Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1996 Feb;178(3):619–624. doi: 10.1128/jb.178.3.619-624.1996

Open reading frame 176 in the photosynthesis gene cluster of Rhodobacter capsulatus encodes idi, a gene for isopentenyl diphosphate isomerase.

F M Hahn 1, J A Baker 1, C D Poulter 1
PMCID: PMC177703  PMID: 8550491

Abstract

Isopentenyl diphosphate (IPP) isomerase catalyzes an essential activation step in the isoprenoid biosynthetic pathway. A database search based on probes from the highly conserved regions in three eukaryotic IPP isomerases revealed substantial similarity with ORF176 in the photosynthesis gene cluster in Rhodobacter capsulatus. The open reading frame was cloned into an Escherichia coli expression vector. The encoded 20-kDa protein, which was purified in two steps by ion exchange and hydrophobic interaction chromatography, catalyzed the interconversion of IPP and dimethylallyl diphosphate. Thus, the photosynthesis gene cluster encodes all of the enzymes required to incorporate IPP into the ultimate carotenoid and bacteriochlorophyll metabolites in R. capsulatus. More recent searches uncovered additional putative open reading frames for IPP isomerase in seed-bearing plants (Oryza sativa, Arabadopsis thaliana, and Clarkia breweri), a worm (Caenorhabiditis elegans), and another eubacterium (Escherichia coli). The R. capsulatus enzyme is the smallest of the IPP isomerases to be identified thus far and may consist mostly of a fundamental catalytic core for the enzyme.

Full Text

The Full Text of this article is available as a PDF (279.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson M. S., Muehlbacher M., Street I. P., Proffitt J., Poulter C. D. Isopentenyl diphosphate:dimethylallyl diphosphate isomerase. An improved purification of the enzyme and isolation of the gene from Saccharomyces cerevisiae. J Biol Chem. 1989 Nov 15;264(32):19169–19175. [PubMed] [Google Scholar]
  2. Armstrong G. A. Eubacteria show their true colors: genetics of carotenoid pigment biosynthesis from microbes to plants. J Bacteriol. 1994 Aug;176(16):4795–4802. doi: 10.1128/jb.176.16.4795-4802.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Ashby M. N., Edwards P. A. Elucidation of the deficiency in two yeast coenzyme Q mutants. Characterization of the structural gene encoding hexaprenyl pyrophosphate synthetase. J Biol Chem. 1990 Aug 5;265(22):13157–13164. [PubMed] [Google Scholar]
  4. Blanc V. M., Pichersky E. Nucleotide sequence of a Clarkia breweri cDNA clone of Ipi1, a gene encoding isopentenyl pyrophosphate isomerase. Plant Physiol. 1995 Jun;108(2):855–856. doi: 10.1104/pp.108.2.855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bollivar D. W., Suzuki J. Y., Beatty J. T., Dobrowolski J. M., Bauer C. E. Directed mutational analysis of bacteriochlorophyll a biosynthesis in Rhodobacter capsulatus. J Mol Biol. 1994 Apr 15;237(5):622–640. doi: 10.1006/jmbi.1994.1260. [DOI] [PubMed] [Google Scholar]
  6. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1006/abio.1976.9999. [DOI] [PubMed] [Google Scholar]
  7. Clarke S. Protein isoprenylation and methylation at carboxyl-terminal cysteine residues. Annu Rev Biochem. 1992;61:355–386. doi: 10.1146/annurev.bi.61.070192.002035. [DOI] [PubMed] [Google Scholar]
  8. Fujisaki S., Hara H., Nishimura Y., Horiuchi K., Nishino T. Cloning and nucleotide sequence of the ispA gene responsible for farnesyl diphosphate synthase activity in Escherichia coli. J Biochem. 1990 Dec;108(6):995–1000. doi: 10.1093/oxfordjournals.jbchem.a123327. [DOI] [PubMed] [Google Scholar]
  9. Goodwin T. W. Biosynthesis of carotenoids and plant triterpenes. Biochem J. 1971 Jul;123(3):293–329. doi: 10.1042/bj1230293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hahn F. M., Poulter C. D. Isolation of Schizosaccharomyces pombe isopentenyl diphosphate isomerase cDNA clones by complementation and synthesis of the enzyme in Escherichia coli. J Biol Chem. 1995 May 12;270(19):11298–11303. doi: 10.1074/jbc.270.19.11298. [DOI] [PubMed] [Google Scholar]
  11. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  13. Matsuoka S., Sagami H., Kurisaki A., Ogura K. Variable product specificity of microsomal dehydrodolichyl diphosphate synthase from rat liver. J Biol Chem. 1991 Feb 25;266(6):3464–3468. [PubMed] [Google Scholar]
  14. Mayer M. P., Hahn F. M., Stillman D. J., Poulter C. D. Disruption and mapping of IDI1, the gene for isopentenyl diphosphate isomerase in Saccharomyces cerevisiae. Yeast. 1992 Sep;8(9):743–748. doi: 10.1002/yea.320080907. [DOI] [PubMed] [Google Scholar]
  15. Rohmer M., Knani M., Simonin P., Sutter B., Sahm H. Isoprenoid biosynthesis in bacteria: a novel pathway for the early steps leading to isopentenyl diphosphate. Biochem J. 1993 Oct 15;295(Pt 2):517–524. doi: 10.1042/bj2950517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Satterwhite D. M. Isopentenyldiphosphate delta-isomerase. Methods Enzymol. 1985;110:92–99. doi: 10.1016/s0076-6879(85)10064-9. [DOI] [PubMed] [Google Scholar]
  17. Sherman M. M., Petersen L. A., Poulter C. D. Isolation and characterization of isoprene mutants of Escherichia coli. J Bacteriol. 1989 Jul;171(7):3619–3628. doi: 10.1128/jb.171.7.3619-3628.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Street I. P., Coffman H. R., Baker J. A., Poulter C. D. Identification of Cys139 and Glu207 as catalytically important groups in the active site of isopentenyl diphosphate:dimethylallyl diphosphate isomerase. Biochemistry. 1994 Apr 12;33(14):4212–4217. doi: 10.1021/bi00180a014. [DOI] [PubMed] [Google Scholar]
  19. Street I. P., Poulter C. D. Isopentenyldiphosphate:dimethylallyldiphosphate isomerase: construction of a high-level heterologous expression system for the gene from Saccharomyces cerevisiae and identification of an active-site nucleophile. Biochemistry. 1990 Aug 14;29(32):7531–7538. doi: 10.1021/bi00484a023. [DOI] [PubMed] [Google Scholar]
  20. Xuan J. W., Kowalski J., Chambers A. F., Denhardt D. T. A human promyelocyte mRNA transiently induced by TPA is homologous to yeast IPP isomerase. Genomics. 1994 Mar 1;20(1):129–131. doi: 10.1006/geno.1994.1139. [DOI] [PubMed] [Google Scholar]
  21. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES