Genomic distribution of genes encoding 68 cytoplasmic ribosomal protein families in rice

• Autorzy: Agarwal S M , Jain M. , Grover A.
• Języki publikacji: EN

Abstrakty

EN

Completion of rice genome sequencing has necessitated identification of transcripts encoded by the genome and their corresponding functions. In the present study we have catalogued cytoplasmic ribosomal protein complement of rice genome corresponding to 68 families. Mining TIGR (The Institute for Genomic Research) rice database and unigene sequences available from National Centre for Biotechnology Information (NCBI) produced a non-redundant set of these sequences. This resulted in identification of 209 candidate r-proteins of which 22 have not been reported previously. The number of genes per family ranges from 1 to 8 distributed throughout the genome with maximum occurrence at chromosome 7. Mapping of r-proteins on BAC clones revealed several small clusters of genes. Unigene sequences correspondtng to most of the reported r-proteins were identified indicating these genes are being expressed.

Słowa kluczowe

EN

duplication; multigene family; human nutrition; protein; cereal; ribosomal protein; rice

• Wydawca: -
• Czasopismo: Acta Physiologiae Plantarum
• Rocznik: 2005
• Tom: 27
• Numer: 4A
• Opis fizyczny: p.439-446,ref.

Twórcy

autor

Agarwal S M

• Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India

autor

Jain M.

autor

Grover A.

Bibliografia

• Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acid. Res., 25: 3389-3402.
• Barakat, A., Szick-Miranda, K., Chang, I., Guyot, R., Blanc, G., Cooke, R., Delseny, M., and Bailey- -Serres J. 2001. The Organization of Cytoplasmic Ribosomal Protein Genes in the Arabidopsis Genome. Plant Physiol., 197: 398-415.
• Bairoch, A. and Apweiler, R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucl. Acid. Res., 28: 45-48.
• Cooke, R., Raynal, M., Laudie, M. and Delseny, M. 1997 Identification of members of gene families in Arabidopsis thaliana by contig construction from partial cDNA sequences: 106 genes encoding 50 cytoplasmic ribosomal proteins. Plant J., 11: 1127-1140.
• Dornelas, M.C., Lejeune, B., Dron, M. and M. Kreis 1997The Arabidopsis SHAGGY-related protein kinase (ASK) gene family: structure organization and evolution. Gene, 212: 249-257.
• Devos, K.M. and Gale, M.D. 2000. Genome relationships: The grass model in current research. Plant Cell, 12: 637-646.
• Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G., Huang, Y., Li, Y., Zhu, J., Liu, Y., Hu, X., Jia, P., Zhang, Y., Zhao, Q., Ying, K., Yu, S., Tang, Y., Weng, Q., Zhang, L., Lu, Y., Mu, J., Lu, Y., Zhang, L.S., Yu, Z., Fan, D., Liu, X., Lu, T., Li, C., Wu, Y., Sun, T., Lei, H., Li, T., Hu, H., Guan, J., Wu, M., Zhang, R., Zhou, B., Chen, Z., Chen, L., Jin, Z., Wang, R., Yin, H., Cai, Z., Ren, S., Lv, G., Gu, W., Zhu, G., Tu, Y., Jia, J., Zhang, Y., Chen, J., Kang, H., Chen, X., Shao, C., Sun, Y., Hu, Q., Zhang, X., Zhang, W., Wang, L., Ding, C., Sheng, H., Gu, J., Chen, S., Ni, L., Zhu, F., Chen, W., Lan, L., Lai, Y., Cheng, Z., Gu, M., Jiang, J., Li, J., Hong, G., Xue, Y. and Han, B. 2002. Sequence and analysis of rice chromosome 4. Nature, 420: 316-320.
• Gantt, J.S. and Key, J.L. 1983. Auxin-induced changes in the level of translatable ribosomal protein messenger ribonucleic acids in soybean hypocotyls. Biochemistry, 22: 4131-4139.
• Geneschik, P., Durr, A., and Fleck, J. 1994. Differential expression of several E2-type ubiquitin carrier protein genes at different developmental stages in Arabidopsis thaliana and Nicotiana sylvestris. Mol. Gen. Genet., 244: 548-556.
• Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., Hadley, D., Hutchison, D., Martin, C., Katagiri, F., Lange, B.M., Moughamer, T., Xia, Y., Budworth, P., Zhong, J., Miguel, T., Paszkowski, U., Zhang, S., Colbert, M., Sun, W.L., Chen, L., Cooper, B., Park, S., Wood, T.C., Mao, L., Quail, P., Wing, R., Dean R., Yu, Y., Zharkikh, A., Shen, R., Sahas- rabudhe, S., Thomas, A., Cannings, R., Gutin, A., Pruss, D., Reid, J., Tavtigian, S., Mitchell, J., Eldredge, G., Scholl, T., Miller, R.M., Bhatnagar, S., Adey, N., Rubano, T., Tusneem, N., Rob-nson, R., Feldhaus, J., Macalma, T., Oliphant, A. and Briggs, S. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296: 92-100.
• Hofte, H., Desprez, T., Amselem, J., Chiapello, H., Caboche, M., Moisan, A., Jourjon, M.F., Charpenteau, J.L., Berthomieu, P., Guerrier, D., Giraudat, J., Quigley, F., Thomas, F., Yu, D.Y., Mache, R., Raynal, M., Cooke, R., Grellet, F., Delseny, M., Parmentier, Y., Marcillac, G., Gigot, C., Fleck, J., Philipps, G., Axelos, M., Bardet, C., Tremousaygue, D. and Lescure, B. 1993. An inventory of1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J., 4: 1051-1061.
• Mager, W.H., Planta, R.J., Ballesta, J.G., Lee, J.C., Mizuta, K., Suzuki, K., Warner, J.R. and Woolford, J. 1997. A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Nucl. Acid Res., 25: 4872-4875.
• Ning, W., Runsheng, C. and Yongxiong, W. 2000. Conservation of ribosomal protein gene ordering in 16 complete genomes. Science in China (Series C), 43: 120-128.
• Raue, H.A. and Planta, R.J. 1991. Ribosome biogenesis in yeast. Prog. Nucleic Acid Res. Mol. Biol., 41: 89-129.
• Santos, M., Gousseau, H., Lis-er, C., Foyer, C., Creissen, G. and Mullineaux, P. 1996. Cytosolic ascorbate peroxidase from Arabidopsis thaliana L. is encoded by a small multigene family. Planta., 198: 64-69.
• Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., Nagamura, Y., Antonio, B.A., Kanamori, H., Hosokawa, S., Masukawa, M., Arikawa, K., Chiden, Y., Hayashi, M., Okamoto, M., Ando, T., Aoki, H., Arita, K., Hamada, M., Harada, C., Hijishita, S., Honda, M., Ichikawa, Y., Idonuma, A., Iijima, M., Ikeda, M., ikeno, M., Ito, S., Ito, T., Ito, Y., Ito, Y., Iwabuchi, A., Kamiya, K., Karasawa, W., Katagiri, S., Kikuta, A., Kobayashi, N., Kono, I., Machita, K., Maehara, T., Mizuno, H., Mizubayashi, T., Mukai, Y., Naga- aki, H., Nakashima, M., Nakama, Y., Nakamichi, Y., Nakamura, M., Namiki, N., Negishi, M., Ohta, I., Ono, N., Saji, S., Sakai, K., Shibata, M., Shimokawa, T., Shomura, A., Song, J., Takazaki, Y., Terasawa, K., Tsuji, K., Waki, K., Yamagata, H., Yamane, H., Yoshiki, S., Yoshihara, R., Yukawa, K., Zhong, H., Iwama, H., Endo, T., Ito, H., Hahn, J.H., Kim, H.L, Eun, M.Y., Yano, M., Jiang, J. and Gojobori, T. 2002. The genome sequence and structure of rice chromot ome. Nature, 420: 312-316.
• Snustad, D.P., Haas, N.A., Kopczack, S.D. and Siflow, C.D. 1992. The small genome of Arabidopsis thaliana contains at least nine expressed b-tubulin genes. Plant Cell, 4: 549-556.
• Takahashi, Y., Mitsuma, T., Hirayama, S. and Odani S. 2002. Identification of ribosomal proteins present in the vicinity of globin mRNA in 40S initiation complex. J. Biochem., 132: 705-711.
• Tatusova, T.A. and Madden, T.L. 1999. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett., 174: 247-50.
• Urao, T., Katagiri, T., Mizoguchi, T., Yama- guchi-Shinozaki, K., Hayashida, N. and Shinozaki, K. 1994. Two genes that encode Ca2+ dependent protein kinases are induced by drought and high-salt stresses in Arabidopsis thaliana. Mol. Gen. Genet., 244: 331-340.
• Warner, J.R. and Nierras, C.R. 1998. Trapping Human Ribosomal Protein Genes. Genome Res., 8: 419-421.
• Wheeler, D.L., Church, D.M., Edgar, R., Federhen. S., Helmberg, W., Madden, T.L., Pontius, J.U., Schuler, G.D., Schriml L.M., Sequeira, E., Suzek, T. O., Tatusova, T.A. and Wagner, L. 2004. Database resources of the National Center for Biotechnology Information: update. Nucl. Acid. Res., 32: D35-D40.
• Wittmann, H.G. 1982. Components of bacterial ribosomes. Annu. Rev. Biochem., 51: 155-183.
• Wool, I.G. 1996. Extraribosomal functions of ribosomal proteins. Trends Biochem Sci., 5: 164-165.
• Wool, I.G., Chan, Y.L. and Gluck, A. 1995. Structure and evolution of mammalian ribosomal proteins. Biochem Cell Biol, 73: 933-947.
• Wu, J.W., Matsui, E., Yamamoto, K., Nagamura, Y., Kurata, N., Sasaki, T., and Minobe, Y. 1995. Genoorganization of 57 ribosomal protein genes in rice (Oryza sativa) through RFLP mapping. Genome, 38: 1189-1200.
• Yoshihama, M., Uechi, T., Asakawa, S., Kawasaki, K., Kato, S., Higa, S., Maeda, N., Minoshima, S., Tanaka, T., Shimizu, N. and Kenmochi, N. 2002. The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. Genome Res., 12: 379-390.
• Yu, J., Hu, S., Wang, J., Wong, G.K, Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., Cao, M., Liu, J., Sun, J., Tang, J., Chen, Y., Huang, X., Lin, W., Ye, C., Tong, W., Cong, L., Geng, J., Han, Y., Li, L., Li, W., Hu, G., Huang, X., Li, W., Li, J., Liu, Z., Li, L., Liu, J., Qi, Q., Liu, J., Li, L., Li, T., Wang, X., Lu, H., Wu, T., Zhu, M., Ni, P., Han, H., Dong, W., Ren, X., Feng, X., Cui, P., Li, X., Wang, H., Xu, X., Zhai, W., Xu, Z., Zhang, J., He, S., Zhang, J., Xu, J., Zhang, K., Zheng, X., Dong, J., Zeng, W., Tao, L., Ye, J., Tan, J., Ren, X., Chen, X., He, J., Liu, D., Tian, W., Tian, C., Xia, H., Bao, Q., Li, G., Gao, H., Cao, T., Wang, J., Zhao, W., Li, P., Chen, W., Wang, X., Zhang, Y., Hu, J., Wang, J., Liu, S., Yang, J., Zhang, G., Xiong, Y., Li, Z., Mao, L., Zhou, C., Zhu, Z., Chen, R., Hao, B., Zheng, W., Chen, S., Guo, W., Li, G., Liu, S., Tao, M., Wang, J., Zhu, L., Yuan, L. and Yang, H. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296: 79-92.