Abstract
The cbbL cbbS and cbbM genes of Thiobacillus denitrificans, encoding form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), respectively, were found to complement a RubisCO-negative mutant of Rhodobacter sphaeroides to autotrophic growth. Endogenous T. denitrificans promoters were shown to function in R. sphaeroides, resulting in high levels of cbbL cbbS and cbbM expression in the R. sphaeroides host. This expression system provided high levels of both T. denitrificans enzymes, each of which was highly purified. The deduced amino acid sequence of the form I enzyme indicated that the large subunit was closely homologous to previously sequenced form I RubisCO enzymes from sulfur-oxidizing bacteria. The form I T. denitrificans enzyme possessed a very low substrate specificity factor and did not exhibit fallover, and yet this enzyme showed a poor ability to recover from incubation with ribulose 1,5-bisphosphate. The deduced amino acid sequence of the form II T. denitrificans enzyme resembled those of other form II RubisCO enzymes. The substrate specificity factor was characteristically low, and the lack of fallover and the inhibition by ribulose 1,5-bisphosphate were similar to those of form II RubisCO obtained from nonsulfur purple bacteria. Both form I and form II RubisCO from T. denitrificans possessed high KCO2 values, suggesting that this organism might suffer in environments containing low levels of dissolved CO2. These studies present the initial description of the kinetic properties of form I and form II RubisCO from a chemoautotrophic bacterium that synthesizes both types of enzyme.
Full Text
The Full Text of this article is available as a PDF (591.1 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Andrews T. J., Ballment B. Active-site carbamate formation and reaction-intermediate-analog binding by ribulosebisphosphate carboxylase/oxygenase in the absence of its small subunits. Proc Natl Acad Sci U S A. 1984 Jun;81(12):3660–3664. doi: 10.1073/pnas.81.12.3660. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chung S. Y., Yaguchi T., Nishihara H., Igarashi Y., Kodama T. Purification of form L2 RubisCO from a marine obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110. FEMS Microbiol Lett. 1993 May 1;109(1):49–53. doi: 10.1111/j.1574-6968.1993.tb06142.x. [DOI] [PubMed] [Google Scholar]
- Codd G. A. Carboxysomes and ribulose bisphosphate carboxylase/oxygenase. Adv Microb Physiol. 1988;29:115–164. doi: 10.1016/s0065-2911(08)60347-1. [DOI] [PubMed] [Google Scholar]
- English R. S., Williams C. A., Lorbach S. C., Shively J. M. Two forms of ribulose-1,5-bisphosphate carboxylase/oxygenase from Thiobacillus denitrificans. FEMS Microbiol Lett. 1992 Jul 1;73(1-2):111–119. doi: 10.1016/0378-1097(92)90593-d. [DOI] [PubMed] [Google Scholar]
- Falcone D. L., Tabita F. R. Expression and regulation of Bradyrhizobium japonicum and Xanthobacter flavus CO2 fixation genes in a photosynthetic bacterial host. J Bacteriol. 1993 Feb;175(3):866–869. doi: 10.1128/jb.175.3.866-869.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Falcone D. L., Tabita F. R. Expression of endogenous and foreign ribulose 1,5-bisphosphate carboxylase-oxygenase (RubisCO) genes in a RubisCO deletion mutant of Rhodobacter sphaeroides. J Bacteriol. 1991 Mar;173(6):2099–2108. doi: 10.1128/jb.173.6.2099-2108.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gibson J. L., Falcone D. L., Tabita F. R. Nucleotide sequence, transcriptional analysis, and expression of genes encoded within the form I CO2 fixation operon of Rhodobacter sphaeroides. J Biol Chem. 1991 Aug 5;266(22):14646–14653. [PubMed] [Google Scholar]
- Gibson J. L., Tabita F. R. Activation of ribulose 1,5-bisphosphate carboxylase from Rhodopseudomonas sphaeroides: probable role of the small subunit. J Bacteriol. 1979 Dec;140(3):1023–1027. doi: 10.1128/jb.140.3.1023-1027.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gibson J. L., Tabita F. R. Different molecular forms of D-ribulose-1,5-bisphosphate carboxylase from Rhodopseudomonas sphaeroides. J Biol Chem. 1977 Feb 10;252(3):943–949. [PubMed] [Google Scholar]
- Gibson J. L., Tabita F. R. Structural differences in the catalytic subunits of form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase from Rhodopseudomonas sphaeroides. J Bacteriol. 1985 Dec;164(3):1188–1193. doi: 10.1128/jb.164.3.1188-1193.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hartman F. C., Harpel M. R. Chemical and genetic probes 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. 1993;67:1–75. doi: 10.1002/9780470123133.ch1. [DOI] [PubMed] [Google Scholar]
- Hartman F. C., Harpel M. R. Structure, function, regulation, and assembly of D-ribulose-1,5-bisphosphate carboxylase/oxygenase. Annu Rev Biochem. 1994;63:197–234. doi: 10.1146/annurev.bi.63.070194.001213. [DOI] [PubMed] [Google Scholar]
- Jordan D. B., Ogren W. L. A Sensitive Assay Procedure for Simultaneous Determination of Ribulose-1,5-bisphosphate Carboxylase and Oxygenase Activities. Plant Physiol. 1981 Feb;67(2):237–245. doi: 10.1104/pp.67.2.237. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jouanneau Y., Tabita F. R. Independent regulation of synthesis of form I and form II ribulose bisphosphate carboxylase-oxygenase in Rhodopseudomonas sphaeroides. J Bacteriol. 1986 Feb;165(2):620–624. doi: 10.1128/jb.165.2.620-624.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Keen N. T., Tamaki S., Kobayashi D., Trollinger D. Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria. Gene. 1988 Oct 15;70(1):191–197. doi: 10.1016/0378-1119(88)90117-5. [DOI] [PubMed] [Google Scholar]
- Kobayashi H., Viale A. M., Takabe T., Akazawa T., Wada K., Shinozaki K., Kobayashi K., Sugiura M. Sequence and expression of genes encoding the large and small subunits of ribulose 1,5-bisphosphate carboxylase/oxygenase from Chromatium vinosum. Gene. 1991 Jan 2;97(1):55–62. doi: 10.1016/0378-1119(91)90009-z. [DOI] [PubMed] [Google Scholar]
- Kusano T., Takeshima T., Inoue C., Sugawara K. Evidence for two sets of structural genes coding for ribulose bisphosphate carboxylase in Thiobacillus ferrooxidans. J Bacteriol. 1991 Nov;173(22):7313–7323. doi: 10.1128/jb.173.22.7313-7323.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Laing W. A., Christeller J. T. A model for the kinetics of activation and catalysis of ribulose 1,5-bisphosphate carboxylase. Biochem J. 1976 Dec 1;159(3):563–570. doi: 10.1042/bj1590563. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Larimer F. W., Harpel M. R., Hartman F. C. Beta-elimination of phosphate from reaction intermediates by site-directed mutants of ribulose-bisphosphate carboxylase/oxygenase. J Biol Chem. 1994 Apr 15;269(15):11114–11120. [PubMed] [Google Scholar]
- Larimer F. W., Soper T. S. Overproduction of Anabaena 7120 ribulose-bisphosphate carboxylase/oxygenase in Escherichia coli. Gene. 1993 Apr 15;126(1):85–92. doi: 10.1016/0378-1119(93)90593-r. [DOI] [PubMed] [Google Scholar]
- Lee E. H., Harpel M. R., Chen Y. R., Hartman F. C. Perturbation of reaction-intermediate partitioning by a site-directed mutant of ribulose-bisphosphate carboxylase/oxygenase. J Biol Chem. 1993 Dec 15;268(35):26583–26591. [PubMed] [Google Scholar]
- Lorimer G. H., Chen Y. R., Hartman F. C. A role for the epsilon-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. 1993 Sep 7;32(35):9018–9024. doi: 10.1021/bi00086a006. [DOI] [PubMed] [Google Scholar]
- McFadden B. A., Denend A. R. Ribulose diphosphate carboxylase from autotrophic microorganisms. J Bacteriol. 1972 May;110(2):633–642. doi: 10.1128/jb.110.2.633-642.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Morse D., Salois P., Markovic P., Hastings J. W. A nuclear-encoded form II RuBisCO in dinoflagellates. Science. 1995 Jun 16;268(5217):1622–1624. doi: 10.1126/science.7777861. [DOI] [PubMed] [Google Scholar]
- Muller E. D., Chory J., Kaplan S. Cloning and characterization of the gene product of the form II ribulose-1,5-bisphosphate carboxylase gene of Rhodopseudomonas sphaeroides. J Bacteriol. 1985 Jan;161(1):469–472. doi: 10.1128/jb.161.1.469-472.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Newman J., Gutteridge S. The X-ray structure of Synechococcus ribulose-bisphosphate carboxylase/oxygenase-activated quaternary complex at 2.2-A resolution. J Biol Chem. 1993 Dec 5;268(34):25876–25886. [PubMed] [Google Scholar]
- ORMEROD J. G., ORMEROD K. S., GEST H. Light-dependent utilization of organic compounds and photoproduction of molecular hydrogen by photosynthetic bacteria; relationships with nitrogen metabolism. Arch Biochem Biophys. 1961 Sep;94:449–463. doi: 10.1016/0003-9861(61)90073-x. [DOI] [PubMed] [Google Scholar]
- Purohit K., McFadden B. A., Cohen A. L. Purification, quaternary structure, composition, and properties of D-ribulose-1,5-bisphosphate carboxylase from Thiobacillus intermedius. J Bacteriol. 1976 Jul;127(1):505–515. doi: 10.1128/jb.127.1.505-515.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Quivey R. G., Jr, Tabita F. R. Cloning and expression in Escherichia coli of the form II ribulose 1,5-bisphosphate carboxylase/oxygenase gene from Rhodopseudomonas sphaeroides. Gene. 1984 Nov;31(1-3):91–101. doi: 10.1016/0378-1119(84)90198-7. [DOI] [PubMed] [Google Scholar]
- Read B. A., Tabita F. R. Amino acid substitutions in the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase that influence catalytic activity of the holoenzyme. Biochemistry. 1992 Jan 21;31(2):519–525. doi: 10.1021/bi00117a031. [DOI] [PubMed] [Google Scholar]
- Read B. A., Tabita F. R. High substrate specificity factor ribulose bisphosphate carboxylase/oxygenase from eukaryotic marine algae and properties of recombinant cyanobacterial RubiSCO containing "algal" residue modifications. Arch Biochem Biophys. 1994 Jul;312(1):210–218. doi: 10.1006/abbi.1994.1301. [DOI] [PubMed] [Google Scholar]
- Schloss J. V., Phares E. F., Long M. V., Norton I. L., Stringer C. D., Hartman F. C. Isolation, characterization, and crystallization of ribulosebisphosphate carboxylase from autotrophically grown Rhodospirillum rubrum. J Bacteriol. 1979 Jan;137(1):490–501. doi: 10.1128/jb.137.1.490-501.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schneider G., Lindqvist Y., Lundqvist T. Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution. J Mol Biol. 1990 Feb 20;211(4):989–1008. doi: 10.1016/0022-2836(90)90088-4. [DOI] [PubMed] [Google Scholar]
- Stein J. L., Haygood M., Felbeck H. Nucleotide sequence and expression of a deep-sea ribulose-1,5-bisphosphate carboxylase gene cloned from a chemoautotrophic bacterial endosymbiont. Proc Natl Acad Sci U S A. 1990 Nov;87(22):8850–8854. doi: 10.1073/pnas.87.22.8850. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stoner M. T., Shively J. M. Cloning and expression of the D-ribulose-1,5-bisphosphate carboxylase/oxygenase form II gene from Thiobacillus intermedius in Escherichia coli. FEMS Microbiol Lett. 1993 Mar 1;107(2-3):287–292. doi: 10.1111/j.1574-6968.1993.tb06044.x. [DOI] [PubMed] [Google Scholar]
- Tabita F. R., McFadden B. A. D-ribulose 1,5-diphosphate carboxylase from Rhodospirillum rubrum. I. Levels, purification, and effects of metallic ions. J Biol Chem. 1974 Jun 10;249(11):3453–3458. [PubMed] [Google Scholar]
- Tabita F. R., McFadden B. A. D-ribulose 1,5-diphosphate carboxylase from Rhodospirillum rubrum. II. Quaternary structure, composition, catalytic, and immunological properties. J Biol Chem. 1974 Jun 10;249(11):3459–3464. [PubMed] [Google Scholar]
- Tabita F. R., McFadden B. A. Regulation of ribulose-1,5-diphosphate carboxylase by 6-phospho-D-gluconate. Biochem Biophys Res Commun. 1972 Sep 5;48(5):1153–1159. doi: 10.1016/0006-291x(72)90831-5. [DOI] [PubMed] [Google Scholar]
- Tabita F. R. Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms. Microbiol Rev. 1988 Jun;52(2):155–189. doi: 10.1128/mr.52.2.155-189.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tabita F. R., Small C. L. 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 U S A. 1985 Sep;82(18):6100–6103. doi: 10.1073/pnas.82.18.6100. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wakabayashi Y., Yamada E., Hasegawa T., Yamada R. Enzymological evidence for the indispensability of small intestine in the synthesis of arginine from glutamate. I. Pyrroline-5-carboxylate synthase. Arch Biochem Biophys. 1991 Nov 15;291(1):1–8. doi: 10.1016/0003-9861(91)90097-3. [DOI] [PubMed] [Google Scholar]
- Weaver K. E., Tabita F. R. Isolation and partial characterization of Rhodopseudomonas sphaeroides mutants defective in the regulation of ribulose bisphosphate carboxylase/oxygenase. J Bacteriol. 1983 Nov;156(2):507–515. doi: 10.1128/jb.156.2.507-515.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Whitney S. M., Shaw D. C., Yellowlees D. Evidence that some dinoflagellates contain a ribulose-1,5-bisphosphate carboxylase/oxygenase related to that of the alpha-proteobacteria. Proc Biol Sci. 1995 Mar 22;259(1356):271–275. doi: 10.1098/rspb.1995.0040. [DOI] [PubMed] [Google Scholar]
- Yaguchi T., Chung S. Y., Igarashi Y., Kodama T. Cloning and sequence of the L2 form of RubisCO from a marine obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110. Biosci Biotechnol Biochem. 1994 Sep;58(9):1733–1737. doi: 10.1271/bbb.58.1733. [DOI] [PubMed] [Google Scholar]
- Zhu G., Jensen R. G. Fallover of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase Activity : Decarbamylation of Catalytic Sites Depends on pH. Plant Physiol. 1991 Dec;97(4):1354–1358. doi: 10.1104/pp.97.4.1354. [DOI] [PMC free article] [PubMed] [Google Scholar]