Plant Molecular Biology

, Volume 67, Issue 6, pp 603–614 | Cite as

Genome-wide survey of the RIP domain family in Oryza sativa and their expression profiles under various abiotic and biotic stresses

  • Shu-Ye Jiang
  • Rengasamy Ramamoorthy
  • Ritu Bhalla
  • Hong-Fen Luan
  • Prasanna Nori Venkatesh
  • Minne Cai
  • Srinivasan Ramachandran


Ribosome-inactivating proteins (RIPs) are N-glycosidases that inhibit protein synthesis by depurinating rRNA. Despite their identification more than 25 years ago, little is known about their biological functions. Here, we report a genome-wide identification of the RIP family in rice based on the complete genome sequence analysis. Our data show that rice genome encodes at least 31 members of this family and they all belong to type 1 RIP genes. This family might have evolved in parallel to species evolution and genome-wide duplications represent the major mechanism for this family expansion. Subsequently, we analyzed their expression under biotic (bacteria and fungus infection), abiotic (cold, drought and salinity) and the phytohormone ABA treatment. These data showed that some members of this family were expressed in various tissues with differentiated expression abundances whereas several members showed no expression under normal growth conditions or various environmental stresses. On the other hand, the expression of many RIP members was regulated by various abiotic and biotic stresses. All these data suggested that specific members of the RIP family in rice might play important roles in biotic and abiotic stress-related biological processes and function as a regulator of various environmental cues and hormone signaling. They may be potentially useful in improving plant tolerance to various abiotic and biotic stresses by over-expressing or suppressing these genes.


Biotic stress Abiotic stress Ectopic expression Ribosome-inactivating protein Rice 





Megnaporthe grisea


Ribosome-inactivating proteins


Xanthomonas oryzae pv oryzae



We would like to thank Dr. Parameswaran Sriram for his help in real-time PCR analysis.

Supplementary material

11103_2008_9342_MOESM1_ESM.xls (21 kb)
(XLS 21 kb)
11103_2008_9342_MOESM2_ESM.xls (34 kb)
(XLS 34 kb)


  1. Barbieri L, Valbonesi P, Bondioli M, Alvarez ML, Dal Monte P, Landini MP, Stirpe F (2001) Adenine glycosylase activity in mammalian tissues: an equivalent of ribosome-inactivating proteins. FEBS Lett 505:196–197PubMedCrossRefGoogle Scholar
  2. Barbieri L, Polito L, Bolognesi A, Ciani M, Pelosi E, Farini V, Jha AK, Sharma N, Vivanco JM, Chambery A et al (2006) Ribosome-inactivating proteins in edible plants and purification and characterization of a new ribosome-inactivating protein from Cucurbita moschata. Biochim Biophys Acta (BBA) 1760:783–792Google Scholar
  3. Barnabas B, Jager K, Feher A (2008) The effect of drought and heat stress on reproductive processes in cereals. Plant Cell Environ 31:11–38PubMedGoogle Scholar
  4. Bass HW, Krawetz JE, OBrian GR, Zinselmeier C, Habben JE, Boston RS (2004) Maize ribosome-inactivating proteins (RIPs) with distinct expression patterns have similar requirements for proenzyme activation. J Exp Bot 55:2219–2233PubMedCrossRefGoogle Scholar
  5. Bieri S, Potrykus I, Fütterer J (2000) Expression of active barley seed ribosome-inactivating protein in transgenic wheat. Theor Appl Genet 100:755–763CrossRefGoogle Scholar
  6. Chaudhry B, Muller-Uri F, Cameron-Mills V, Gough S, Simpson D, Skriver K, Mundy J (1994) The barley 60 KDa jasmonate-induced protein (JIP60) is a novel ribosome-inactivating protein. Plant J 6:815–824PubMedCrossRefGoogle Scholar
  7. Desmyter S, Vandenbussche F, Hao Q, Proost P, Peumans WJ, Van Damme EJ (2003) Type-1 ribosome-inactivating protein from iris bulbs: a useful agronomic tool to engineer virus resistance? Plant Mol Biol 51:567–576PubMedCrossRefGoogle Scholar
  8. Ding ZJ, Wu XH, Wang T (2002) The rice tapetum-specific gene RA39 encodes a type I ribosome-inactivating protein. Sex Plant Reprod 15:205–212CrossRefGoogle Scholar
  9. Dowd PF, Mehta AD, Boston RS (1998) Relative toxicity of the maize endosperm ribosome-inactivating protein to insects. J Agric Food Chem 46:3775–3779CrossRefGoogle Scholar
  10. Ferreras JM, Barbieri L, Girbés T, Battelli MG, Rojo MA, Arias FJ, Rocher MA, Soriano F, Mendéz E, Stirpe F (1993) Distribution and properties of major ribosome-inactivating proteins (28 S rRNA N-glycosidases) of the plant Saponaria officinalis, L. (Caryophyllaceae). Biochim Biophys Acta 1216:31–42PubMedGoogle Scholar
  11. Gatehouse A, Barbieri L, Stirpe F, Croy RRD (1990) Effects of ribosome inactivating proteins on insect development—differences between Lepidoptera and Coleoptera. Entomol Exp Appl 54:43–51CrossRefGoogle Scholar
  12. Girbes T, de Torre C, Iglesias R, Ferreras JM, Mendez E (1996) RIP for viruses. Nature 379:777–778CrossRefGoogle Scholar
  13. Girbes T, Ferreras JM, Arias FJ, Stirpe F (2004) Description, distribution, activity and phylogenetic relationship of ribosome-inactivating proteins in plants, fungi and bacteria. Mini Rev Med Chem 4:467–482Google Scholar
  14. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. Japonica). Science 296:92–100PubMedCrossRefGoogle Scholar
  15. Gorschen E, Dunaeva M, Hause B, Reeh I, Wasternack C, Parthier B (1997) Expression of the ribosome-inactivating protein JIP60 from barely in transgenic tobacco leads to an abnormal phenotype and alterations on the level of translation. Planta 202:470–478PubMedCrossRefGoogle Scholar
  16. Hu H, Dai M, Yao J, Xiao B, Li X, Zhang Q, Xiong L (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci USA 103:12987–12992PubMedCrossRefGoogle Scholar
  17. Huang H, Chan H, Wang YY, Ouyang DY, Zheng YT, Tam SC (2006) Trichosanthin suppresses the elevation of p38 MAPK, and Bcl-2 induced by HSV-1 infection in Vero cells. Life Sci 79:1287–1292PubMedCrossRefGoogle Scholar
  18. Iglesias R, Perez Y, de Torre C, Ferreras JM, Antolin P, Jimenez P, Rojo MA, Mendez E, Girbes T (2005) Molecular characterization and systemic induction of single-chain ribosome-inactivating proteins (RIPs) in sugar beet (Beta vulgaris) leaves. J Exp Bot 56:1675–1684PubMedCrossRefGoogle Scholar
  19. Ishizaki T, Megumi C, Komai F, Masuda K, Oosawa K (2002) Accumulation of a 31-kDa glycoprotein in association with the expression of embryogenic potential by spinach callus in culture. Physiol Plant 114:109–115PubMedCrossRefGoogle Scholar
  20. Jach G, Gornhardt B, Mundy J, Logemann J, Pinsdorf E, Leah R, Schell J, Maas C (1995) Enhanced quantitative resistance against fungal disease by combinatorial expression of different barley antifungal proteins in transgenic tobacco. Plant J 8:97–109PubMedCrossRefGoogle Scholar
  21. Jefferson RA (1987) Assaying chimeric genes in plants, the GUS gene fusion system. Plant Mol Biol Rep 5:387–405CrossRefGoogle Scholar
  22. Jiang SY, Ramachandran S (2006) Comparative and evolutionary analysis of genes encoding small GTPases and their activating proteins in eukaryotic genomes. Physiol Genomics 24:235–251PubMedGoogle Scholar
  23. Jiang SY, Bachmann D, La H, Ma Z, Venkatesh PN, Ramamoorthy R, Ramachandran S (2007) Ds insertion mutagenesis as an efficient tool to produce diverse variations for rice breeding. Plant Mol Biol 65:385–402PubMedCrossRefGoogle Scholar
  24. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H et al (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from Japonica rice. Science 301:376–379PubMedCrossRefGoogle Scholar
  25. Kim JK, Duan X, Wu R, Seok SJ, Boston RS, Jang IC, Eun MY, Nahm BH (1999) Molecular and genetic analysis of transgenic rice plants expressing the ribosome inactivating protein b-32 gene and the herbicide resistance bar gene. Mol Breed 5:85–94CrossRefGoogle Scholar
  26. Kumar MA, Timm DE, Neet KE, Owen WG, Peumans WJ, Rao AG (1993) Characterization of the lectin from the bulbs of Eranthis hyemalis (winter aconite) as an inhibitor of protein synthesis. J Biol Chem 268:25176–25183PubMedGoogle Scholar
  27. Lafitte HR, Ismail A, Bennett J (2004) Abiotic stress tolerance in rice for Asia: progress and the future. Proceedings of the 4th international crop science congress, Brisbane, AustraliaGoogle Scholar
  28. Lanceras JC, Pantuwan G, Jongdee B, Toojinda T (2004) Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiol 135:384–399PubMedCrossRefGoogle Scholar
  29. Lauchli A, Grattan SR (2007) Plant growth and development under salinity stress. In: Jenks MA, Hasegawa P, Jain SM (eds) Advances in molecular breeding toward drought and salt tolerant crops. Springer, Netherlands, pp 1–32CrossRefGoogle Scholar
  30. Li XD, Liu WY, Niu CI (1996) Purification of a new ribosome-inactivating protein from the seeds of Cinnamumum porrectum and characterization of the RNA N-glycosidase activity of the toxic protein. Biol Chem 377:825–831PubMedGoogle Scholar
  31. Li XD, Chen WF, Liu WY, Wang GH (1997) Large-scale preparation of two new ribosome-inactivating proteins––cinnamomin and camphorin from the seeds of Cinnamomum camphora. Protein Expr Purif 10:27–31PubMedCrossRefGoogle Scholar
  32. Lin JY, Liu K, Chen CC, Tung TC (1971) Effect of crystalline ricin on the biosynthesis of protein, RNA, and DNA in experimental tumor cells. Cancer Res 31:921–924PubMedGoogle Scholar
  33. Lodge JK, Kaniewski WK, Tumer NE (1993) Broad-spectrum virus resistance in transgenic plants expressing pokeweed antiviral protein. Proc Natl Acad Sci USA 90:7089–7093PubMedCrossRefGoogle Scholar
  34. Logemann J, Jach G, Tommerup H, Mundy J, Schell J (1992) Expression of a barley ribosome-inactivating protein leads to increased fungal protection in transgenic tobacco plants. Nat Biotechnol 10:305–308CrossRefGoogle Scholar
  35. Lutts S, Kinet JM, Bouharnont J (1995) Changes in plant response to NaCl during development of rice (Oryza sativa L.) varieties differing in salinity resistance. J Exp Bot 46:1843–1852CrossRefGoogle Scholar
  36. Maddaloni M, Forlani F, Balmas V, Donini G, Stasse L, Corazza L, Motto M (1997) Tolerance to the fungal pathogen Rhizoctonia solani AG4 of transgenic tobacco expressing the maize ribosome-inactivating protein b-32. Transgenic Res 6:393–402CrossRefGoogle Scholar
  37. Mendez E, Girbes T (2005) Molecular characterization and systemic induction of single-chain ribosome-inactivating proteins (RIPs) in sugar beet (Beta vulgaris) leaves. J Exp Bot 56:1675–1684PubMedCrossRefGoogle Scholar
  38. Montanaro L, Sperti S, Stirpe F (1973) Inhibition by ricin of protein synthesis in vitro. Ribosomes as the target of the toxin. Biochem J 136:677–683PubMedGoogle Scholar
  39. Motto M, Lupotto E (2004) The genetics and properties of cereal ribosome-inactivating proteins. Mini Rev Med Chem 4:493–503PubMedGoogle Scholar
  40. Muller M, Dues G, Balconi C, Salamini F, Thompson RD (1997) Nitrogen and hormonal responsiveness of the 22 KDa alpha-zein and b-32 genes in maize endosperm is displayed in the absence of the transcriptional regulator Opaque-2. Plant J 12:281–291PubMedCrossRefGoogle Scholar
  41. Nielsen K, Boston RS (2001) Ribosome-inactivating proteins: a plant perspective. Annu Rev Plant Physiol Plant Mol Biol 52:785–816PubMedCrossRefGoogle Scholar
  42. Obrig TG, Irvin JD, Hardesty B (1973) The effect of an antiviral peptide on the ribosomal reactions of the peptide elongation enzymes, EF-I and EF-II. Arch Biochem Biophys 155:278–289PubMedCrossRefGoogle Scholar
  43. Park SW, Vepachedu R, Sharma N, Vivanco JM (2004) Ribosome-inactivating proteins in plant biology. Planta 219:1093–1096PubMedCrossRefGoogle Scholar
  44. Peumans WJ, Hao Q, Van Damme EJM (2001) Ribosome-inactivating proteins from plants: more than RNA N-glycosidases? FASEB J 15:1493–1506PubMedCrossRefGoogle Scholar
  45. Reddy PR, Goss JA (1971) Effect of salinity on pollen I. Pollen viability as altered by increasing osmotic pressure with NaCl, MgCl2, and CaCl2. Am J Bot 58:721–725CrossRefGoogle Scholar
  46. Reinbothe S, Reinbothe C, Lehmann J, Becker W, Apel K, Parthier B (1994) JIP60, a methyl jasmonate-induced ribosome-inactivating protein involved in plant stress reactions. Proc Natl Acad Sci USA 91:7012–7016PubMedCrossRefGoogle Scholar
  47. Rippmann JF, Michalowski CB, Nelson DE, Bohnert HJ (1997) Induction of a ribosome-inactivating protein upon environmental stress. Plant Mol Biol 35:701–709PubMedCrossRefGoogle Scholar
  48. Saini HS (1997) Effects of water stress on male gametophyte development in plants. Sex Plant Reprod 10:67–73CrossRefGoogle Scholar
  49. Schaefer SC, Gasic K, Cammue B, Broekaert W, van Damme EJ, Peumans WJ, Korban SS (2005) Enhanced resistance to early blight in transgenic tomato lines expressing heterologous plant defense genes. Planta 222:858–866PubMedCrossRefGoogle Scholar
  50. Sharma N, Park SW, Vepachedu R, Barbieri L, Ciani M, Stirpe F, Savary BJ, Vivanco JM (2004) Isolation and characterization of an RIP (ribosome-inactivating protein)-like protein from tobacco with dual enzymatic activity. Plant Physiol 134:171–181PubMedCrossRefGoogle Scholar
  51. Shinozaki K, Yamaguchi-Schinozaki K, Seki M (2003) Regulatory network of gene expression in the drought and cold stress responses. Curr Opin Plant Biol 6:410–417PubMedCrossRefGoogle Scholar
  52. Song SK, Choi Y, Moon YH, Kim SG, Choi YD, Lee JS (2000) Systemic induction of a Phytolacca insularis antiviral protein gene by mechanical wounding, jasmonic acid, and abscisic acid. Plant Mol Biol 43:439–450PubMedCrossRefGoogle Scholar
  53. Stirpe F, Battelli MG (2006) Ribosome-inactivating proteins: progress and problems. Cell Mol Life Sci 63:1850–1866PubMedCrossRefGoogle Scholar
  54. Stirpe F, Barbieri L, Gorini P, Valbonesi P, Bolognesi A, Polito L (1996) Activities associated with the presence of ribosome-inactivating proteins increase in senescent and stressed leaves. FEBS Lett 382:309–312PubMedCrossRefGoogle Scholar
  55. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882PubMedCrossRefGoogle Scholar
  56. Vepachedu R, Bais HP, Vivanco JM (2003) Molecular characterization and post-transcriptional regulation of ME1, a type-I ribosome-inactivating protein from Mirabilis expansa. Planta 217:498–506PubMedCrossRefGoogle Scholar
  57. Vivanco JM, Savary BJ, Flores HE (1999) Characterization of two novel type I ribosome-inactivating proteins from the storage roots of the Andean crop Mirabilis expansa. Plant Physiol 119:1447–1456PubMedCrossRefGoogle Scholar
  58. Walsh TA, Morgan AE, Hey TD (1991) Characterization and molecular cloning of a proenzyme form of a ribosome-inactivating protein from maize: novel mechanism of proenzyme activation by proteolytic removal of a 2.8-kilodalton internal peptide segment. J Biol Chem 266:23422–23427PubMedGoogle Scholar
  59. Wei Q, Huang MX, Xu Y, Zhang XS, Chen F (2005) Expression of a ribosome inactivating protein (curcin 2) in Jatropha curcas is induced by stress. J Biosci 30:351–357CrossRefGoogle Scholar
  60. Wong RNS, Mak NK, Choi WT, Law PTW (1995) Increased accumulation of trichosanthin in Trichosanthes kirilowii induced by microorganisms. J Exp Bot 46:355–358CrossRefGoogle Scholar
  61. Xu J, Wang H, Fan J (2007) Expression of a ribosome-inactivating protein gene in bitter melon is induced by Sphaerotheca fuliginea and abiotic stimuli. Biotechnol Lett 29:1605–1610PubMedCrossRefGoogle Scholar
  62. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. Indica). Science 296:79–92PubMedCrossRefGoogle Scholar
  63. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3(e38):0266–0281Google Scholar
  64. Yuan H, Ming X, Wang L, Hu P, An C, Chen Z (2002) Expression of a gene encoding trichosanthin in transgenic rice plants enhances resistance to fungus blast disease. Plant Cell Rep 20:992–998CrossRefGoogle Scholar
  65. Zhou X, Li XD, Yuan JZ, Tang ZH, Liu WY (2000) Toxicity of cinnamomin—a new type II ribosome-inactivating protein to bollworm and mosquito. Insect Biochem Mol Biol 30:259–264PubMedCrossRefGoogle Scholar
  66. Zoubenko O, Uckun F, Hur Y, Chet I, Tumer N (1997) Plant resistance to fungal infection induced by nontoxic pokeweed antiviral protein mutants. Nat Biotechnol 15:992–996PubMedCrossRefGoogle Scholar
  67. Zoubenko O, Hudak K, Tumer NE (2000) A non-toxic pokeweed antiviral protein mutant inhibits pathogen infection via a novel salicylic acid-independent pathway. Plant Mol Biol 44:219–229PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Shu-Ye Jiang
    • 1
  • Rengasamy Ramamoorthy
    • 1
  • Ritu Bhalla
    • 1
  • Hong-Fen Luan
    • 1
  • Prasanna Nori Venkatesh
    • 1
  • Minne Cai
    • 1
  • Srinivasan Ramachandran
    • 1
  1. 1.Rice Functional Genomics Group, Temasek Life Sciences Laboratory, 1 Research LinkThe National University of SingaporeSingaporeSingapore

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