Summary
Carotenoid pigments are essential for the protection of both photosynthetic and non-photosynthetic tissues from photooxidative damage. Although carotenoid biosynthesis has been studied in many organisms from bacteria to higher plants, little is known about carotenoid biosynthetic enzymes, or the nature and regulation of the genes encoding them. We report here the first DNA sequence of carotenoid genes from any organism. We have determined the complete nucleotide sequence (11 039 bp) of a gene cluster encoding seven of the eight previously known carotenoid genes (crt A, B, C, D, E, F, I) and a new gene, designated crtK, from Rhodobacter capsulatus, a purple non-sulfur photosynthetic bacterium. The 5′ flanking regions of crtA, I, D and E contain a highly conserved palindromic sequence homologous to the consensus binding site for a variety of prokaryotic DNA-binding regulatory proteins. This putative regulatory palindrome is also found 5′ to the puc operon, encoding the light-harvesting II antenna polypeptides. Escherichia coli-like σ70 promoter sequences are located 5′ to crtI and crtD, suggesting for the first time that such promoters may exist in purple photosynthetic bacteria. The crt genes form a minimum of four distinct operons, crtA, crtIBK, crtDC and crtEF, based on inversions of transcriptional orientation within the gene cluster. Possible rho-independent transcription terminators are located 3′ to crtI, B, K, C and F. The 3′ end of crtA may overlap transcription initiation signals for a downstream gene required for bacteriochlorophyll biosynthesis. We have also observed two regions of exceptional amino acid homology between CrtI and CrtD, both of which are dehydrogenases.
Similar content being viewed by others
References
Bauer CE, Young DA, Marrs BL (1988) Analysis of the Rhodobacter capsulatus puf operon. J Biol Chem 263:4820–4827
Beyer P, Weiss G, Kleinig H (1985) Solubilization and reconstitution of the membrane-bound carotenogenic enzymes from daffodil chromoplasts. Eur J Biochem 153:341–346
Bolivar F (1978) Construction and characterization of new cloning vehicles: III. Derivatives of plasmid pBR322 carrying the EcoRI sites for selection of EcoRI generated recombinant DNA molecules. Gene 4:121–136
Bolivar F, Rodriguez RL, Greene PJ, Betlach MC, Heynecker HL, Boyer HW (1977) Construction and characterization of new cloning vehicles: II. A multipurpose cloning system. Gene 2:95–113
Bramley P (1985) The in vitro biosynthesis of carotenoids. In: Paoletti R, Kritchensky D (eds) Advances in lipid research, vol 21. Academic Press, Orlando, Florida, pp 243–279
Bramley PM, Taylor RF (1985) The solubilization of carotenogenic enzymes of Phycomyces blakesleeanus. Biochim Biophys Acta 839:155–160
Buck M, Miller S, Drummond M, Dixon R (1986) Upstream activator sequences are present in the promoters of nitrogen fixation genes. Nature 320:374–378
Camara B, Bardat F, Moneger R (1982) Sites of biosynthesis of carotenoids in Capsicum chromoplasts. Eur J Biochem 127:255–258
Chen EY, Seeburg H (1985) Laboratory methods — supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA 4:165–170
Chen CY, Beatty JT, Cohen SN, Belasco JG (1988) An intercistronic stem-loop structure functions as an mRNA decay terminator necessary but insufficient for puf mRNA stability. Cell 52:609–619
Clark WG, Davidson E, Marrs BL (1984) Variation of levels of mRNA coding for antenna and reaction center polypeptides in Rhodopseudomonas capsulata in response to changes in oxygen concentration. J Bacteriol 157:945–948
Daldal F, Chen S, Applebaum J, Davidson E, Prince RC (1986) Cytochrome c 2 is not essential for photosynthetic growth of Rhodopseudomonas capsulata. Proc Natl Acad Sci USA 83:2012–2016
Davidson E, Daldal F (1987) fbc operon, encoding the Rieske Fe-S protein, cytochrome b, and cytochrome c 1 apoproteins previously described from Rhodopseudomonas sphaeroides, is from Rhodopseudomonas capsulata. J Mol Biol 195:25–29
Drews G (1985) Structure and functional organization of light-harvesting complexes and photochemical reaction centers in membranes of phototrophic bacteria. Microbiol Rev 49:59–70
Drews G, Oelze J (1981) Organization and differentiation of membranes of phototrophic bacteria. Adv Microb Physiol 22:1–92
Gabellini N, Sebald W (1986) Nucleotide sequence and transcription of the fbc operon from Rhodopseudomonas sphaeroides. Eur J Biochem 154:569–579
Gicquel-Sanzey B, Cossart P (1982) Homologies between different procaryotic DNA-binding regulatory proteins and between their sites of action. EMBO J 1:591–595
Giuliano G, Pollock D, Scolnik PA (1986) The crtI gene mediates the conversion of phytoene into colored carotenoids in Rhodopseudomonas capsulata. J Biol Chem 261:12925–12929
Giuliano G, Pollock D, Stapp H, Scolnik PA (1988) A geneticphysical map of the Rhodobacter capsulatus carotenoid biosynthesis gene cluster. Mol Gen Genet 213:78–83
Goodwin TW (1980) The Biochemistry of the Carotenoids, vol 1, Plants. Chapman and Hall, New York
Gussin GN, Ronson CW, Ausubel FM (1986) Regulation of nitrogen fixation genes. Annu Rev Genet 20:567–591
Harding RW, Shropshire W (1980) Photocontrol of carotenoid biosynthesis. Annu Rev Plant Physiol 31:217–238
Imhoff JF, Trüper HG, Pfennig N (1984) Rearrangements of the species and genera of the phototrophic “purple nonsulfur bacteria”. Int J Syst Bacteriol 34:340–343
Johnson JA, Wong WKR, Beatty JT (1986) Expression of cellulase genes in Rhodobacter capsulatus by the use of plasmid expression vectors. J Bacteriol 167:604–610
Jones BL, Porter JW (1986) Biosynthesis of carotenes in higher plants. CRC Crit Rev Plant Sci 3:295–324
Kiley PJ, Kaplan S (1987) Cloning, DNA sequence and expression of the Rhodobacter sphaeroides light-harvesting B800-850-α and B800-850-β genes. J Bacteriol 169:3268–3275
Kiley PJ, Kaplan S (1988) Molecular genetics of photosynthetic membrane biosynthesis in Rhodobacter sphaeroides. Microbiol Rev 52:50–69
Klug G, Kaufmann N, Drews G (1985) Gene expression of pigment-binding proteins of the bacterial photosynthetic apparatus: transcription and assembly in the membrane of Rhodopseudomonas capsulata. Proc Natl Acad Sci USA 82:6485–6489
Kreuz K, Beyer P, Kleinig H (1982) The site of carotenogenic enzymes in chromoplasts from Narcissus pseudonarcissus L. Planta 154:66–69
Krinsky NI (1971) Function. In: Isler O, Gutmann H, Solms U (eds) Carotenoids. Birkheuser Verlag, Basel, pp 669–716
Maniatis T, Fritsch EF, Sambrook J (1982) Molecular Cloning. A laboratory manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
Marrs B (1981) Mobilization of the genes for photosynthesis from Rhodopseudomonas capsulata by a promiscuous plasmid. J Bacteriol 146:1003–1012
Masepohl B, Klipp W, Pühler A (1988) Genetic characterization and sequence analysis of the duplicated nifA/nifB region of R. capsulatus. Mol Gen Genet 212:27–37
McClure WR (1985) Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem 54:171–204
Messing J, Crea R, Seeburg PH (1981) A system for shotgun DNA sequencing. Nucleic Acids Res 9:309–321
Pemberton JM, Harding CM (1986) Cloning of carotenoid biosynthesis genes from Rhodopseudomonas sphaeroides. Curr Microbiol 14:25–29
Pemberton JM, Harding CM (1987) Expression of Rhodopseudomonas sphaeroides carotenoid photopigment genes in phylogenetically related nonphotosynthetic bacteria. Curr Microbiol 15:67–71
Pitt GAJ (1971) Vitamin A. In: Isler O, Gutmann H, Solms U (eds) Carotenoids. Birkheuser Verlag, Basel, pp 717–742
Platt T (1986) Transcription termination and the regulation of gene expression. Annu Rev Biochem 55:339–372
Pustell J, Kafatos F (1982) A convenient and adaptable package of DNA sequence analysis programs for microcomputers. Nucleic Acids Res 10:51–59
Raibaud O, Schwartz M (1984) Positive control of transcription initiation in bacteria. Annu Rev Genet 18:173–206
Reznikoff WS, Siegele DA, Cowing DW, Gross C (1985) The regulation of transcription initiation in bacteria. Annu Rev Genet 19:355–387
Sandmann G, Bramley P (1985) Carotenoid biosynthesis by Aphanocapsa homogenates coupled to a phytoene-generating system from Phycomyces blakesleeanus. Planta 164:259–263
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
Schumann J, Waitches G, Scolnik P (1986) A DNA fragment hybridizing to a nif probe in Rhodobacter capsulatus is homologous to a 16 S rRNA gene. Gene 48:79–90
Scolnik PA, Marrs BL (1987) Genetic research with photosynthetic bacteria. Annu Rev Microbiol 41:703–726
Scolnik PA, Walker MA, Marrs BL (1980) Biosynthesis of carotenoids derived from neurosporene in Rhodopseudomonas capsulata. J Biol Chem 255:2427–2432
Sharp PM, Li W-H (1986) Codon usage in regulatory genes in Escherichia coli does not reflect selection for ‘rare’ codons. Nucleic Acids Res 14:7737–7749
Shine J, Dalgarno L (1974) The 3′-terminal sequence of Escherichia coli 16 S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci USA 71:1342–1346
Stormo GD (1986) Translation initiation. In: Reznikoff W, Gold L (eds) Maximizing Gene Expression. Butterworths, Stoneham, Massachusetts, pp 195–224
Sweet RM, Eisenberg D (1983) Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J Mol Biol 171:479–488
Taylor DP, Cohen SN, Clark WG, Marrs BL (1983) Alignment of the genetic and restriction maps of the photosynthesis region of the Rhodopseudomonas capsulata chromosome by a conjugation-mediated marker rescue technique. J Bacteriol 154:580–590
Yanisch-Perron C, Vieira J, Messing J (1985) Improved M13 cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103–119
Yen HC, Marrs B (1976) Map of genes for carotenoid and bacteriochlorophyll biosynthesis in Rhodopseudomonas capsulata. J Bacteriol 126:619–629
Youvan DC, Ismail S (1985) Light-harvesting II (B800-B850 complex) structural genes from Rhodopseudomonas capsulata. Proc Natl Acad Sci USA 82:58–62
Youvan DC, Bylina EJ, Alberti M, Begusch H, Hearst JE (1984a) Nucleotide and deduced polypeptide sequences of the photosynthetic reaction-center, B870 antenna, and flanking polypeptides from R. capsulata. Cell 37:949–957
Youvan DC, Alberti M, Begusch H, Bylina EJ, Hearst JE (1984b) Reaction center and light-harvesting genes from Rhodopseudomonas capsulata. Proc Natl Acad Sci USA 81:189–192
Zhu YS, Hearst JE (1986) Regulation of the expression of the genes for light-harvesting antenna proteins LH-I and LH-II; reaction center polypeptides RC-L, RC-M, and RC-H; and enzymes of bacteriochlorophyll and carotenoid biosynthesis in Rhodobacter capsulatus by light and oxygen. Proc Natl Acad Sci USA 83:7613–7617
Zhu YS, Cook DN, Leach F, Armstrong GA, Alberti M, Hearst JE (1986) Oxygen-regulated mRNAs for light-harvesting and reaction center complexes and for bacteriochlorophyll and carotenoid biosynthesis in Rhodobacter capsulatus during the shift from anaerobic to aerobic growth. J Bacteriol 168:1180–1188
Zsebo KM, Hearst JE (1984) Genetic-physical mapping of a photosynthetic gene cluster from R. capsulata. Cell 37:937–947
Zucconi AP, Beatty JT (1988) Post-transcriptional regulation by light of the steady-state levels of mature B800-850 light-harvesting complexes in Rhodobacter capsulatus. J Bacteriol 170:877–882
Author information
Authors and Affiliations
Additional information
Communicated by H. Saedler
Rights and permissions
About this article
Cite this article
Armstrong, G.A., Alberti, M., Leach, F. et al. Nucleotide sequence, organization, and nature of the protein products of the carotenoid biosynthesis gene cluster of Rhodobacter capsulatus . Mol Gen Genet 216, 254–268 (1989). https://doi.org/10.1007/BF00334364
Received:
Issue Date:
DOI: https://doi.org/10.1007/BF00334364