Advertisement

Planta

, Volume 241, Issue 5, pp 1119–1129 | Cite as

Rice RING E3 ligase may negatively regulate gamma-ray response to mediate the degradation of photosynthesis-related proteins

  • Yong Chan Park
  • Jung Ju Kim
  • Dong Sub Kim
  • Cheol Seong Jang
Original Article
First Online:
Received:
Accepted:

Abstract

Main conclusion

In this study, our findings regarding the regulation of GA irradiation-induced OsGIRP1 in relation to the levels of photosynthesis-related proteins such as OsrbcL1 and OsrbcS1 and hypersensitive responses of overexpressing plants to GR irradiation provide insight into the molecular functions of OsGIRP1 as a negative regulator in response to the stress of radiation.

Abstract

The RING (Really Interesting New Gene) finger proteins are known to play crucial roles in various abiotic stresses in plants. Here, we report on RING finger E3 ligase, Oryza sativa gamma rays-induced RING finger protein1 gene (OsGIRP1), which is highly induced by gamma rays (GR) irradiation. In vitro ubiquitination assay demonstrated that a single amino acid substitution (OsGIRP1C196A) of the RING domain showed no E3 ligase activity, supporting the notion that the activity of most E3s is specified by a RING domain. We isolated at least 6 substrate proteins of OsGIRP1, including 2 Rubisco subunits, OsrbcL1 and OsrbcSl, via yeast two-hybridization and bimolecular fluorescence complementation assays. OsGIRP1 and its partner proteins were targeted to the cytosol and the cytosol or chloroplasts, respectively; however, florescence signals of the complexes with OsGIPR1 were observed in the cytosol. Protein degradation in cell extracts showed that OsGIRP1 mediates proteolysis of 2 substrates, OsrbcS1 and OsrbcL1, via the 26S proteasome degradation pathway. The Arabidopsis plants overexpressing OsGIRP1 clearly exhibited increased sensitivity to GR irradiation. These results might suggest that OsGIRP1 acts as a negative regulator of GR response to mediate the degradation of photosynthesis-related proteins.

Keywords

26S proteasome Gamma rays RING E3 ligase Rubisco subunits Ubiquitination 

Abbreviations

RING

Really interesting new gene

GR

Gamma rays

BiFC

Bimolecular fluorescence complementation

Rubisco

Ribulose biphosphate carboxylase/oxygenase

DDO/X/A

Synthetic defined medium lacking Leu and Trp supplemented with 40 μg ml−1 X-α-Gal and 70 ng ml−1 aureobasidin A (AbA)

QDO/X/A

Synthetic defined medium lacking Ade, His, Leu, and Trp with 40 μg ml−1 X-α-Gal and 70 ng ml−1 AbA

This is a preview of subscription content, log in to check access.

Notes

Acknowledgments

This work was supported by the National Research Foundation of Korea Funded by the Ministry of Education, Science, and Technology (NRF-2013R1A1A4A01011064) and by grants from the Nuclear R&D Program of the Ministry of Science, ICT, and Future Planting (MSIP), Republic of Korea.

Supplementary material

425_2015_2242_MOESM1_ESM.pdf (269 kb)
Supplementary material 1 (PDF 269 kb) Fig. S1 Subcellular localization and BiFC assay of 4 OsGIRP1-interacting proteins. Four full-length genes were cloned into 35S:EYFP vector (for subcellular localization) and SPYNE(R) vector (for BiFC assay), respectively. Each construct vector was transfected into rice protoplasts. OsPPT1 (a), OsDNLZ1 (b), OsMSR1 (c), and Os4NPP1 (d) were separately transfected for subcellular localization, and transfected with OsGIRP1-SPYCE(M) for BiFC assay into rice protoplastsFig. S2 Semi-quantitative RT-PCR of OsGIRP1-overexpressing Arabidopsis and control plants. Two-week-old seedlings of each of T3 transgenic plants were used for RT-PCR. AtUBC was used for the internal controlFig. S3 The transcript levels of OsrbcS1 (a) and OsrbcL1 (b) genes in irradiated rice. Irradiated rice samples were used for quantitative RT-PCR. The cDNA was mixed with a with TOPreal™ qPCR2XPreMix with SYBR green (Enzynomics, South Korea) and 10 pmol of each of the primers. PCR was performed using the CFX96 real-Time PCR Detection System (BioRad). The transcript level was standardized on the basis of cDNA amplification with Actinll as an internal control
425_2015_2242_MOESM2_ESM.pdf (115 kb)
Supplementary material 2 (PDF 114 kb) Table S1 Primer list for cloning and semi-quantitative RT-PCR used in this study

References

  1. Al-Salhi M, Ghannam MM, Al-Ayed MS, El-Kameesy SU, Roshdy S (2004) Effect of gamma-irradiation on the biophysical and morphological properties of corn. Nahrung 48:95–98CrossRefPubMedGoogle Scholar
  2. Bauer J, Chen K, Hiltbunner A, Wehrli E, Eugster M, Schnell D, Kessler F (2000) The major protein import receptor of plastids is essential for chloroplast biogenesis. Nature 403:203–207CrossRefPubMedGoogle Scholar
  3. Clough SJ (2004) Floral dip: Agrobacterium-mediated germ line transformation. Methods Mol Biol 286:91–101Google Scholar
  4. Deshaies RJ, Joazeiro CA (2009) RING domain E3 ubiquitin ligases. Annu Rev Biochem 78:399–434CrossRefPubMedGoogle Scholar
  5. Dong CH, Agarwal M, Zhang Y, Xie Q, Zhu JK (2006) The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proc Natl Acad Sci USA 103:8281–8286CrossRefPubMedCentralPubMedGoogle Scholar
  6. Freemont PS, Hanson IM, Trowsdale J (1991) A novel cysteine-rich sequence motif. Cell 64:483–484CrossRefPubMedGoogle Scholar
  7. Gailey FB, Tolbert NE (1958) Effect of ionizing radiation on the development of photosynthesis in etiolated wheat leaves. Arch Biochem Biophys 76:188–195CrossRefPubMedGoogle Scholar
  8. Gao T, Wu Y, Zhang Y, Liu L, Ning Y, Wang D, Tong H, Chen S, Chu C, Xie Q (2011) OsSDIR1 overexpression greatly improves drought tolerance in transgenic rice. Plant Mol Biol 76:145–156CrossRefPubMedGoogle Scholar
  9. Heller H, Hershko A (1990) A ubiquitin-protein ligase specific for type III protein substrates. J Biol Chem 265:6532–6535PubMedGoogle Scholar
  10. Hurley JH, Lee S, Prag G (2006) Ubiquitin-binding domains. Biochem J 399:361–372CrossRefPubMedCentralPubMedGoogle Scholar
  11. Hwang JE, Hwang S-G, Kim SH, Lee KJ, Jang CS, Kim JB, Kim SH, Ha BK, Ahn J-W, Kang S-Y, Kim DS (2014) Transcriptome profiling in response to different types of ionizing radiation and identification of multiple radio marker genes in rice. Physiol Plant 150:604–619CrossRefPubMedGoogle Scholar
  12. Jacobson AD, Zhang NY, Xu P, Han KJ, Noone S, Peng J, Liu CW (2009) The lysine 48 and lysine 63 ubiquitin conjugates are processed differently by the 26s proteasome. J Biol Chem 284:35485–35494CrossRefPubMedCentralPubMedGoogle Scholar
  13. Jung CG, Lim SD, Hwang S-G, Jang CS (2012) Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene 505:9–18CrossRefPubMedGoogle Scholar
  14. Kim JH, Chung BY, Kim JS, Wi SG (2005) Effects of in planta gamma-irradiation on growth, photosynthesis, and antioxidative capacity of red pepper (Capsicum annuum L.) plants. J Plant Biol 48:47–56CrossRefGoogle Scholar
  15. Kim DS, Kim JB, Goh EJ, Kim W-J, Kim SH, Seo YW, Jang CS, Kang S-Y (2011) Antioxidant response of Arabidopsis plants gamma irradiation: genome-wide expression profiling of the ROS scavenging and signal transduction pathways. J Plant Physiol 168:1960–1971CrossRefPubMedGoogle Scholar
  16. Kim SH, Song M, Lee KJ, Hwang SG, Jang CS, Kim JB, Ha BK, Kang SY, Kim DS (2012) Genome-wide transcriptome profiling of ROS scavenging and signal transduction pathways in rice (Oryza sativa L.) in response to different types of ionizing radiation. Mol Biol Rep 39:11231–11248CrossRefPubMedGoogle Scholar
  17. Kim SH, Hwang SG, Hwang JE, Jang CS, Velusamy V, Kim JB, Kim SH, Ha B-K, Kang S-Y, Kim DS (2013) The identification of candidate radio marker genes using a coexpression network analysis in gamma-irradiated rice. Physiol Plant 149:554–570CrossRefGoogle Scholar
  18. Kovacs E, Keresztes A (2002) Effect of gamma and UV-B/C radiation on plant cells. Micron 33:199–210CrossRefPubMedGoogle Scholar
  19. Kuzin AM, Uzorin EK, Chirkovskii VI (1963) Examination of remote post-irradiation effects in some plant species of the Nicotiana family following gamma irradiation of the seed. Radiobiologiia 3:903–908PubMedGoogle Scholar
  20. Lee H, Xiong L, Gong Z, Ishitani M, Stevenson B, Zhu JK (2001) The Arabidopsis HOS1 gene negatively regulates cold signal transduction and encodes a RING finger protein that displays cold-regulated nucleo-cytoplasmic partitioning. Genes Dev 15:912–924CrossRefPubMedCentralPubMedGoogle Scholar
  21. Lim SD, Yim WC, Moon JC, Kim DS, Lee BM, Jang CS (2010) A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol Biol 72:369–380CrossRefPubMedGoogle Scholar
  22. Lim SD, Cho HY, Park YC, Ham DJ, Lee JK, Jang CS (2013a) The rice RING finger E3 ligase, OsHCI1, drives nuclear export of multiple substrate proteins and its heterogeneous overexpression enhances acquired thermotolerance. J Exp Bot 64:2899–2914CrossRefPubMedCentralPubMedGoogle Scholar
  23. Lim SD, Hwang JG, Jung CG, Hwang SG, Moon JC, Jang CS (2013b) Comprehensive analysis of the rice RING E3 ligase family reveals their functional diversity in response to abiotic stress. DNA Res 20:299–314CrossRefPubMedCentralPubMedGoogle Scholar
  24. Lim SD, Hwang JG, Han AR, Park YC, Lee C, Ok YS, Jang CS (2014a) Positive regulation of rice RING E3 ligase OsHIR1 in arsenic and cadmium uptakes. Plant Mol Biol 85:365–379CrossRefPubMedGoogle Scholar
  25. Lim SD, Lee C, Jang CS (2014b) The rice RING E3 ligase, OsCTR1, inhibits trafficking to the chloroplasts of OsCP12 and OsRP1, and its overexpression confers drought tolerance in Arabidopsis. Plant Cell Environ 37:1097–1113CrossRefPubMedGoogle Scholar
  26. Lin H, Wang H, Ding H, Chen YL, Li QZ (2009) Prediction of subcellular localization of apoptosis protein using Chou’s pseudo amino acid composition. Acta Biotheor 57:321–330CrossRefPubMedGoogle Scholar
  27. Mehta RA, Fawcett TW, Porath D, Mattoo AK (1992) Oxidative stress causes rapid membrane translocation and in vivo degradation of rubulose-1-5-bisphosphate carboxylase/oxygenase. J Biol Chem 267:2810–2816PubMedGoogle Scholar
  28. Minoda A, Weber APM, Tanaka L, Miyagishima SY (2010) Nucleus-independent control of the Rubisco operon by the plastid-encoded transcription factor Ycf30 in the red alga Cyanidioschyzon merolae. Plant Physiol 154:1532–1540CrossRefPubMedCentralPubMedGoogle Scholar
  29. Mukhopadhyay D, Riezman H (2007) Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science 315:201–205CrossRefPubMedGoogle Scholar
  30. Penate L, Martin O, Cardenas R, Agusti S (2010) Short-term effects of gamma ray bursts on oceanic photosynthesis. Astrophys Space Sci 330:211–217CrossRefGoogle Scholar
  31. Shyu YJ, Hiatt SM, Duren HM, Ellis RE, Kerppola TK, Hu CD (2008) Visualization of protein interactions in living Caenorhabditis elegans using bimolecular fluorescence complementation analysis. Nat Protoc 3:588–596CrossRefPubMedGoogle Scholar
  32. Smalle J, Vierstra RD (2004) The ubiquitin 26S proteasome proteolytic pathway. Annu Rev Plant Biol 55:555–590CrossRefPubMedGoogle Scholar
  33. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630CrossRefPubMedGoogle Scholar
  34. Stone SL, Hauksdottir H, Troy A, Herschleb J, Kraft E, Callis J (2005) Functional analysis of the RING-type ubiquitin ligase family of Arabidopsis. Plant Physiol 137:13–30CrossRefPubMedCentralPubMedGoogle Scholar
  35. Vierstra RD (2009) The ubiquitin-26S proteasome system at the nexus of plant biology. Nat Rev Mol Cell Biol 10:385–397CrossRefPubMedGoogle Scholar
  36. von Arnim AG, Deng XW (1994) Light inactivation of Arabidopsis photomorphogenic repressor COP1 involves a cell-specific regulation of its nucleocytoplasmic partitioning. Cell 79:1035–1045CrossRefGoogle Scholar
  37. Wakasugi T, Tsudzuki T, Sugiura M (2001) The genomics of land plant chloroplasts: gene content and alteration of genomic information by RNA editing. Photosynth Res 70:107–118CrossRefPubMedGoogle Scholar
  38. Wi SG, Chung BY, Kim JH, Baek MH, Yang DH, Lee JW, Kim JS (2005) Ultrastructural changes of cell organelles in Arabidopsis stems after gamma irradiation. J Plant Biol 48:195–200CrossRefGoogle Scholar
  39. Wi SG, Chung BY, Kim JS, Kim JH, Baek MH, Lee JW, Kim YS (2007) Effects of gamma irradiation on morphological changes and biological responses in plants. Micron 38:553–564CrossRefPubMedGoogle Scholar
  40. Zhang YY, Yang CW, Li Y, Zheng NY, Chen H, Zhao QZ, Gao T, Guo HS, Xie Q (2007) SDIR1 is a RING finger E3 ligase that positively regulates stress-responsive abscisic acid signaling in Arabidopsis. Plant Cell 19:1912–1929CrossRefPubMedCentralPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Yong Chan Park
    • 1
  • Jung Ju Kim
    • 1
  • Dong Sub Kim
    • 2
  • Cheol Seong Jang
    • 1
  1. 1.Plant Genomics Lab, Department of Applied Plant SciencesKangwon National UniversityChuncheonRepublic of Korea
  2. 2.Advanced Radiation Technology Institute, Korea Atomic Energy Research InstituteJeongeupSouth Korea

Personalised recommendations