chem. 249:3459-3464
56. Tabita, F. R., and C. L. Small. 1985. Expression and assembly of active cyanobacterial ribulose-1,5-bisphosphate carboxylase/oxygenase in Escherichia coli containing stoichiometric amounts of large and small subunits. Proc. Natl. Acad. Sci USA 82:6100-6103.
57. Wagner, S. J., S. E. Stevens, B. T. Nixon, D. H. Lambert, R. G. Quivey, and F. R. Tabita. 1988. Nucleotide and deduced amino acid sequence of the Rhodobacter sphaeroides gene encoding form II ribulose-1,5-bisphosphate carboxylase/oxygenase and comparison with other deduced form I and II sequences FEMS Microbiol. Lett. 55:217-222.
58. Weaver, K. E., and F. R. Tabita. 1983. Isolation and partial characterization of Rhodopseudomonas sphaeroides mutants defective in the regulation of ribulose bisphosphate carboxylase/oxygenase J. Bacteriol. 156:507-515.
59. Whitney, S. M., D. C. Shaw, and D. Yellowlees. 1995. Evidence that some dinofiagellates contain a ribulose-1,5-bisphosphate carboxylase/oxygenase related to that of the α-proteobacteria. Proc. R. Soc. Lond. Ser. B 259:271-275.
60. 2 form of RubisCO from a marine obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110. Biosci. Biotechnol Biochem. 58:1733-1737
61. Yokota, A., and S. Kitaoka. 1989 Linearity and functioning forms in the carboxylase reaction of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase. Plant Cell Physiol. 30:183-191.
62. Zhu, G., and R. G. Jensen. 1991. Fallover of ribulose-1,5-bisphosphate carboxylase/oxygenase activity. Decarbamylation of catalytic sites depends on pH. Plant Physiol. (Bethesda) 97:1354-1358.