Hostname: page-component-cd9895bd7-gbm5v Total loading time: 0 Render date: 2024-12-26T07:30:00.523Z Has data issue: false hasContentIssue false
  • English
  • Français

Molecular cloning, gene expression and functional expression of a phosphoenolpyruvate carboxylase Osppc1 in developing rice seeds: implication of involvement in nitrogen accumulation

Published online by Cambridge University Press:  07 January 2014

Naoki Yamamoto ,
Tatsuya Kubota ,
Takehiro Masumura ,
Naomasa Shiraishi ,
Kunisuke Tanaka ,
Toshio Sugimoto  and
Yoshikiyo Oji
Naoki Yamamoto
Affiliation:
Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe657-8501, Japan
Tatsuya Kubota
Affiliation:
Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe657-8501, Japan
Takehiro Masumura
Affiliation:
Laboratory of Genetic Engineering, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Kyoto606-8522, Japan Kyoto Prefectural Institute of Agricultural Biotechnology, Kitainayazuma, Seika-cho, Soraku-gun, Kyoto619-0244, Japan
Naomasa Shiraishi
Affiliation:
Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe657-8501, Japan
Kunisuke Tanaka
Affiliation:
Laboratory of Genetic Engineering, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Kyoto606-8522, Japan Kyoto Prefectural Institute of Agricultural Biotechnology, Kitainayazuma, Seika-cho, Soraku-gun, Kyoto619-0244, Japan
Toshio Sugimoto*
Affiliation:
Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe657-8501, Japan
Yoshikiyo Oji
Affiliation:
Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe657-8501, Japan
*
*Correspondence E-mail: sugimoto@kobe-u.ac.jp
Get access Rights & Permissions [Opens in a new window]

Abstract

We isolated two cDNAs of phosphoenolpyruvate carboxylase (PEPC) from developing rice seeds, Osppc1 and Osppc3. The deduced amino acid sequences of both cDNAs share several conserved motifs with other non-photosynthetic PEPCases, and these common motifs are known to be functionally important to their regulatory properties. The deduced protein sequence of Osppc1 was clustered into a monocotyledonous plant-specific clade, and Osppc3 was clustered into a gramineous plant-specific clade in the phylogenetic tree of plant PEPCases. The mRNA accumulations of Osppc1 and Osppc3 were found in developing rice seeds throughout the grain-filling stages, although their expression patterns differed: Osppc1 was strongly expressed at 7 d after flowering, and Osppc3 was strongly expressed at 4 d after flowering. The kinetic properties of the Osppc1 recombinant protein were quite similar to those of maize root-type PEPCase, except that the sensitivity for malate at pH 7.3 was weaker. Mining rice microarray data, we observed that Osppc1 was co-expressed with aspartate aminotransferase and alanine aminotransferase, which are involved in seed nitrogen metabolism. Moreover, reannotation of the co-expressed genes revealed that Osppc1, the two aminotransferases and the enolase were mapped on to the consecutive reaction from 2-phosphoglycerate to glutamate and pyruvate in the cytosol. These results imply that Osppc1 functions cooperatively with the two aminotransferases in the synthesis of amino acids that are used for storage protein synthesis in developing rice seeds.

Keywords

amino acid synthesiskineticsnitrogen accumulationphosphoenolpyruvate carboxylaseproteinriceseeds
Type
Research Papers
Information
Seed Science Research , Volume 24 , Issue 1 , March 2014 , pp. 23 - 36
Check for updates
Copyright
Copyright © Cambridge University Press 2014 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Albert, H.A., Martin, T. and Sun, S.S.M. (1992) Structure and expression of a sugarcane gene coding a housekeeping phosphoenolpyruvate carboxylase. Plant Molecular Biology 20, 663–671.Google Scholar
Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Muertter, R.N., Holko, M., Ayanbule, O., Yefanov, A. and Soboleva, A. (2010) NCBI GEO: archive for functional genomics data sets – 10 years on. Nucleic Acids Research 39, D1005–D1010.CrossRefGoogle Scholar
Bläsing, O.E., Westhoff, P. and Svensson, P. (2000) Evolution of C4 phosphoenolpyruvate carboxylase in Flaveria, a conserved serine residue in the carboxyl-terminal part of the enzyme is a major determinant for C4-specific characteristics. Journal of Biological Chemistry 275, 27917–27923.Google Scholar
Blonde, J.D. and Plaxton, W.C. (2003) Structural and kinetic properties of high and low molecular mass phosphoenolpyruvate carboxylase isoforms from the endosperm of developing castor oilseeds. Journal of Biological Chemistry 278, 11867–11873.CrossRefGoogle ScholarPubMed
Bradford, M.M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry 72, 248–254.Google Scholar
Champagne, E.T., Bett-Garber, K.L., Thomson, J.L. and Fitzgerald, M.A. (2001) Unraveling the impact of nitrogen nutrition on cooked rice flavor and texture. Cereal Chemistry 86, 274–280.Google Scholar
Champagne, E.T., Bett-Garber, K.L., McClung, A.M. and Bergman, C. (2004) Sensory characteristics of diverse rice cultivars as influenced by genetic and environmental factors. Cereal Chemistry 81, 237–243.Google Scholar
Champagne, E.T., Bett-Garher, K.L., Grimm, C.C. and McClung, A.M. (2007) Effects of organic fertility management on physicochemical properties and sensory quality of diverse rice cultivars. Cereal Chemistry 84, 320–327.Google Scholar
Derycke, V., Veraverbeke, W.S., Vandeputte, G.E., De Man, W., Hoseney, R.C. and Deleour, J.A. (2005) Impact of proteins on pasting and cooking properties of nonparboiled and parboiled rice. Cereal Chemistry 82, 468–474.Google Scholar
Diebold, R., Schuster, J., Däschner, K. and Binder, S. (2002) The branched-chain amino acid transaminase gene family in Arabidopsis encodes plastid and mitochondrial proteins. Plant Physiology 129, 540–550.Google Scholar
Dong, L.Y., Masuda, T., Kawamura, T., Hata, S. and Izui, K. (1998) Cloning, expression, and characterization of a root-form phosphoenolpyruvate carboxylase from Zea mays: comparison with the C4-form enzyme. Plant & Cell Physiology 39, 865–873.Google Scholar
Duff, S.M.G. and Chollet, R. (1995) In vivo regulation of wheat-leaf phosphoenolpyruvate carboxylase by reversible phosphorylation. Plant Physiology 107, 775–782.Google Scholar
Echevarria, C., Pacquit, V., Bakrim, N., Osuna, L., Delgado, B., Arrio-Dupont, M. and Vidal, J. (1994) The effect of pH on the covalent and metabolic control of C4 phosphoenolpyruvate carboxylase from sorghum leaf. Archives of Biochemistry and Biophysics 315, 425–430.Google Scholar
Furukawa, S., Tanaka, K., Masumura, T., Ogihara, Y., Kiyokawa, Y. and Wakai, Y. (2006) Influence of rice proteins on eating quality of cooked rice and on aroma and flavor of sake. Cereal Chemistry 83, 439–446.Google Scholar
Gennidakis, S., Rao, S., Greenham, K., Uhrig, R.G., O'Leary, B., Snedden, W.A., Lu, C. and Plaxton, W.C. (2007) Bacterial- and plant-type phosphoenolpyruvate carboxylase polypeptides interact in the hetero-oligomeric Class-2 PEPC complex of developing castor oil seeds. The Plant Journal 52, 839–849.Google Scholar
Golombek, S., Heim, U., Horstmann, C., Wobus, U. and Weber, H. (1999) Phosphoenolpyruvate carboxylase in developing seeds of Vicia faba L.: gene expression and metabolic regulation. Planta 208, 66–72.CrossRefGoogle ScholarPubMed
González, M.C., Osuna, L., Echevarría, C., Vidal, J. and Cejudo, F.J. (1998) Expression and localization of phosphoenolpyruvate carboxylase in developing and germinating wheat grains. Plant Physiology 116, 1249–1258.Google Scholar
Gout, E., Boisson, A., Aubert, S., Douce, R. and Bligny, R. (2001) Origin of the cytoplasmic pH changes during anaerobic stress in higher plant cells. Carbon-13 and phosphorus-31 nuclear magnetic resonance studies. Plant Physiology 125, 912–925.Google Scholar
Hamada, K., Hongo, K., Suwabe, K., Shimizu, A., Nagayama, T., Abe, R., Kikuchi, S., Yamamoto, N., Fujii, T., Yokoyama, K., Tsuchida, H., Sano, K., Mochizuki, T., Oki, N., Horiuchi, Y., Fujita, M., Watanabe, M., Matsuoka, M., Kurata, N. and Yano, K. (2011) OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. Plant & Cell Physiology 52, 220–229.Google Scholar
Hamaker, B.R. and Griffin, V.K. (1990) Changing the viscoelastic properties of cooked rice through protein disruption. Cereal Chemistry 67, 261–264.Google Scholar
Huppe, H.C. and Turpin, D.H. (1994) Integration of carbon and nitrogen metabolism in plant and algal cells. Annual Review of Plant Physiology and Plant Molecular Biology 45, 577–607.Google Scholar
Igawa, T., Fujiwara, M., Tanaka, I., Fukao, Y. and Yanagawa, Y. (2010) Characterization of bacterial-type phosphoenolpyruvate carboxylase expressed in male gametophyte of higher plants. BMC Plant Biology 10, 200.CrossRefGoogle ScholarPubMed
International Year of Rice Secretariat (2004) The international year of rice 2004: Concept Paper. Available at http://www.fao.org/docrep/MEETING/007/J1225e/J1225e00.HTM (accessed accessed 19 December 2013).Google Scholar
Irizarry, R.A. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249–264.Google Scholar
Iwasaki, Y., Mae, T., Makino, A., Ohira, K. and Ojima, K. (1992) Nitrogen accumulation in the inferior spikelet of rice ear during ripening. Soil Science and Plant Nutrition 38, 517–525.CrossRefGoogle Scholar
Juliano, B.O., Onate, L.U. and del Mundo, A.M. (1965) Relation of starch composition, protein content and gelatinization temperature to cooking and eating qualities of milled rice. Food Technology 19, 1006–1011.Google Scholar
Kai, Y., Matsumura, H. and Izui, K. (2003) Phosphoenolpyruvate carboxylase: three-dimensional structure and molecular mechanisms. Archives of Biochemistry and Biophysics 414, 170–179.Google Scholar
Kikuchi, H., Hirose, S., Toki, S., Akama, K. and Takaiwa, F. (1999) Molecular characterization of a gene for alanine aminotransferase from rice (Oryza sativa). Plant Molecular Biology 39, 149–159.Google Scholar
Laemmli, U.K. (1970) Cleavage of structural protein during the assembly of the head of bacteriophage T4. Nature 227, 680–685.Google Scholar
Lin, C.F., Wei, C., Jiang, L.Z., Li, K.G., Qian, X.Y., Attia, K. and Yang, J.S. (2004) Isolation, characterization and expression analysis of a leaf-specific phosphoenolpyruvate carboxylase gene in Oryza sativa . DNA Sequence 15, 269–276.Google Scholar
Macnicol, P.K. and Jacobsen, J.V. (1992) Endosperm acidification and related metabolic changes in the developing barley grain. Plant Physiology 98, 1098–1104.CrossRefGoogle ScholarPubMed
Mamedov, T.G., Moellering, E.R. and Chollet, R. (2005) Identification and expression analysis of two inorganic C- and N-responsive genes encoding novel and distinct molecular forms of eukaryotic phosphoenolpyruvate carboxylase in the green microalga Chlamydomonas reinhardtii . The Plant Journal 42, 832–843.CrossRefGoogle Scholar
Martin, M. and Fitzgerald, M.A. (2002) Proteins in rice grains influence cooking properties! Journal of Cereal Science 36, 285–294.CrossRefGoogle Scholar
Masumoto, C., Miyazawa, S., Ohkawa, H., Fukuda, T., Taniguchi, Y., Murayama, S., Kusano, M., Saito, K., Fukayama, H. and Miyao, M. (2010) Phosphoenolpyruvate carboxylase intrinsically located in the chloroplast of rice plays a crucial role in ammonium assimilation. Proceedings of the National Academy of Sciences, USA 107, 5226–5231.Google Scholar
Masumura, T., Hibino, T., Kidzu, K., Mitsukawa, N., Tanaka, K. and Fujii, S. (1990) Cloning and characterization of a cDNA encoding a rice 13 kDa prolamin. Molecular and General Genetics 221, 1–7.CrossRefGoogle ScholarPubMed
Matsuoka, M. and Hata, S. (1987) Comparative studies of phosphoenolpyruvate carboxylase from C3 and C4 plants. Plant Physiology 85, 947–951.Google Scholar
Okadome, H., Kurihara, M., Kusuda, O., Toyoshimna, H., Kim, J., Shimotsubo, K., Matsuda, T. and Ohtsubo, K. (1999) Multiple measurements of physical properties of cooked rice grains with different nitrogenous fertilizers. Japanese Journal of Crop Science 68, 211–216, (in Japanese).CrossRefGoogle Scholar
O'Leary, B., Park, J. and Plaxton, W.C. (2011) The remarkable diversity of plant PEPC (phosphoenolpyruvate carboxylase): recent insights into the physiological functions and post-translational controls of non-photosynthetic PEPCs. Biochemical Journal 436, 15–34.Google Scholar
Onate, T.U., del Mundo, A.M. and Juliano, B.O. (1964) Relationship between protein content and eating quality of milled rice. Philippine Agriculturist 47, 441–444.Google Scholar
Park, J.K., Kim, S.S. and Kim, O.K. (2001) Effect of milling ratio on sensory properties of cooked rice and on physicochemical properties of milled and cooked rice. Cereal Chemistry 78, 151–156.Google Scholar
Perez, C.M., Juliano, B.O., Liboon, S.P., Alcantara, J.M. and Cassman, K.G. (1996) Effects of late nitrogen fertilizer application on head rice yield, protein content, and grain quality of rice. Cereal Chemistry 73, 556–560.Google Scholar
Podesta, F.E. and Plaxton, W.C. (1994a) Regulation of cytosolic carbon metabolism in germinating Ricinus communis cotyledons. I. Developmental profiles for the activity, concentration, and molecular structure of the pyrophosphate- and ATP-dependent phosphofructokinases, phosphoenolpyruvate carboxylase and pyruvate kinase. Planta 194, 374–380.CrossRefGoogle Scholar
Podesta, F.E. and Plaxton, W.C. (1994b) Regulation of cytosolic carbon metabolism in germinating Ricinus communis cotyledons. II. Properties of phosphoenolpyruvate carboxylase and cytosolic pyruvate kinase associated with the regulation of glycolysis and nitrogen assimilation. Planta 194, 381–387.Google Scholar
Roberts, J.K., Hooks, M.A., Miaullis, A.P., Edwards, S. and Webster, C. (1992) Contribution of malate and amino acid metabolism to cytoplasmic pH regulation in hypoxic maize root tips studied using nuclear magnetic resonance spectroscopy. Plant Physiology 98, 480–487.Google Scholar
Rolletschek, H., Radchuk, R., Klukas, C., Schreiber, F., Wobus, U. and Borisjuk, L. (2005) Evidence of a key role for photosynthetic oxygen release in oil storage in developing soybean seeds. New Phytologist 167, 777–786.CrossRefGoogle ScholarPubMed
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406–425.Google Scholar
Sánchez, R. and Cejudo, F.J. (2003) Identification and expression analysis of a gene encoding a bacterial-type phosphoenolpyruvate carboxylase from Arabidopsis and rice. Plant Physiology 132, 949–957.Google Scholar
Sato, Y., Takehisa, H., Kamatsuki, K., Minami, H., Namiki, N., Ikawa, H., Ohyanagi, H., Sugimoto, K., Antonio, B.A. and Nagamura, Y. (2013) RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. Nucleic Acids Research Database issue, D1206–D1213.CrossRefGoogle ScholarPubMed
Sentoku, N., Taniguchi, M., Sugiyama, T., Ishimaru, K., Ohsugi, R., Takaiwa, F. and Toki, S. (2000) Analysis of the transgenic tobacco plants expressing Panicum miliaceum aspartate aminotransferase genes. Plant Cell Reports 19, 598–603.CrossRefGoogle ScholarPubMed
Song, J., Yamamoto, K., Shomura, A., Yano, M., Minobe, Y. and Sasaki, T. (1996) Characterization and mapping of cDNA encoding aspartate aminotransferase in rice, Oryza sativa L. DNA Research 3, 303–310.CrossRefGoogle ScholarPubMed
Sugiharto, B. and Sugiyama, T. (1992) Effects of nitrate and ammonium on gene expression of phosphoenolpyruvate carboxylase and nitrogen metabolism in maize leaf tissue during recovery from nitrogen stress. Plant Physiology 98, 1403–1408.Google Scholar
Sugimoto, T., Tanaka, K., Monma, M., Kawamura, Y. and Saio, K. (1989) Phosphoenolpyruvate carboxylase level in soybean seed highly correlates to its contents of protein and lipid. Agricultural and Biological Chemistry 53, 885–887.Google Scholar
Sugimoto, T., Kawasaki, T., Kato, T., Whittier, R.F., Shibata, D. and Kawamura, Y. (1992) cDNA sequence and expression of a phosphoenolpyruvate carboxylase gene from soybean. Plant Molecular Biology 20, 743–747.Google Scholar
Sugimoto, T., Sueyoshi, K. and Oji, Y. (1997) Increase of PEPC activity in developing rice seeds with nitrogen application at flowering stage. pp. 811–812 in Ando, T.; Fujita, K.; Mae, T.; Matsumoto, H.; Mori, S.; Sekiya, J. (Eds) Plant nutrition for sustainable food production and environment – proceedings of the XIII international plant nutrition colloquium, 13–19 September, Tokyo, Japan. Netherlands, Springer.Google Scholar
Sullivan, S., Jenkins, G.I. and Nimmo, H.G. (2004) Roots, cycles and leaves. Expression of the phosphoenolpyruvate carboxylase kinase gene family in soybean. Plant Physiology 135, 2078–2087.Google Scholar
Suzuki, I., Crétin, C., Omata, T. and Sugiyama, T. (1994) Transcriptional and posttranscriptional regulation of nitrogen-responding expression of phosphoenolpyruvate carboxylase gene in maize. Plant Physiology 105, 1223–1229.Google Scholar
Svensson, P., Bläsing, O. and Westhoff, P. (1997) Evolution of the enzymatic characteristics of C4 phosphoenolpyruvate carboxylase. A comparison of the orthologous PPCA phosphoenolpyruvate carboxylases of Flaveria trinervia (C4) and Flaveria pringlei (C3). European Journal of Biochemistry 246, 452–460.Google Scholar
Tamaki, M., Ebata, M., Tashiro, T. and Ishikawa, M. (1989) Physicoecological studies on quality formation of rice kernel. I. Effects of nitrogen top-dressed at full heading time and air temperature during ripening period on quality of rice kernel. Japanese Journal of Crop Science 58, 653–658.Google Scholar
Tournaire-Roux, C., Sutka, M., Javot, H., Gout, E., Gerbeau, P., Luu, D.T., Bligny, R. and Maurel, C. (2003) Cytosolic pH regulates root water transport during anoxic stress through gating of aquaporins. Nature 425, 393–397.Google Scholar
Van Quy, L. and Champigny, M.L. (1992) Nitrate enhances the kinase activity for phosphorylation of phosphoenolpyruvate carboxylase and sucrose phosphate synthase proteins in wheat leaves. Plant Physiology 99, 344–347.Google Scholar
Van Quy, L., Foyer, C. and Champigny, M.L. (1991) Effect of light and nitrate on wheat leaf phosphoenolpyruvate carboxylase activity. Evidence for covalent modulation of C3 enzyme. Plant Physiology 97, 1476–1482.Google Scholar
Xia, J.H. and Saglio, P.H. (1992) Lactic acid efflux as a mechanism of hypoxic acclimation of maize root tips to anoxia. Plant Physiology 100, 40–46.Google Scholar
Xie, L., Chen, N., Duan, B., Zhu, Z. and Liao, X. (2008) Impact of proteins on pasting and cooking properties of waxy and non-waxy rice. Journal of Cereal Science 47, 372–379.Google Scholar
Yamagata, H., Sugimoto, T., Tanaka, K. and Kasai, Z. (1982) Biosynthesis of storage proteins in developing rice seeds. Plant Physiology 70, 1094–1100.CrossRefGoogle ScholarPubMed
Yan-Lin, T., Jing-Feng, H., Shao-Hong, C. and Ren-Chao, W. (2007) Nitrogen content of rice panicle and paddy by hyperspectral remote sensing. Pakistan Journal of Biological Sciences 10, 4420–4425.Google Scholar
Zhang, X-Q., Bin, L. and Chollet, R. (1995) In vivo regulatory phosphorylation of soybean nodule phosphoenolpyruvate carboxylase. Plant Physiology 108, 1561–1568.Google Scholar
Zhou, Y., Cai, H., Xiao, J., Li, X., Zhang, Q. and Lian, X. (2009) Over-expression of aspartate aminotransferase genes in rice resulted in altered nitrogen metabolism and increased amino acid content in seeds. Theoretical and Applied Genetics 118, 1381–1390.Google Scholar
Zhu, C., Naqvi, S., Breitenbach, J., Sandmann, G., Christou, P. and Capell, T. (2008) Combinatorial genetic transformation generates a library of metabolic phenotypes for the carotenoid pathway in maize. Proceedings of the National Academy of Sciences, USA 105, 18232–18237.Google Scholar
Supplementary material: File

Yamamoto Supplementary Material

Figures

Download Yamamoto Supplementary Material(File)
File 150 KB
Supplementary material: File

Yamamoto Supplementary Material

Table S1

Download Yamamoto Supplementary Material(File)
File 43 KB
Supplementary material: File

Yamamoto Supplementary Material

Table S2

Download Yamamoto Supplementary Material(File)
File 18.4 KB