Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis

  • Neetu Chaudhary
  • Aashima Nijhawan
  • Jitendra P. Khurana
  • Paramjit Khurana
Original Paper


Carotenoids, important lipid-soluble antioxidants in photosynthetic tissues, are known to be completely absent in rice endosperm. Many studies, involving transgenic manipulations of carotenoid biosynthesis genes, have been performed to get carotenoid-enriched rice grain. Study of genes involved in their biosynthesis can provide further information regarding the abundance/absence of carotenoids in different tissues. We have identified 16 and 34 carotenoid biosynthesis genes in rice and Populus genomes, respectively. A detailed analysis of the domain structure of carotenoid biosynthesis enzymes in rice, Populus and Arabidopsis has shown that highly conserved catalytic domains, along with other domains, are present in these proteins. Phylogenetic analysis of rice genes with Arabidopsis and other characterized carotenoid biosynthesis genes has revealed that homologous genes exist in these plants, and the duplicated gene copies probably adopt new functions. Expression of rice and Populus genes has been analyzed by full-length cDNA- and EST-based expression profiling. In rice, this analysis was complemented by real-time PCR, microarray and signature-based expression profiling, which reveal that carotenoid biosynthesis genes are highly expressed in light-grown tissues, have differential expression pattern during vegetative/reproductive development and are responsive to stress.


Carotenoids Microarray MPSS Populus Phylogenetic analysis Rice 



This work was financially supported by the Department of Biotechnology, Government of India, the University Grants Commission and the Council of Scientific and Industrial Research, New Delhi (research fellowship to N. C. and A. N.). The TIGR, KOME, TAIR, NCBI and Populus database resources are gratefully acknowledged for the detailed sequence information.

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  1. Adams MD, Kerlavage AR, Fleischmann RD, Fuldner RA, Bult CJ, Lee NH, Kirkness EF, Weinstock KG, Gocayne JD, White O et al (1995) Initial assessment of human genome diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377:3–17PubMedGoogle Scholar
  2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefPubMedGoogle Scholar
  3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  4. Audran C, Liotenberg S, Gonneau M, North H, Frey A, Tap-Waksman K, Vartanian N, Marion-Poll A (2001) Localization and expression of zeaxanthin epoxidase mRNA in Arabidopsis in response to drought stress and during seed development. Aust J Plant Physiol 28:1161–1173Google Scholar
  5. Bashton M, Chothia C (2007) The generation of new protein functions by the combination of domains. Structure 15:85–99CrossRefPubMedGoogle Scholar
  6. Beveridge CA, Gresshoff PM, Rameau C, Turnbull CGN (2003) Additional signaling compounds are required to orchestrate plant development. J Plant Growth Regul 22:15–24CrossRefGoogle Scholar
  7. Borsani O, Valpuesta V, Botella MA (2001) Evidence for a role of salicylic acid in the oxidative damage generated by NaCl and osmotic stress in Arabidopsis seedlings. Plant Physiol 126:1024–1030CrossRefPubMedGoogle Scholar
  8. Bouvier F, Dogbo O, Camara B (2003a) Biosynthesis of the food and cosmetic plant pigment bixin (annatto). Science 300:2089–2091CrossRefPubMedGoogle Scholar
  9. Bouvier F, Suire C, Mutterer J, Camara B (2003b) Oxidative remodeling of chromoplast carotenoids: identification of the carotenoid dioxygenase CsCCD and CsZCD genes involved in Crocus secondary metabolite biogenesis. Plant Cell 15:47–62CrossRefPubMedGoogle Scholar
  10. Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unraveling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433–438CrossRefPubMedGoogle Scholar
  11. Britton G, Jensen SL, Pfander H (2004) Carotenoids handbook. Birkhäuser Verlag, BaselGoogle Scholar
  12. Burkhardt P, Beyer P, Wunn J, Kloti A, Armstrong G, Schledz M, von Lintig J, Potrykus I (1997) Transgenic rice (Oryza sativa) endosperm expressing daffodil (Narcissus pseudonarcissus) phytoene synthase accumulates phytoene, a key intermediate of provitamin A biosynthesis. Plant J 11:1071–1078CrossRefPubMedGoogle Scholar
  13. Calucci L, Capocchi A, Galleschi L, Ghiringhelli S, Pinzino C, Saviozzi F, Zandomeneghi M (2004) Antioxidants, free radicals, storage proteins, puroindolines, and proteolytic activities in bread wheat (Tritium aestivum) seeds during accelerated aging. J Agric Food Chem 52:4274–4281CrossRefPubMedGoogle Scholar
  14. Chen J, Agrawal V, Rattray M, West MAL, St Clair DA, Michelmore RW, Coughlan SJ, Meyers BC (2007) A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis. BMC Genomics 8:414CrossRefPubMedGoogle Scholar
  15. Dall’Osto L, Lico C, Alric J, Giuliano G, Havaux M, Bassi R (2006) Lutein is needed for efficient chlorophyll triplet quenching in the major LHCII antenna complex of higher plants and effective photoprotection in vivo under strong light. BMC Plant Biol 6:32CrossRefPubMedGoogle Scholar
  16. Dall’Osto L, Fiore A, Cazzaniga S, Giuliano G, Bassi R (2007) Different roles of alpha- and beta-branch xanthophylls in photosystem assembly and photoprotection. J Biol Chem 282:35056–35068CrossRefPubMedGoogle Scholar
  17. Davidson PA, Hunter CN, Horton P (2002) Overexpression of beta-carotene hydroxylase enhances stress tolerance in Arabidopsis. Nature 418:203–206CrossRefGoogle Scholar
  18. Dellapenna D, Pogson BJ (2006) Vitamin synthesis in plants: tocopherols and carotenoids. Annu Rev Plant Biol 57:711–738CrossRefPubMedGoogle Scholar
  19. Durbin R, Eddy SR, Krogh A, Mitchison GJ (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press, LondonGoogle Scholar
  20. Fang J, Chu C (2008) Abscisic acid and the pre-harvest sprouting in cereals. Plant Signal Behav 3:1046–1048PubMedGoogle Scholar
  21. Franco AC, Matsubara S, Orthen B (2007) Photoinhibition, carotenoid composition and the co-regulation of photochemical and non-photochemical quenching in neotropical savanna trees. Tree Physiol 27:717–725PubMedGoogle Scholar
  22. Fraser PD, Kiano JW, Truesdale MR, Schuch W, Bramley PM (1999) Phytoene synthase-2 enzyme activity in tomato does not contribute to carotenoid synthesis in ripening fruit. Plant Mol Biol 40:687–698CrossRefPubMedGoogle Scholar
  23. Gallagher CE, Matthews PD, Li F, Wurtzel ET (2004) Gene duplication in the carotenoid biosynthetic pathway preceded evolution of grasses. Plant Physiol 135:1776–1783CrossRefPubMedGoogle Scholar
  24. Hable WE, Oishi KK, Schumaker KS (1998) Viviparous-5 encodes phytoene desaturase, an enzyme essential for abscisic acid (ABA) accumulation and seed development in maize. Mol Gen Genet 257:167–176CrossRefPubMedGoogle Scholar
  25. Harjes C, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG et al (2008) Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319:330–333CrossRefPubMedGoogle Scholar
  26. Havaux M, Niyogi KK (1999) The violaxanthin cycle protects plants from photooxidative damage by more than one mechanism. Proc Natl Acad Sci USA 96:8762–8767CrossRefPubMedGoogle Scholar
  27. Holt NE, Zigmantas D, Valkunas L, Li XP, Niyogi KK, Fleming GR (2005) Carotenoid cation formation and the regulation of photosynthetic light harvesting. Science 307:433–436CrossRefPubMedGoogle Scholar
  28. Howitt CA, Pogson BJ (2006) Carotenoid accumulation and function in seeds and non-green tissues. Plant Cell Environ 29:435–445CrossRefPubMedGoogle Scholar
  29. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800CrossRefGoogle Scholar
  30. Jeffery SW, Douce R, Benson AA (1974) Carotenoid transformations in the chloroplast envelope. Proc Natl Acad Sci USA 71:807–810CrossRefGoogle Scholar
  31. Jordan IK, Makarova KS, Spouge JL, Wolf YI, Koonin EV (2001) Lineage-specific gene expansions in bacterial and archaeal genomes. Genome Res 11:555–565CrossRefPubMedGoogle Scholar
  32. Kato M, Ikoma Y, Matsumoto H, Sugiura M, Hyodo H, Yano M (2004) Accumulation of carotenoids and expression of carotenoid biosynthetic genes during maturation in citrus fruit. Plant Physiol 134:824–837CrossRefPubMedGoogle Scholar
  33. Kulheim C, Agren J, Jansson S (2002) Rapid regulation of light harvesting and plant fitness in the field. Science 308:267–269Google Scholar
  34. Lespinet O, Wolf YI, Koonin EV, Aravind L (2002) The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res 12:1048–1059CrossRefPubMedGoogle Scholar
  35. Li L, Paolillo DJ, Parthasarathy MV, DiMuzio EM, Garvin DF (2001) A novel gene mutation that confers abnormal patterns of β-carotene accumulation in cauliflower (Brassica oleracea var. botrytis). Plant J 26:59–67CrossRefPubMedGoogle Scholar
  36. Li X, Duan X, Jiang H, Sun Y, Tang Y, Yuan Z, Guo J, Liang W, Chen L, Yin J, Ma H, Wang J, Zhang D (2006) Genome-wide analysis of basic/helix–loop–helix transcription factor family in rice and Arabidopsis. Plant Physiol 141:1167–1184CrossRefPubMedGoogle Scholar
  37. Li F, Vallabhaneni R, Wurtzel ET (2008a) PSY3, a new member of the phytoene synthase gene family conserved in the Poaceae and regulator of abiotic stress-induced carotenogenesis. Plant Physiol 146:1333–1345CrossRefPubMedGoogle Scholar
  38. Li F, Vallabhaneni R, Yu J, Rocheford T, Wurtzel ET (2008b) The maize phytoene synthase gene family: overlapping roles for carotenogenesis in endosperm, photomorphogenesis and thermal stress tolerance. Plant Physiol 147:1334–1346CrossRefPubMedGoogle Scholar
  39. Lokstein H, Tian L, Polle JEW, Dellapenna D (2002) Xanthophyll biosynthetic mutants of Arabidopsis thaliana: altered nonphotochemical quenching of chlorophyll fluorescence is due to changes in photosystem II antenna size and stability. Biochim Biophys Acta 1553:309–319CrossRefPubMedGoogle Scholar
  40. Lopez AB, Van Eck J, Conlin BJ, Paolillo DJ, O’Neill J, Li L (2008) Effect of the cauliflower or transgene on carotenoid accumulation and chromoplast formation in transgenic potato tubers. J Exp Bot 59:213–223CrossRefPubMedGoogle Scholar
  41. López-Ráez JA, Charnikhova T, Gómez-Roldán V, Matusova R, Kohlen W, De Vos R, Verstappen F, Puech-Pages V, Bécard G, Mulder P, Bouwmeester H (2008) Tomato strigolactones are derived from carotenoids and their biosynthesis is promoted by phosphate starvation. New Phytol 178:863–874CrossRefPubMedGoogle Scholar
  42. Lu S, Li L (2008) Carotenoid metabolism: biosynthesis, regulation and beyond. J Integr Plant Biol 50:778–785CrossRefPubMedGoogle Scholar
  43. McNulty HP, Byun J, Lockwood SF, Jacob RF, Mason RP (2007) Differential effects of carotenoids on lipid peroxidation due to membrane interactions: X-ray diffraction analysis. BBA Biomembranes 1768:167–174CrossRefPubMedGoogle Scholar
  44. McSteen P, Leyser O (2005) Shoot branching. Annu Rev Plant Biol 56:353–374CrossRefPubMedGoogle Scholar
  45. Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15:1771–1780CrossRefPubMedGoogle Scholar
  46. Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, Meyers BC (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 34:D731–D735CrossRefPubMedGoogle Scholar
  47. Nambara E, Marion-Poll A (2005) Abscisic acid biosynthesis and catabolism. Annu Rev Plant Biol 56:165–185CrossRefPubMedGoogle Scholar
  48. Niyogi KK (1999) Photoprotection revisited: genetic and molecular approaches. Annu Rev Plant Biol 56:165–185Google Scholar
  49. Nobuta K, Venu RC, Lu C, Beló A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ, Wang G, Meyers BC (2007) An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol 25:473–477CrossRefPubMedGoogle Scholar
  50. Oudes AJ, Roach JC, Walashek LS, Eichner LJ, True LD, Vessella RL, Liu AY (2005) Application of Affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression. BMC Cancer 5:86CrossRefPubMedGoogle Scholar
  51. Paine JA, Shipton CA, Chaggar S, Howells RM, Kennedy MJ, Vernon G, Wright SY, Hinchliffe E, Adams JL, Silverstone AL, Drake R (2005) A new version of golden rice with increased pro-vitamin A content. Nat Biotechnol 23:482–487CrossRefPubMedGoogle Scholar
  52. Park H, Kreunen SS, Cuttriss AJ, Dellapenna D, Pogson BJ (2002) Identification of the carotenoid isomerase provides insight into carotenoid biosynthesis, prolamellar body formation, and photomorphogenesis. Plant Cell 14:321–332CrossRefPubMedGoogle Scholar
  53. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556CrossRefPubMedGoogle Scholar
  54. Pogson BJ, Niyogi KK, Bjorkman O, Dellapenna D (1998) Altered xanthophylls compositions adversely affect chlorophyll accumulation and nonphotochemical quenching in Arabidopsis mutants. Proc Natl Acad Sci USA 95:13324–13329CrossRefPubMedGoogle Scholar
  55. Quinlan RF, Jaradat TT, Wurtzel ET (2007) Escherichia coli as a platform for functional expression of plant P450 carotene hydroxylases. Arch Biochem Biophys 458:146–157CrossRefPubMedGoogle Scholar
  56. Raes J, Rohde A, Christensen JH, van de Peer Y, Boerjan W (2003) Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol 133:1051–1071CrossRefPubMedGoogle Scholar
  57. Rivier L, Léonard JF, Cottier JP (1983) Rapid effect of osmotic stress on the content and exodiffusion of abscisic acid in Zea mays roots. Plant Sci Lett 83:133–137Google Scholar
  58. Rossel JB, Wilson IW, Pogson BJ (2002) Global changes in gene expression in response to high light in Arabidopsis. Plant Physiol 130:1109–1120CrossRefPubMedGoogle Scholar
  59. Rouze P, Pavy N, Rombauts S (1999) Genome annotation: which tools do we have for it? Curr Opin Plant Biol 2:90–95CrossRefPubMedGoogle Scholar
  60. Segerman B, Jansson S, Karlsson J (2007) Characterization of genes with narrow expression patterns in Populus. Tree Genet Genomes 3:351–362CrossRefGoogle Scholar
  61. Shan H, Zhang N, Liu C, Xu G, Zhang J, Chen Z et al (2007) Patterns of gene duplication and functional diversification during the evolution of the AP1/SQUA subfamily of plant MADS-box genes. Mol Phylogenet Evol 44:26–41CrossRefPubMedGoogle Scholar
  62. Siefermann-Harms D, Joyard J, Douce R (1978) Light-induced changes of the carotenoid levels in chloroplast envelopes. Plant Physiol 61:530–533CrossRefPubMedGoogle Scholar
  63. Simkin AJ, Schwartz SH, Auldridge M, Taylor MG, Jee HJ (2004a) The tomato carotenoid cleavage dioxygenase I gene contributes to the formation of the flavor volatiles beta-ionone, pseudo ionone, and geranylacetone. Plant J 40:882–892CrossRefPubMedGoogle Scholar
  64. Simkin AJ, Underwood BA, Auldridge M, Loucas HM, Shibuya K, Schmelz E et al (2004b) Circadian regulation of the PhCCD1 carotenoid cleavage dioxygenase controls emission of β-ionone, a fragrance volatile of petunia flowers. Plant Physiol 136:3504–3514CrossRefPubMedGoogle Scholar
  65. Singh G, Kumar S, Singh P (2003) A quick method to isolate RNA from wheat and other carbohydrate-rich seeds. PMB Report 21:93a-fGoogle Scholar
  66. Sun ZR, Gantt E, Cunningham FX (1996) Cloning and functional analysis of the beta-carotene hydroxylase of Arabidopsis thaliana. J Biol Chem 271:24349–24352CrossRefPubMedGoogle Scholar
  67. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  68. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTALX Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedGoogle Scholar
  69. Thompson AJ, Jackson AC, Parker RA, Morpeth DR, Burbidge A, Taylor IB (2000a) Abscisic acid biosynthesis in tomato: regulation of zeaxanthin epoxidase and 9-cis-epoxycarotenoid dioxygenase mRNAs by light/dark cycles, water stress and abscisic acid. Plant Mol Biol 42:833–845CrossRefPubMedGoogle Scholar
  70. Thompson AJ, Jackson AC, Symonds RC, Mulholland BJ, Dadswell AR, Blake PS, Burbidge A, Taylor IB (2000b) Ectopic expression of a tomato 9-cis-epoxycarotenoid dioxygenase gene causes over-production of abscisic acid. Plant J 23:363–374CrossRefPubMedGoogle Scholar
  71. Thompson AJ, Mulholland BJ, Jackson AC, McKee JM, Hilton HW, Symonds RC, Sonneveld T, Burbidge A, Stevenson P, Taylor IB (2007) Regulation and manipulation of ABA biosynthesis in roots. Plant Cell Environ 30:67–78CrossRefPubMedGoogle Scholar
  72. Tian L, DellaPenna D (2001) Characterization of a second carotenoid β-hydroxylase gene from Arabidopsis and its relationship to the LUT1 locus. Plant Mol Biol 47:379–388CrossRefPubMedGoogle Scholar
  73. Tian L, Musetti V, Kim J, Magallanes-Lundback M, Dellapenna D (2004) The Arabidopsis LUT1 locus encodes a member of the cytochrome P450 family that is required for carotenoid epsilon-ring hydroxylation activity. Proc Natl Acad Sci USA 101:402–407CrossRefPubMedGoogle Scholar
  74. Tuskan GA et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604CrossRefPubMedGoogle Scholar
  75. Tuteja N (2007) Abscisic acid and abiotic stress signaling. Plant Signal Behav 2:135–138PubMedGoogle Scholar
  76. van Norman, Jaimie M, Sieburth, Leslie E (2007) Dissecting the biosynthetic pathway for the bypass1 root-derived signal. Plant J 49:619–628CrossRefPubMedGoogle Scholar
  77. Vishnevetsky M, Ovadis M, Zuker A, Vainstein A (1999) Molecular mechanisms underlying carotenogenesis in the chromoplast: multilevel regulation of carotenoid-associated genes. Plant J 20:423–431CrossRefPubMedGoogle Scholar
  78. von Lintig J, Welsch R, Bonk M, Giuliano G, Batschauer A, Kleinig H (1997) Light-stimulated carotenoid biosynthesis occurs at the level of phytoene synthase expression and is mediated by phytochrome in Sinapis alba and Arabidopsis thaliana seedlings. Plant J 12:625–634CrossRefGoogle Scholar
  79. Welsch R, Beyer P, Hugueney P, Kleinig H, von Lintig J (2000) Regulation and activation of phytoene synthase, a key enzyme in carotenoid biosynthesis, during photomorphogenesis. Planta 211:846–854CrossRefPubMedGoogle Scholar
  80. Welsch R, Wüst F, Bär C, Al-Babili S, Beyer P (2008) A third phytoene synthase is devoted to abiotic stress-induced abscisic acid formation in rice and defines functional diversification of phytoene synthase genes. Plant Physiol 147:367–380CrossRefPubMedGoogle Scholar
  81. Woitsch S, Römer S (2003) Expression of xanthophyll biosynthetic genes during light-dependent chloroplast differentiation. Plant Physiol 132:1508–1517CrossRefPubMedGoogle Scholar
  82. Ye XD, Al-Babili S, Kloti A, Zhang J, Lucca P, Beyer P, Potrykus I (2000) Engineering the provitamin A (β-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science 287:303–305CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Neetu Chaudhary
    • 1
  • Aashima Nijhawan
    • 1
  • Jitendra P. Khurana
    • 1
  • Paramjit Khurana
    • 1
  1. 1.Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia

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