Plant Molecular Biology

, Volume 74, Issue 6, pp 617–629 | Cite as

Molecular characterization, expression pattern, and functional analysis of the OsIRL gene family encoding intracellular Ras-group-related LRR proteins in rice

  • Changjun You
  • Xiaoxia Dai
  • Xingwang Li
  • Lei Wang
  • Guoxing Chen
  • Jinghua Xiao
  • Changyin Wu


Leucine-rich repeat proteins constitute a large gene family and play important roles in plant growth and development. Among them, Arabidopsis PIRL is a plant-specific class of intracellular Ras-group-related leucine-rich repeat proteins. In this study, we identified eight homologues of PIRLs in rice and designated them as OsIRL proteins. We described the gene structures, chromosome localizations, protein motifs, and phylogenetic relationships of the OsIRL gene family. The expression profiles of OsIRL genes were analyzed throughout the entire rice life cycle, along with light and three hormone stress conditions, using quantitative RT-PCR and microarray data. All OsIRL genes were expressed in at least one experimental stage and exhibited divergent expression patterns, with several genes showing preferential expression at specific stages. OsIRL4 and OsIRL5 showed higher expression levels under light compared to dark. OsIRL4 and OsIRL7 exhibited significant differential expression in response to hormone treatments. Six T-DNA or Tos17 insertion lines for five individual OsIRL genes were identified and examined morphologically. The comprehensive expression profile elucidated in this investigation together with the characterized insertion lines will provide a solid foundation for in-depth dissection of OsIRL functions.


Oryza sativa OsIRL Segmental duplication Expression profile Insertion mutant 



Leucine-rich repeat


Plant intracellular Ras-group-related LRR


Oryza sativa intracellular Ras-group-related LRR


Reverse transcription polymerase chain reaction


Gibberellic acid


Naphthalene acetic acid





We thank Gynheung An, Hongwei Xue, and Hirohiko Hirochika for providing mutant seeds. This research was supported by grants from the National Science Foundation of China and the National Special Key Project of China on Functional Genomics of Major Plants and Animals.

Supplementary material

11103_2010_9704_MOESM1_ESM.doc (2.1 mb)
Supplementary material 1 (DOC 2150 kb)


  1. Baumberger N, Doesseger B, Guyot R, Diet A, Parsons RL, Clark MA, Simmons MP, Bedinger P, Goff SA, Ringli C, Keller B (2003) Whole-genome comparison of leucine-rich repeat extensins in Arabidopsis and rice. A conserved family of cell wall proteins form a vegetative and a reproductive clade. Plant Physiol 131:1313–1326CrossRefPubMedGoogle Scholar
  2. Bella J, Hindle KL, McEwan PA, Lovell SC (2008) The leucine-rich repeat structure. Cell Mol Life Sci 65:2307–2333CrossRefPubMedGoogle Scholar
  3. Buchanan SG, Gay NJ (1996) Structural and functional diversity in the leucine-rich repeat family of proteins. Prog Biophys Mol Biol 65:1–44CrossRefPubMedGoogle Scholar
  4. Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4:10CrossRefPubMedGoogle Scholar
  5. Claudianos C, Campbell HD (1995) The novel flightless-I gene brings together two gene families, actin-binding proteins related to gelsolin and leucine-rich-repeat proteins involved in Ras signal transduction. Mol Biol Evol 12:405–414PubMedGoogle Scholar
  6. Cutler ML, Bassin RH, Zanoni L, Talbot N (1992) Isolation of rsp-1, a novel cDNA capable of suppressing v-Ras transformation. Mol Cell Biol 12:3750–3756PubMedGoogle Scholar
  7. DeYoung BJ, Innes RW (2006) Plant NBS-LRR proteins in pathogen sensing and host defense. Nat Immunol 7:1243–1249CrossRefPubMedGoogle Scholar
  8. Di Matteo A, Bonivento D, Tsernoglou D, Federici L, Cervone F (2006) Polygalacturonase-inhibiting protein (PGIP) in plant defence: a structural view. Phytochemistry 67:528–533CrossRefPubMedGoogle Scholar
  9. Dievart A, Clark SE (2004) LRR-containing receptors regulating plant development and defence. Development 131:251–261CrossRefPubMedGoogle Scholar
  10. Forsthoefel NR, Cutler K, Port MD, Yamamoto T, Vernon DM (2005) PIRLs: a novel class of plant intracellular leucine-rich repeat proteins. Plant Cell Physiol 46:913–922CrossRefPubMedGoogle Scholar
  11. Gendron JM, Wang ZY (2007) Multiple mechanisms modulate brassinosteroid signaling. Curr Opin Plant Biol 10:436–441CrossRefPubMedGoogle Scholar
  12. Guyon V, Tang WH, Monti MM, Raiola A, Lorenzo GD, McCormick S, Taylor LP (2004) Antisense phenotypes reveal a role for SHY, a pollen-specific leucine-rich repeat protein, in pollen tube growth. Plant J 39:643–654CrossRefPubMedGoogle Scholar
  13. Han MJ, Jung KH, Yi G, Lee DY, An G (2006) Rice Immature Pollen 1 (RIP1) is a regulator of late pollen development. Plant Cell Physiol 47:1457–1472CrossRefPubMedGoogle Scholar
  14. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143:1467–1483CrossRefPubMedGoogle Scholar
  15. Jung KH, Lee J, Dardick C, Seo YS, Cao P et al (2008) Identification and functional analysis of light-responsive unique genes and gene family members in rice. PLoS Genet 4:e1000164CrossRefPubMedGoogle Scholar
  16. Kajava AV (1998) Structural diversity of leucine-rich repeat proteins. J Mol Biol 277:519–527CrossRefPubMedGoogle Scholar
  17. Kajava AV, Vassart G, Wodak SJ (1995) Modeling of the three-dimensional structure of proteins with the typical leucine-rich repeats. Structure 3:867–877CrossRefPubMedGoogle Scholar
  18. Kobe B, Deisenhofer J (1994) The leucine-rich repeat: a versatile binding motif. Trends Biochem Sci 19:415–421CrossRefPubMedGoogle Scholar
  19. Kobe B, Kajava AV (2001) The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol 11:725–732CrossRefPubMedGoogle Scholar
  20. Kong H, Landherr LL, Frohlich MW, Leebens-Mack J, Ma H, dePamphilis CW (2007) Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. Plant J 50:873–885CrossRefPubMedGoogle Scholar
  21. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5:150–163CrossRefPubMedGoogle Scholar
  22. Kurepin LV, Emery RJ, Pharis RP, Reid DM (2007) The interaction of light quality and irradiance with gibberellins, cytokinins and auxin in regulating growth of Helianthus annuus hypocotyls. Plant Cell Environ 30:147–155CrossRefPubMedGoogle Scholar
  23. Kuroda H, Takahashi N, Shimada H, Seki M, Shinozaki K, Matsui M (2002) Classification and expression analysis of Arabidopsis F-box-containing protein genes. Plant Cell Physiol 43:1073–1085CrossRefPubMedGoogle Scholar
  24. Long TA, Brady SM, Benfey PN (2008) Systems approaches to identifying gene regulatory networks in plants. Annu Rev Cell Dev Biol 24:81–103CrossRefPubMedGoogle Scholar
  25. Lynch M, Conery J (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151–1155CrossRefPubMedGoogle Scholar
  26. Muller B, Sheen J (2008) Cytokinin and auxin interaction in root stem-cell specification during early embryogenesis. Nature 453:1094–1097CrossRefPubMedGoogle Scholar
  27. Nibau C, Wu HM, Cheung AY (2006) RAC/ROP GTPases: ‘hubs’ for signal integration and diversification in plants. Trends Plant Sci 11:309–315CrossRefPubMedGoogle Scholar
  28. Padmanabhan M, Cournoyer P, Dinesh-Kumar SP (2009) The leucine-rich repeat domain in plant innate immunity: a wealth of possibilities. Cell Microbiol 11:191–198CrossRefPubMedGoogle Scholar
  29. Rensink WA, Buell CR (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci 10:603–609CrossRefPubMedGoogle Scholar
  30. Seo M, Nambara E, Choi G, Yamaguchi S (2009) Interaction of light and hormone signals in germinating seeds. Plant Mol Biol 69:463–472CrossRefPubMedGoogle Scholar
  31. Sieburth DS, Sun Q, Han M (1998) SUR-8, a conserved Ras-binding protein with leucine-rich repeats, positively regulates Ras-mediated signaling in C. elegans. Cell 94:119–130CrossRefPubMedGoogle Scholar
  32. Stratford S, Barne W, Hohorst DL, Sagert JG, Cotter R, Golubiewski A, Showalter AM, McCormick S, Bedinger P (2001) A leucine-rich repeat region is conserved in pollen extensin-like (Pex) proteins in monocots and dicots. Plant Mol Biol 46:43–56CrossRefPubMedGoogle Scholar
  33. Suzuki N, Choe HR, Nishida Y, Yamawaki-Kataoka Y, Ohnishi S, Tamaoki T, Kataoka T (1990) Leucine-rich repeats and carboxyl terminus are required for interaction of yeast adenylate cyclase with RAS proteins. Proc Natl Acad Sci USA 87:8711–8715CrossRefPubMedGoogle Scholar
  34. 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 25:4876–4882CrossRefPubMedGoogle Scholar
  35. van der Hoorn RA, Wulff BB, Rivas S, Durrant MC, van der Ploeg A, de Wit PJ, Jones JD (2005) Structure-function analysis of cf-9, a receptor-like protein with extracytoplasmic leucine-rich repeats. Plant Cell 17:1000–1015CrossRefPubMedGoogle Scholar
  36. Wang X, Shi X, Hao B, Ge S, Luo J (2005) Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 165:937–946CrossRefPubMedGoogle Scholar
  37. Wang L, Xie W, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, Xu C, Xiao J, Zhang Q (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J 61:752–766CrossRefPubMedGoogle Scholar
  38. Wu C, Li X, Yuan W, Chen G, Kilian A, Li J, Xu C, Zhou DX, Wang S, Zhang Q (2003) Development of enhancer trap lines for functional analysis of the rice genome. Plant J 35:418–427CrossRefPubMedGoogle Scholar
  39. Xiang Y, Huang Y, Xiong L (2007) Characterization of stress-responsive CIPK genes in rice for stress tolerance improvement. Plant Physiol 144:1416–1428CrossRefPubMedGoogle Scholar
  40. Xu Y, McCouch SR, Zhang Q (2005) How can we use genomics to improve cereals with rice as a reference genome? Plant Mol Biol 59:7–26CrossRefPubMedGoogle Scholar
  41. 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:e38CrossRefPubMedGoogle Scholar
  42. Zhang J, Guo D, Chang Y, You C, Li X et al (2007) Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library. Plant J 49:947–959CrossRefPubMedGoogle Scholar
  43. Zheng ZL, Yang Z (2000) The Rop GTPase: an emerging signaling switch in plants. Plant Mol Biol 44:1–9CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Changjun You
    • 1
  • Xiaoxia Dai
    • 1
  • Xingwang Li
    • 1
  • Lei Wang
    • 1
  • Guoxing Chen
    • 1
  • Jinghua Xiao
    • 1
  • Changyin Wu
    • 1
  1. 1.National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina

Personalised recommendations