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PLOS Genetics  2008 

Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice

DOI: 10.1371/journal.pgen.1000164

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Functional redundancy limits detailed analysis of genes in many organisms. Here, we report a method to efficiently overcome this obstacle by combining gene expression data with analysis of gene-indexed mutants. Using a rice NSF45K oligo-microarray to compare 2-week-old light- and dark-grown rice leaf tissue, we identified 365 genes that showed significant 8-fold or greater induction in the light relative to dark conditions. We then screened collections of rice T-DNA insertional mutants to identify rice lines with mutations in the strongly light-induced genes. From this analysis, we identified 74 different lines comprising two independent mutant lines for each of 37 light-induced genes. This list was further refined by mining gene expression data to exclude genes that had potential functional redundancy due to co-expressed family members (12 genes) and genes that had inconsistent light responses across other publicly available microarray datasets (five genes). We next characterized the phenotypes of rice lines carrying mutations in ten of the remaining candidate genes and then carried out co-expression analysis associated with these genes. This analysis effectively provided candidate functions for two genes of previously unknown function and for one gene not directly linked to the tested biochemical pathways. These data demonstrate the efficiency of combining gene family-based expression profiles with analyses of insertional mutants to identify novel genes and their functions, even among members of multi-gene families.


[1]  Brown DM, Zeef LA, Ellis J, Goodacre R, Turner SR (2005) Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17: 2281–2295.
[2]  AbuQamar S, Chen X, Dhawan R, Bluhm B, Salmeron J, et al. (2006) Expression profiling and mutant analysis reveals complex regulatory networks involved in Arabidopsis response to Botrytis infection. Plant J 48: 28–44.
[3]  Khanna R, Shen Y, Toledo-Ortiz G, Kikis EA, Johannesson H, et al. (2006) Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation. Plant Cell 18: 2157–2171.
[4]  Jung KH, An G, Ronald PC (2008) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat Rev Genet 9: 91–101.
[5]  Walia H, Wilson C, Condamine P, Liu X, Ismail AM, et al. (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 139: 822–835.
[6]  Jung KH, Han MJ, Lee YS, Kim YW, Hwang I, et al. (2005) Rice Undeveloped Tapetum1 is a major regulator of early tapetum development. Plant Cell 17: 2705–2722.
[7]  Shimono M, Sugano S, Nakayama A, Jiang CJ, Ono K, et al. (2007) Rice WRKY45 Plays a Crucial Role in Benzothiadiazole-Inducible Blast Resistance. Plant Cell 19: 2064–2076.
[8]  Jiao Y, Lau OS, Deng XW (2007) Light-regulated transcriptional networks in higher plants. Nat Rev Genet 8: 217–230.
[9]  Yu J, Wang J, Lin W, Li S, Li H, et al. (2005) The Genomes of Oryza sativa: a history of duplications. PLoS Biol 3: e38.
[10]  Jiao Y, Yang H, Ma L, Sun N, Yu H, et al. (2003) A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol 133: 1480–1493.
[11]  Ma L, Zhao H, Deng XW (2003) Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Development 130: 969–981.
[12]  Alonso JM, Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet 7: 524–536.
[13]  Stangeland B, Nestestog R, Grini PE, Skrbo N, Berg A, et al. (2005) Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5′ end of genes. J Exp Bot 56: 2495–2505.
[14]  Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, et al. (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63–66.
[15]  Pasek S, Risler JL, Brezellec P (2006) The role of domain redundancy in genetic robustness against null mutations. J Mol Biol 362: 184–191.
[16]  Pelaz S, Ditta GS, Baumann E, Wisman E, Yanofsky MF (2000) B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature 405: 200–203.
[17]  Kuusk S, Sohlberg JJ, Magnus Eklund D, Sundberg E (2006) Functionally redundant SHI family genes regulate Arabidopsis gynoecium development in a dose-dependent manner. Plant J 47: 99–111.
[18]  Miki D, Itoh R, Shimamoto K (2005) RNA silencing of single and multiple members in a gene family of rice. Plant Physiol 138: 1903–1913.
[19]  Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KF, et al. (2004) Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell 16: 1220–1234.
[20]  Tian C, Wan P, Sun S, Li J, Chen M (2004) Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol 54: 519–532.
[21]  Miyao A, Iwasaki Y, Kitano H, Itoh J, Maekawa M, et al. (2007) A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes. Plant Mol Biol 63: 625–635.
[22]  Budziszewski GJ, Lewis SP, Glover LW, Reineke J, Jones G, et al. (2001) Arabidopsis genes essential for seedling viability: isolation of insertional mutants and molecular cloning. Genetics 159: 1765–1778.
[23]  Tzafrir I, Pena-Muralla R, Dickerman A, Berg M, Rogers R, et al. (2004) Identification of genes required for embryo development in Arabidopsis. Plant Physiol 135: 1206–1220.
[24]  Kubis S, Patel R, Combe J, Bedard J, Kovacheva S, et al. (2004) Functional specialization amongst the Arabidopsis Toc159 family of chloroplast protein import receptors. Plant Cell 16: 2059–2077.
[25]  Townsend JP, Cavalieri D, Hartl DL (2003) Population genetic variation in genome-wide gene expression. Mol Biol Evol 20: 955–963.
[26]  Jung KH, Hur J, Ryu CH, Choi Y, Chung YY, et al. (2003) Characterization of a rice chlorophyll-deficient mutant using the T-DNA gene-trap system. Plant Cell Physiol 44: 463–472.
[27]  Zhang H, Li J, Yoo JH, Yoo SC, Cho SH, et al. (2006) Rice Chlorina-1 and Chlorina-9 encode ChlD and ChlI subunits of Mg-chelatase, a key enzyme for chlorophyll synthesis and chloroplast development. Plant Mol Biol 62: 325–337.
[28]  Tottey S, Block MA, Allen M, Westergren T, Albrieux C, et al. (2003) Arabidopsis CHL27, located in both envelope and thylakoid membranes, is required for the synthesis of protochlorophyllide. Proc Natl Acad Sci U S A 100: 16119–16124.
[29]  Lee S, Kim JH, Yoo ES, Lee CH, Hirochika H, et al. (2005) Differential regulation of chlorophyll a oxygenase genes in rice. Plant Mol Biol 57: 805–818.
[30]  Fujino K, Sekiguchi H, Kiguchi T (2005) Identification of an active transposon in intact rice plants. Mol Genet Genomics 273: 150–157.
[31]  Carretero-Paulet L, Cairo A, Botella-Pavia P, Besumbes O, Campos N, et al. (2006) Enhanced flux through the methylerythritol 4-phosphate pathway in Arabidopsis plants overexpressing deoxyxylulose 5-phosphate reductoisomerase. Plant Mol Biol 62: 683–695.
[32]  Barrero JM, Piqueras P, Gonzalez-Guzman M, Serrano R, Rodriguez PL, et al. (2005) A mutational analysis of the ABA1 gene of Arabidopsis thaliana highlights the involvement of ABA in vegetative development. J Exp Bot 56: 2071–2083.
[33]  Coschigano KT, Melo-Oliveira R, Lim J, Coruzzi GM (1998) Arabidopsis gls mutants and distinct Fd-GOGAT genes. Implications for photorespiration and primary nitrogen assimilation. Plant Cell 10: 741–752.
[34]  Kashino Y, Lauber WM, Carroll JA, Wang Q, Whitmarsh J, et al. (2002) Proteomic analysis of a highly active photosystem II preparation from the cyanobacterium Synechocystis sp. PCC 6803 reveals the presence of novel polypeptides. Biochemistry 41: 8004–8012.
[35]  Suorsa M, Aro EM (2007) Expression, assembly and auxiliary functions of photosystem II oxygen-evolving proteins in higher plants. Photosynth Res 93: 89–100.
[36]  Chen H, Zhang D, Guo J, Wu H, Jin M, et al. (2006) A Psb27 homologue in Arabidopsis thaliana is required for efficient repair of photodamaged photosystem II. Plant Mol Biol 61: 567–575.
[37]  Agrawal GK, Yamazaki M, Kobayashi M, Hirochika R, Miyao A, et al. (2001) Screening of the rice viviparous mutants generated by endogenous retrotransposon Tos17 insertion. Tagging of a zeaxanthin epoxidase gene and a novel ostatc gene. Plant Physiol 125: 1248–1257.
[38]  Kuromori T, Wada T, Kamiya A, Yuguchi M, Yokouchi T, et al. (2006) A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis. Plant J 47: 640–651.
[39]  Lin Y, Cheng CL (1997) A chlorate-resistant mutant defective in the regulation of nitrate reductase gene expression in Arabidopsis defines a new HY locus. Plant Cell 9: 21–35.
[40]  Muller-Moule P, Havaux M, Niyogi KK (2003) Zeaxanthin deficiency enhances the high light sensitivity of an ascorbate-deficient mutant of Arabidopsis. Plant Physiol 133: 748–760.
[41]  Muller-Moule P, Golan T, Niyogi KK (2004) Ascorbate-deficient mutants of Arabidopsis grow in high light despite chronic photooxidative stress. Plant Physiol 134: 1163–1172.
[42]  Voll LM, Jamai A, Renne P, Voll H, McClung CR, et al. (2006) The photorespiratory Arabidopsis shm1 mutant is deficient in SHM1. Plant Physiol 140: 59–66.
[43]  Kitami T, Nadeau JH (2002) Biochemical networking contributes more to genetic buffering in human and mouse metabolic pathways than does gene duplication. Nat Genet 32: 191–194.
[44]  Harrison R, Papp B, Pal C, Oliver SG, Delneri D (2007) Plasticity of genetic interactions in metabolic networks of yeast. Proc Natl Acad Sci U S A 104: 2307–2312.
[45]  Miki D, Shimamoto K (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 45: 490–495.
[46]  Fare TL, Coffey EM, Dai H, He YD, Kessler DA, et al. (2003) Effects of atmospheric ozone on microarray data quality. Anal Chem 75: 4672–4675.
[47]  Kinoshita T, Doi M, Suetsugu N, Kagawa T, Wada M, et al. (2001) Phot1 and phot2 mediate blue light regulation of stomatal opening. Nature 414: 656–660.
[48]  Masuda T, Fusada N, Oosawa N, Takamatsu K, Yamamoto YY, et al. (2003) Functional analysis of isoforms of NADPH: protochlorophyllide oxidoreductase (POR), PORB and PORC, in Arabidopsis thaliana. Plant Cell Physiol 44: 963–974.
[49]  Jiao Y, Ma L, Strickland E, Deng XW (2005) Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17: 3239–3256.
[50]  Ma L, Chen C, Liu X, Jiao Y, Su N, et al. (2005) A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 15: 1274–1283.
[51]  Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498–2504.
[52]  Edwards JW, Coruzzi GM (1989) Photorespiration and light act in concert to regulate the expression of the nuclear gene for chloroplast glutamine synthetase. Plant Cell 1: 241–248.
[53]  Douce R, Neuburger M (1999) Biochemical dissection of photorespiration. Curr Opin Plant Biol 2: 214–222.
[54]  Takahashi S, Bauwe H, Badger M (2007) Impairment of the photorespiratory pathway accelerates photoinhibition of photosystem II by suppression of repair but not acceleration of damage processes in Arabidopsis. Plant Physiol 144: 487–494.
[55]  Wingler A, Lea PJ, Quick WP, Leegood RC (2000) Photorespiration: metabolic pathways and their role in stress protection. Philos Trans R Soc Lond B Biol Sci 355: 1517–1529.
[56]  Reumann S, Weber AP (2006) Plant peroxisomes respire in the light: some gaps of the photorespiratory C2 cycle have become filled–others remain. Biochim Biophys Acta 1763: 1496–1510.
[57]  Leegood RC (2007) A welcome diversion from photorespiration. Nat Biotechnol 25: 539–540.
[58]  Khan MS (2007) Engineering photorespiration in chloroplasts: a novel strategy for increasing biomass production. Trends Biotechnol 25: 437–440.
[59]  Sharma A, Komatsu S (2002) Involvement of a Ca(2+)-dependent protein kinase component downstream to the gibberellin-binding phosphoprotein, RuBisCO activase, in rice. Biochem Biophys Res Commun 290: 690–695.
[60]  Burlat V, Oudin A, Courtois M, Rideau M, St-Pierre B (2004) Co-expression of three MEP pathway genes and geraniol 10-hydroxylase in internal phloem parenchyma of Catharanthus roseus implicates multicellular translocation of intermediates during the biosynthesis of monoterpene indole alkaloids and isoprenoid-derived primary metabolites. Plant J 38: 131–141.
[61]  Schwarte S, Bauwe H (2007) Identification of the photorespiratory 2-phosphoglycolate phosphatase, PGLP1, in Arabidopsis. Plant Physiol 144: 1580–1586.
[62]  Consortium. TGO (2008) The Gene Ontology project in 2008. Nucleic Acids Res 36: D440–444.
[63]  Werner T (2008) Bioinformatics applications for pathway analysis of microarray data. Curr Opin Biotechnol 19: 50–54.
[64]  Somerville SC, Ogren WL (1983) An Arabidopsis thaliana mutant defective in chloroplast dicarboxylate transport. Proc Natl Acad Sci U S A 80: 1290–1294.
[65]  Giordano M, Beardall J, Raven JA (2005) CO2 concentrating mechanisms in algae: mechanisms, environmental modulation, and evolution. Annu Rev Plant Biol 56: 99–131.
[66]  Price GD, Coleman JR, Badger MR (1992) Association of Carbonic Anhydrase Activity with Carboxysomes Isolated from the Cyanobacterium Synechococcus PCC7942. Plant Physiol 100: 784–793.
[67]  Seemann M, Tse Sum Bui B, Wolff M, Miginiac-Maslow M, Rohmer M (2006) Isoprenoid biosynthesis in plant chloroplasts via the MEP pathway: direct thylakoid/ferredoxin-dependent photoreduction of GcpE/IspG. FEBS Lett 580: 1547–1552.
[68]  Boucher Y, Doolittle WF (2000) The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways. Mol Microbiol 37: 703–716.
[69]  Lichtenthaler HK, Schwender J, Disch A, Rohmer M (1997) Biosynthesis of isoprenoids in higher plant chloroplasts proceeds via a mevalonate-independent pathway. FEBS Lett 400: 271–274.
[70]  Schwender J, Seemann M, Lichtenthaler HK, Rohmer M (1996) Biosynthesis of isoprenoids (carotenoids, sterols, prenyl side-chains of chlorophylls and plastoquinone) via a novel pyruvate/glyceraldehyde 3-phosphate non-mevalonate pathway in the green alga Scenedesmus obliquus. Biochem J 316 (Pt 1): 73–80.
[71]  Eisenreich W, Schwarz M, Cartayrade A, Arigoni D, Zenk MH, et al. (1998) The deoxyxylulose phosphate pathway of terpenoid biosynthesis in plants and microorganisms. Chem Biol 5: R221–233.
[72]  Guevara-Garcia A, San Roman C, Arroyo A, Cortes ME, de la Luz Gutierrez-Nava M, et al. (2005) Characterization of the Arabidopsis clb6 mutant illustrates the importance of posttranscriptional regulation of the methyl-D-erythritol 4-phosphate pathway. Plant Cell 17: 628–643.
[73]  Lichtenthaler HK (1999) The 1-Deoxy-D-Xylulose-5-Phosphate Pathway of Isoprenoid Biosynthesis in Plants. Annu Rev Plant Physiol Plant Mol Biol 50: 47–65.
[74]  Rohmer M (1999) The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants. Nat Prod Rep 16: 565–574.
[75]  Aharoni A, Jongsma MA, Bouwmeester HJ (2005) Volatile science? Metabolic engineering of terpenoids in plants. Trends Plant Sci 10: 594–602.
[76]  Hsieh MH, Goodman HM (2006) Functional evidence for the involvement of Arabidopsis IspF homolog in the nonmevalonate pathway of plastid isoprenoid biosynthesis. Planta 223: 779–784.
[77]  Hsieh MH, Goodman HM (2005) The Arabidopsis IspH homolog is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis. Plant Physiol 138: 641–653.
[78]  Estevez JM, Cantero A, Romero C, Kawaide H, Jimenez LF, et al. (2000) Analysis of the expression of CLA1, a gene that encodes the 1-deoxyxylulose 5-phosphate synthase of the 2-C-methyl-D-erythritol-4-phosphate pathway in Arabidopsis. Plant Physiol 124: 95–104.
[79]  Page JE, Hause G, Raschke M, Gao W, Schmidt J, et al. (2004) Functional analysis of the final steps of the 1-deoxy-D-xylulose 5-phosphate (DXP) pathway to isoprenoids in plants using virus-induced gene silencing. Plant Physiol 134: 1401–1413.
[80]  Gutierrez-Nava Mde L, Gillmor CS, Jimenez LF, Guevara-Garcia A, Leon P (2004) CHLOROPLAST BIOGENESIS genes act cell and noncell autonomously in early chloroplast development. Plant Physiol 135: 471–482.
[81]  Ahn CS, Pai HS (2008) Physiological function of IspE, a plastid MEP pathway gene for isoprenoid biosynthesis, in organelle biogenesis and cell morphogenesis in Nicotiana benthamiana. Plant Mol Biol 66: 503–517.
[82]  Rodriguez-Concepcion M, Fores O, Martinez-Garcia JF, Gonzalez V, Phillips MA, et al. (2004) Distinct light-mediated pathways regulate the biosynthesis and exchange of isoprenoid precursors during Arabidopsis seedling development. Plant Cell 16: 144–156.
[83]  Ma S, Gong Q, Bohnert HJ (2007) An Arabidopsis gene network based on the graphical Gaussian model. Genome Res 17: 1614–1625.
[84]  Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136: 2621–2632.
[85]  Jung KH, Han MJ, Lee DY, Lee YS, Schreiber L, et al. (2006) Wax-deficient anther1 is involved in cuticle and wax production in rice anther walls and is required for pollen development. Plant Cell 18: 3015–3032.
[86]  Rocke DM (2004) Design and analysis of experiments with high throughput biological assay data. Semin Cell Dev Biol 15: 703–713.
[87]  Berger JA, Hautaniemi S, Jarvinen AK, Edgren H, Mitra SK, et al. (2004) Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinformatics 5: 194–206.
[88]  Monte E, Tepperman JM, Al-Sady B, Kaczorowski KA, Alonso JM, et al. (2004) The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Proc Natl Acad Sci U S A 101: 16091–16098.


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