Chlorophyll biosynthesis and transcriptome profiles of chlorophyll b-deficient type 2b rice (Oryza sativa L.)

  • Minh Khiem NGUYEN Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei 115 (TW)
  • Chi-Ming Yang Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei 115 (TW)
  • Tin-Han SHIH Biodiversity Research Center, Academia Sinica, Nangang, Taipei 115 (TW)
  • Szu-Hsien LIN Biodiversity Research Center, Academia Sinica, Nangang, Taipei 115 (TW)
  • Giang Tuyet PHAM Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000 (VN)
  • Hoang Chinh NGUYEN Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000 (VN)
Keywords: chl b-deficient mutant, chlorophyll, gene expression, photosynthesis, transcriptome profiles


Photosynthetic and transcriptomic characteristics of a chlorophyll (Chl) b-deficient mutant type 2b rice (ch14) were investigated in this study. The ultrastructure of chloroplast in ch14 demonstrated irregular chloroplast enhancement (loss of starch granules, indistinct membranes, and thinner grana). Ch14 had significantly lower carotenoid, Chl a, Chl b, and total Chl contents, but a higher ratio of Chl a to Chl b than a wide-type rice. 3,594 genes were differentially expressed in ch14, among which 309 transcription factors were related to Chl degradation and biosynthesis, chloroplast formations, and the photosynthesis capacity. PsbR, GSA-AT, PBGD, PPOX, MgMT, and POR genes were down-regulated, reducing Chl content and photosynthetic capacity in the ch14. This study suggests that Chl degradation may be attributed to abnormal chloroplast development and down-regulation of gene expression in the common pathway and Mg branch and the rise in Chl a to Chl b ratio may be involved in the alternative Chl b degradation pathway.


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Allen JF (1992). How does protein phosphorylation regulate photosynthesis? Trends in Biochemical Sciences 17:12-17.

Allen KD, Duysen ME, Staehelin LA (1998). Biogenesis of thylakoid membranes is controlled by light intensity in the conditional chlorophyll b-deficient CD3 mutant of wheat. The Journal of Cell Biology 107:907-919.

Amarnath K, Bennett DI, Schneider AR, Fleming GR (2016). Multiscale model of light harvesting by photosystem II in plants. Proceedings of the National Academy of Sciences 113:1156-1161.

Barber J (1982). Influence of surface charges on thylakoid structure and function. Annual Review of Plant Physiology 33:261-295.

Bennett J (1991). Protein phosphorylation in green plant chloroplasts. Annual Review of Plant Physiology 42:281-311.

Blankenship RE (2014). Molecular mechanisms of photosynthesis. John Wiley & Sons.

Bujaldon S, Kodama N, Rappaport F, Subramanyam R, de Vitry C, Takahashi Y, Wollman FA (2017). Functional accumulation of antenna proteins in chlorophyll b-less mutants of Chlamydomonas reinhardtii. Molecular Plant 10:115-130.

Cha KW, Lee YJ, Koh HJ, Lee BM, Nam YW, Paek NC (2002). Isolation, characterization, and mapping of the stay green mutant in rice. Theoretical and Applied Genetics 104:526-232.

Chu P, Yan GX, Yang Q, Zhai LN, Zhang C, Zhang FQ, Guan RZ (2015). iTRAQ-based quantitative proteomics analysis of Brassica napus leaves reveals pathways associated with chlorophyll deficiency. Journal of Proteomics 113:244-259.

Demirbaş A (2001). Biomass resource facilities and biomass conversion processing for fuels and chemicals. Energy Conversion and Management 42:1357-1378.

Dubreuil C, Jin X, de Dios Barajas-López J, Hewitt TC, Tanz SK, Dobrenel T, ... Small I (2018). Establishment of photosynthesis through chloroplast development is controlled by two distinct regulatory phases. Plant Physiology 176:1199-1214.

Dutta S, Mohanty S, Tripathy BC (2009). Role of temperature stress on chloroplast biogenesis and protein import in pea. Plant Physiology 150:1050-1061.

Evans LT, Evans LTE, Evans LT, Evans LT (1998). Feeding the ten billion: plants and population growth. Cambridge University Press.

Flood PJ, Kruijer W, Schnabel SK, van der Schoor R, Jalink H, Snel JF, ... Aarts MG (2016). Phenomics for photosynthesis, growth and reflectance in Arabidopsis thaliana reveals circadian and long-term fluctuations in heritability. Plant Methods 12:1-4.

Fujita Y (1996). Protochlorophyllide reduction: a key step in the greening of plants. Plant Cell Physiology 37:411-421.

Goral TK, Johnson MP, Duffy CD, Brain AP, Ruban AV, Mullineaux CW (2012). Light‐harvesting antenna composition controls the macrostructure and dynamics of thylakoid membranes in Arabidopsis. The Plant Journal 69:289-301.

Gupta J (2013). Climate change and water law. In: Grover VI (Ed). Impact of Climate Change on Water and Health. CRC Press, Taylor & Francis Group, Boca Raton, pp 30-45.

Hong ZH, Zhou YY, Hong Z, He SZ, Ning ZH, Liu QC (2019). Transcriptome profiling reveals insights into the molecular mechanism of drought tolerance in sweetpotato. Journal of Integrative Agriculture 18:9-23.

Hopkins WG, Hayden DB, Neuffer MG (1980). A light-sensitive mutant in maize (Zea mays L.) I. Chlorophyll, chlorophyll-protein and ultrastructural studies. Zeitschrift für Pflanzenphysiologie 99:417-426.

Huang J, Qin F, Zang G, Kang Z, Zou H, Hu F, ... Wang G (2013). Mutation of OsDET1 increases chlorophyll content in rice. Plant Science 210:241-249.

Hunter MC, Smith RG, Schipanski ME, Atwood LW, Mortensen DA (2017). Agriculture in 2050: recalibrating targets for sustainable intensification. Bioscience 67:386-391.

Ito H, Ohtsuka T, Tanaka A (1996). Conversion of chlorophyll b to chlorophyll a via 7-hydroxymethyl chlorophyll. Journal of Biological Chemistry 271:1475-1479.

Jenny A, Mark W, Robin G W, Caroline A H, Alexander V R, Peter H, Stefan J (2003). Absence of the Lhcb1 and Lhcb2 proteins of the light‐harvesting complex of photosystem II–effects on photosynthesis, grana stacking and fitness. The Plant Journal 35:350-361.

Jung KH, Hur J, Ryu CH, Choi Y, Chung YY, Miyao A, ... An G (2003). Characterization of a rice chlorophyll-deficient mutant using the T-DNA gene-trap system. Plant and Cell Physiology 44:463-472.

Kato KK, Palmer RG (2004). Duplicate chlorophyll-deficient loci in soybean. Genome 47:190-198.

Kim EH, Li XP, Razeghifard R, Anderson JM, Niyogi KK, Pogson BJ, Chow WS (2009). The multiple roles of light-harvesting chlorophyll a/b-protein complexes define structure and optimize function of Arabidopsis chloroplasts: a study using two chlorophyll b-less mutants. Biochimica et Biophysica Acta (BBA)-Bioenergetics 1787:973-984.

Landi M, Zivcak M, Sytar O, Brestic M, Allakhverdiev SI (2020). Plasticity of photosynthetic processes and the accumulation of secondary metabolites in plants in response to monochromatic light environments: A review. Biochimica et Biophysica Acta (BBA)-Bioenergetics 1861:148131.

Levicán G, Katz A, De Armas M, Núñez H, Orellana O (2007). Regulation of a glutamyl-tRNA synthetase by the heme status. Proceedings of the National Academy of Sciences 104:3135-3140.

Li CF, Xu YX, Ma JQ, Jin JQ, Huang DJ, Yao MZ, ... Chen L (2016). Biochemical and transcriptomic analyses reveal different metabolite biosynthesis profiles among three color and developmental stages in ‘Anji Baicha’(Camellia sinensis). BMC Plant Biology 16:195.

Li WX, Yang SB, Lu Z, He ZC, Ye YL, Zhao BB, ... Jin B (2018). Cytological, physiological, and transcriptomic analyses of golden leaf coloration in Ginkgo biloba L. Horticulture Research 5:12.

Li Y, Zhang Z, Wang P, Ma L, Li L, Yang R, Ma Y, Wang Q (2015). Comprehensive transcriptome analysis discovers novel candidate genes related to leaf color in a Lagerstroemia indica yellow leaf mutant. Genes & Genomics 37:851-863.

Liu W, Fu Y, Hu G, Si H, Zhu L, Wu C, Sun Z (2007). Identification and fine mapping of a thermo-sensitive chlorophyll deficient mutant in rice (Oryza sativa L.). Planta 226:785-795.

Liu X, Li L, Li M, Su L, Lian S, Zhang B, ... Li L (2018). AhGLK1 affects chlorophyll biosynthesis and photosynthesis in peanut leaves during recovery from drought. Scientific Reports 8:2250.

Livak KJ, Schmittgen TD (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402-408.

Lokstein H, Härtel H, Hoffmann P, Renger G (1993). Comparison of chlorophyll fluorescence quenching in leaves of wild-type with a chlorophyll-b-less mutant of barley (Hordeum vulgare L.). Journal of Photochemistry and Photobiology B: Biology 19:217-225.

Long SP, ZHU XG, Naidu SL, Ort DR (2006). Can improvement in photosynthesis increase crop yields? Plant, Cell & Environment 29:315-330.

Masuda T, Fujita Y (2008). Regulation and evolution of chlorophyll metabolism. Photochemical & Photobiological Sciences 7:1131-1149.

Milovanovic V, Smutka L (2017). Asian countries in the global rice market. ACTA Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 65:679-688.

Morita R, Kusaba M, Yamaguchi H, Amano E, Miyao A, Hirochika H, Nishimura M (2005). Characterization of chlorophyllide a oxygenase (CAO) in rice. Breeding Science 55:361-364.

Murchie EH, Pinto M, Horton P (2009). Agriculture and the new challenges for photosynthesis research. New Phytologist 181:532-552.

Nelson N, Yocum CF (2006). Structure and function of photosystems I and II. Annual Review of Plant Biology 2006 57:521-565.

Nomata J, Swem LR, Bauer CE, Fujita Y (2005). Overexpression and characterization of dark-operative protochlorophyllide reductase from Rhodobacter capsulatus. Biochimica et Biophysica Acta (BBA)-Bioenergetics 1708:229-237.

Nguyen MK, Shih TH, Lin SH, Huang WD, Yang CM (2020). Transcription analysis of chlorophyll biosynthesis in wildtype and chlorophyll b-lacking rice (Oryza sativa L.). Photosynthetica 58:702-711.

Oster U, Tanaka R, Tanaka A, Rüdiger W (2000). Cloning and functional expression of the gene encoding the key enzyme for chlorophyll b biosynthesis (CAO) from Arabidopsis thaliana. The Plant Journal 21:305-310.

Ray DK, Mueller ND, West PC, Foley JA (2013). Yield trends are insufficient to double global crop production by 2050. PLoS One 8:66428.

Rüdiger W (2002). Biosynthesis of chlorophyll b and the chlorophyll cycle. Photosynthesis Research 74:187-193.

Sager JC, McFarlane JC (1997). Radiation. In: Langhans RW, Tibbitts TW (Eds). Plant growth chamber handbook. Iowa Agricultural and Home Economics Experiment Station.

Schoefs B (2001). The protochlorophyllide–chlorophyllide cycle. Photosynthesis Research 70:257-271.

Shi LX, Hall M, Funk C, Schröder WP (2012). Photosystem II, a growing complex: updates on newly discovered components and low molecular mass proteins. Biochimica et Biophysica Acta (BBA)-Bioenergetics 1817:13-25.

Shimoda Y, Ito H, Tanaka A (2012). Conversion of chlorophyll b to chlorophyll a precedes magnesium dechelation for protection against necrosis in Arabidopsis. Plant Journal 72:501-511.

Spurr AR (1969). A low-viscosity epoxy resin embedding medium for electron microscopy. Journal of Ultrastructure Research 26:31-43.

Standfuss J, Terwisscha van Scheltinga AC, Lamborghini M, Kühlbrandt W (2005). Mechanisms of photoprotection and nonphotochemical quenching in pea light‐harvesting complex at 2.5 Å resolution. The EMBO Journal 24:919-928.

Tanaka A, Ito H, Tanaka R, Tanaka NK, Yoshida K, Okada K (1998). Chlorophyll a oxygenase (CAO) is involved in chlorophyll b formation from chlorophyll a. Proceedings of the National Academy of Sciences 95:12719-12723.

Terao T, Yamashita A, Katoh S (1985). Chlorophyll b-deficient mutants of rice: I. Absorption and fluorescence spectra and chlorophyll a/b ratios. Plant and Cell Physiology 26:1361-1367.

Tomitani A, Okada K, Miyashita H, Matthijs HC, Ohno T, Tanaka A (1999). Chlorophyll b and phycobilins in the common ancestor of cyanobacteria and chloroplasts. Nature 400:159-162.

Voitsekhovskaja OV, Tyutereva EV (2015). Chlorophyll b in angiosperms: functions in photosynthesis, signaling and ontogenetic regulation. Journal of Plant Physiology 189:51-64.

Von Wettstein D, Gough S, Kannangara CG (1995). Chlorophyll biosynthesis. The Plant Cell 7:1039.

Wang Z, Gerstein M, Snyder M (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10:57-63.

Warren MJ, Cooper JB, Wood SP, Shoolingin-Jordan PM (1998). Lead poisoning, haem synthesis and 5-aminolaevulinic acid dehydratase. Trends in Biochemical Sciences 23:217-221.

Wu Z, Zhang X, He B, Diao L, Sheng S, Wang J, ... Wang C (2007). A chlorophyll-deficient rice mutant with impaired chlorophyllide esterification in chlorophyll biosynthesis. Plant Physiology 145:29-40.

Wu ZM, Zhang X, Wang JL, Wan JM. Leaf chloroplast ultrastructure and photosynthetic properties of a chlorophyll-deficient mutant of rice. Photosynthetica 52:217-222.

Yamazaki J (2010). Changes in the photosynthetic characteristics and photosystem stoichiometries in wt and Chl b-deficient mutant rice seedlings under various irradiances. Photosynthetica 48:521-529.

Yang CM, Chang KW, Yin MH, Huang HM (1998). Methods for the determination of the chlorophylls and their derivatives. Taiwania 43:116-122.

Yang CM, Chen HY (1996). Grana stacking is normal in a chlorophyll-deficient LT8 mutant of rice. Botanical Bulletin of Academia Sinica 37:31-34.

Yang HY, Xia XW, Fang W, Fu Y, An MM, Zhou MB (2015). Identification of genes involved in spontaneous leaf color variation in Pseudosasa japonica. Genetic and Molecular Research 14:11827-11840.

Yang Y, Chen X, Xu B, Li Y, Ma Y, Wang G (2015). Phenotype and transcriptome analysis reveals chloroplast development and pigment biosynthesis together influenced the leaf color formation in mutants of Anthurium andraeanum ‘Sonate’. Frontiers in Plant Science 6:139.

Zhao X, Chen T, Feng B, Zhang C, Peng S, Zhang X, ... Tao L (2017). Non-photochemical quenching plays a key role in light acclimation of rice plants differing in leaf color. Frontiers in Plant Science 7:1968.

Zhao X, Nishimura Y, Fukumoto Y, Li J (2011). Effect of high temperature on active oxygen species, senescence and photosynthetic properties in cucumber leaves. Environmental and Experimental Botany 70:212-216.

Zhu XG, Long SP, Ort DR (2010). Improving photosynthetic efficiency for greater yield. Annual Review of Plant Biology 61:235-261.

How to Cite
NGUYEN, M. K., Yang, C.-M., SHIH, T.-H., LIN, S.-H., PHAM, G. T., & NGUYEN, H. C. (2021). Chlorophyll biosynthesis and transcriptome profiles of chlorophyll b-deficient type 2b rice (Oryza sativa L.). Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 49(3), 12380.
Research Articles
DOI: 10.15835/nbha49312380

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