Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis
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.
KeywordsCarotenoids 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.
- 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
- Britton G, Jensen SL, Pfander H (2004) Carotenoids handbook. Birkhäuser Verlag, BaselGoogle Scholar
- 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
- 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
- Durbin R, Eddy SR, Krogh A, Mitchison GJ (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press, LondonGoogle Scholar
- Kulheim C, Agren J, Jansson S (2002) Rapid regulation of light harvesting and plant fitness in the field. Science 308:267–269Google Scholar
- 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
- 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
- Niyogi KK (1999) Photoprotection revisited: genetic and molecular approaches. Annu Rev Plant Biol 56:165–185Google Scholar
- 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
- 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
- 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