DOI QR코드

DOI QR Code

Comparative Analysis of the Conserved Functions of Arabidopsis DRL1 and Yeast KTI12

  • Jun, Sang Eun (Department of Molecular Biotechnology, Dong-A University) ;
  • Cho, Kiu-Hyung (Department of Molecular Biotechnology, Dong-A University) ;
  • Hwang, Ji-Young (Department of Molecular Biotechnology, Dong-A University) ;
  • Abdel-Fattah, Wael (Institut fur Biologie, FG Mikrobiologie, Universitat Kassel) ;
  • Hammermeister, Alexander (Institut fur Biologie, FG Mikrobiologie, Universitat Kassel) ;
  • Schaffrath, Raffael (Department of Genetics, University of Leicester) ;
  • Bowman, John L. (School of Biological Sciences, Monash University) ;
  • Kim, Gyung-Tae (Department of Molecular Biotechnology, Dong-A University)
  • Received : 2014.11.05
  • Accepted : 2014.12.03
  • Published : 2015.03.31

Abstract

Patterning of the polar axis during the early leaf developmental stage is established by cell-to-cell communication between the shoot apical meristem (SAM) and the leaf primordia. In a previous study, we showed that the DRL1 gene, which encodes a homolog of the Elongator-associated protein KTI12 of yeast, acts as a positive regulator of adaxial leaf patterning and shoot meristem activity. To determine the evolutionally conserved functions of DRL1, we performed a comparison of the deduced amino acid sequence of DRL1 and its yeast homolog, KTI12, and found that while overall homology was low, well-conserved domains were presented. DRL1 contained two conserved plant-specific domains. Expression of the DRL1 gene in a yeast KTI12-deficient yeast mutant suppressed the growth retardation phenotype, but did not rescue the caffeine sensitivity, indicating that the role of Arabidopsis Elongator-associated protein is partially conserved with yeast KTI12, but may have changed between yeast and plants in response to caffeine during the course of evolution. In addition, elevated expression of DRL1 gene triggered zymocin sensitivity, while overexpression of KTI12 maintained zymocin resistance, indicating that the function of Arabidopsis DRL1 may not overlap with yeast KTI12 with regards to toxin sensitivity. In this study, expression analysis showed that class-I KNOX genes were downregulated in the shoot apex, and that YAB and KAN were upregulated in leaves of the Arabidopsis drl1- 101 mutant. Our results provide insight into the communication network between the SAM and leaf primordia required for the establishment of leaf polarity by mediating histone acetylation or through other mechanisms.

Keywords

Arabidopsis thaliana;DRL1;elognator-associated protein;leaf polarity;yeast KTI12

Acknowledgement

Supported by : National Research Foundation of Korea

References

  1. Butler, A.R., White, J.H., Folawiyo, Y., Edlin, A., Gardiner, D., and Stark, M.J. (1994). Two Saccharomyces cerevisiae gene which control sensitivity to G1 arrest induced by Kluyveromyces lactis toxin. Mol. Cell. Biol. 14, 6306-6316. https://doi.org/10.1128/MCB.14.9.6306
  2. Chen, Z., Zhang, H., Jablonowski, D., Zhou, X., Ren, Z., Hong, X., Schaffrath, R., Zhu, J.-K., and Gong, Z. (2006). Mutations of ABO/ELO2, a subunit of holo-Elongator, increase abscisic acid sensitivity and drought tolerance in Arabidopsis thaliana. Mol. Cell. Biol. 26, 6902-6912. https://doi.org/10.1128/MCB.00433-06
  3. Cho, K.-H., Choi, H., Seki, M., Jun, S.E., Yi, Y.B., Shinozaki, K., Tsukaya, H., and Kim, G.-T. (2007). DRL1 regulates adaxial leaf patterning and shoot apical meristem activity in Arabidopsis. J. Plant Biol. 50, 467-474. https://doi.org/10.1007/BF03030684
  4. Chitwood, D.H., Nogueira, F.T., Howell, M.D., Montgomery, T.A., Carrington, J.C., and Timmermans, M.C. (2009). Pattern formation via small RNA mobility. Genes Dev. 23, 549-554. https://doi.org/10.1101/gad.1770009
  5. Chua, Y.L., Channeliere, S., Mott, E., and Gray, J.C. (2005). The bromodomain protein GTE6 controls leaf development in Arabidopsis by histone acetylation at ASYMMETRIC LEAVES 1. Genes Dev. 19, 2245-2254. https://doi.org/10.1101/gad.352005
  6. DeFraia, C.T., Zhang, X., and Mou, Z. (2010). Elongator subunit 2 is an accelerator of immune responses in Arabidopsis thaliana. Plant J. 64, 511-523. https://doi.org/10.1111/j.1365-313X.2010.04345.x
  7. Dewitte, W., Riou-Khamlichi, C., Scofield, S., Healy, J.M.S., Jacqmard, A., Kilby, N.J, and Murray, J.A.H. (2003). Altered cell cycle distribution, hyperplasia, and inhibited differentiation in Arabidopsis caused by the D-type cyclin CYCD3. Plant Cell 15, 79-92. https://doi.org/10.1105/tpc.004838
  8. Dinkel, H., Van Roey, K., Michael, S., Davey, N.E., Weatheritt, R.J., Born, D., Speck, T., Kruger, D., Grebnev, G., Kuba, M., et al. (2013). The eukaryotic linear motif resource ELM:10 years and counting. Nucleic Acids Res. 42, D259-266.
  9. Eshed, Y., Baum, S.F., Perea, J.V., and Bowman, J.L. (2001). Establishment of polarity in lateral organs of plants. Curr. Biol. 11, 1251-1260. https://doi.org/10.1016/S0960-9822(01)00392-X
  10. Eshed, Y., Izhaki, A., Bam, S.F., Floyd, S.K., and Bowman, J.L. (2004). Asymmetric leaf development and blade expransion in Arabidopsis are mediated by KANADI and YABBY activities. Development 131, 2997-3006. https://doi.org/10.1242/dev.01186
  11. Fichtner, L., and Schaffrath, R. (2002). KTI11 and KTI13, Saccharomyces cerevisiae genes controlling sensitivity to G1 arrest induced by Kluyveromyces lactis zymocin. Mol. Microbiol. 44, 865-875. https://doi.org/10.1046/j.1365-2958.2002.02928.x
  12. Fichtner, L., Frohlof, F., Burkner, K., Larsen, M., Breunig, K.D., and Schaffrath, R. (2002). Molecular analysis of KTI12/TOT4, a Saccharomyces cerevisiae gene required for Kluyveromyces lactis zymocin action. Mol. Microbiol. 43, 783-791. https://doi.org/10.1046/j.1365-2958.2002.02794.x
  13. Frohloff, F., Fichtner, L., Jablonowski, D., Breunig, K.D., and Schaf frath, R. (2001). Saccharomyces cerevisiae Elongator mutations confer resistance to the Kluyveromyces lactis zymocin. EMBO J. 20, 1993-2003. https://doi.org/10.1093/emboj/20.8.1993
  14. Gillmor, C.S., Park, M.Y., Smith, M.R., Pepitone, R., Kerstetter, R.A., and Poethig, R.S. (2010). The MED12-MED13 module of Mediator regulates the timing of embryo patterning in Arabidopsis. Development 137, 113-122. https://doi.org/10.1242/dev.043174
  15. Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A., and Enright, A.J. (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acid Res. 34, D140-D144. https://doi.org/10.1093/nar/gkj112
  16. Hasson, A., Blein, T., and Laufs, P. (2010). Leaving the meristem behind: the genetic and molecular control of leaf patterning and morphogenesis. C. R. Biol. 333, 650-360.
  17. Hu, Y., Xie, Q., and Chua, N.H. (2003) The Arabidopsis auxininducible gene ARGOS controls lateral organ size. Plant Cell 15, 1951-1961. https://doi.org/10.1105/tpc.013557
  18. Huang, B., Johansson, M.J., and Bystrom, A.S. (2005). An early step in wobble uridine tRNA modification requires the Elongator complex. RNA 11, 424-436. https://doi.org/10.1261/rna.7247705
  19. Huang, W., Pi, L., Liang, W., Xu, B., Wang, H., Cai, R., and Huang, H. (2006). The proteolytic function of the Arabidopsis 26S proteasome is required for specifying leaf adaxial identity. Plant Cell 18, 2479-2492. https://doi.org/10.1105/tpc.106.045013
  20. Hunter, C., Willmann, M.R., Wu, G., Yoshikawa, M., De La Luz Gutierrez-Nava, M., and Poethig, S.R. (2006). Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heterblasty in Arabidopsis. Development 133, 2973-2981. https://doi.org/10.1242/dev.02491
  21. Ishibashi, N., Kanamaru, K., Ueno, Y., Kojima, S., Kobayashi, T., Machda, C., and Machida, Y. (2012). ASYMMETRIC-LEAVES2 and an ortholog of eukaryotic NudC domain proteins repress expression of AUXIN-RESPONSE-FACTOR and class 1 KNOX homeobox genes for development of flat symmetric leaves in Arabidopsis. Biol. Open 1, 197-207 https://doi.org/10.1242/bio.2012406
  22. Izhaki, A., and Bowman, J.L. (2007). KANADI and class III HD-ZIP gene families regulate embryo patterning and modulate auxin flow during embryogenesis in Arabidopsis. Plant Cell 19, 495-508 https://doi.org/10.1105/tpc.106.047472
  23. Jablonowski, D., and Schaffrath, R. (2007). Zymocin, a composite chitinase and tRNase killer toxin from yeast. Biochem. Soc. Trans. 35, 1533-1537 https://doi.org/10.1042/BST0351533
  24. Jablonowski, D., Zink, S., Mehlgarten, C., Daum, G., and Schaffrath, R. (2006). tRNA Glu wobble uridine methylation by Trm9 identifies Elongator's key role for zymocin-induced cell death in yeast. Mol. Microbiol. 59, 677-688 https://doi.org/10.1111/j.1365-2958.2005.04972.x
  25. Kidner, C.A., and Martienssen, R.A. (2004). Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428, 81-84. https://doi.org/10.1038/nature02366
  26. Kojima, S., Iwasaki, M., Takahashi, H., Imai, T., Matsumura, Y., Fleury, D., Van Lijsebettens, M., Machida, Y., and Machida, C. (2011). ASYMMETRIC LEAVES2 and Elongator, a histone acetyltransferase complex, mediate the establishment of polarity in leaves of Arabidopsis thaliana. Plant Cell Physiol. 52, 1259-1273. https://doi.org/10.1093/pcp/pcr083
  27. Kornberg, R.D. (2005). Mediator and the mechanism of transcriptional activation. Trends. Biochem. Sci. 30, 235-239 https://doi.org/10.1016/j.tibs.2005.03.011
  28. Kyte, J., and Doolittle, R.F. (1982). A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132. https://doi.org/10.1016/0022-2836(82)90515-0
  29. Lu, J., Huang, B., Esberg, A., Johansson, M.J., and Bystrom, A.S. (2005). The Kluyveromyces lactis gamma-toxin targets tRNA anticodons. RNA 11, 1648-1654. https://doi.org/10.1261/rna.2172105
  30. Mehlgarten, C., Jablonowski, D., Wrackmeyer, U., Tschitschmann, S., Sondermann, D., Jager, G., Gong, Z., Bystrom, A.S., Schaffrath, R., and Breunig, K.D. (2010). Elongator function in tRNA wobble uridine modification is conserved between yeast and plants. Mol. Microbiol. 75, 1082-1094.
  31. Mizukami, Y., and Fischer, R.L. (2000) Plant organ size control: AINTEGUMENTA regulates growth and cell numbers during organogenesis. Proc. Natl. Acad. Sci. USA 97, 942-947 https://doi.org/10.1073/pnas.97.2.942
  32. Nandakumar, J., Schwer, B., Schaffrath, R., and Shuman, S. (2008). RNA repair: an antidote to cytotoxic eukaryal RNA damage. Mol. Cell 31, 278-286. https://doi.org/10.1016/j.molcel.2008.05.019
  33. Nelissen, H., Clarke, J.H., De Block, M., De Block, S., Vanderhaeghen, R., Zielinski, R.E., Dyer, T., Lust, S., Inze, D., and Lijsebettens, M.V. (2003). DRL1, a homolog of the Yeast TOT4/KTI12 protein, has a function in meristem activity and organ growth in plants. Plant Cell 15, 639-654. https://doi.org/10.1105/tpc.007062
  34. Nelissen, H., Fleury, D., Bruno, L., Robles, P., De Veylder, L., Traas, J., Micol, J.L., Van Montagu, M., Inze, D., and Van Lijsebettens, M. (2005). The elongata mutants identify a functional Elongator complex in plants with a role in cell proliferation during organ growth. Proc. Natl. Acad. Sci. USA 102, 7754-7759 https://doi.org/10.1073/pnas.0502600102
  35. Nelissen, H., De Groeve, S., Fleury, D., Neyt, P., Bruno, L., Bitonti, M.B., Vandenbussche, F., Van der Straeten, D., Yamaguchi, T., Tsukaya, H., et al. (2010). Plant Elongator regulates auxinrelated genes during RNA polymerase II transcription elongation. Proc. Natl. Acad. Sci. USA 107, 1678-1683. https://doi.org/10.1073/pnas.0913559107
  36. Otero, G., Fellows, J., Li, Y., de Bizemont, T., Dirac, A.M., Gustafsson, C.M., Erdjument-Bromage, H., Tempst, P., and Svejstrup, J.Q. (1999). Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Mol. Cell 3, 109-118 https://doi.org/10.1016/S1097-2765(00)80179-3
  37. Petrakis, T.G., Sogaard, M.M., Erdjument-Bromage, H., Tempst, P., and Svejstrup, J.Q. (2005). Physical and functional interaction between elongator and the chromatin-associated Kti12 protein. J. Biol. Chem. 280, 19454-19460. https://doi.org/10.1074/jbc.M413373200
  38. Poss, Z.C., Ebmeier, C.C., and Taatjes, D.J. (2013). The Mediator complex and transcription regulation. Crit. Rev. Biochem. Mol. Biol. 48, 575-608 https://doi.org/10.3109/10409238.2013.840259
  39. Reddy, G.V. (2008). Live-imaging stem-cell homeostasis in the Arabidopsis shoot apex. Curr. Opin. Plant. Biol. 11, 88-93. https://doi.org/10.1016/j.pbi.2007.10.012
  40. Sanmartin, M., Sauer, M., Munoz, A., Zouhar, J., Ordonez, A., van de Ven, W.T.G., Caro, E., de la Paz Sanchez, M., Raikhel, N.V., Gutierrez, C., et al. (2011). A molecular switch for initiating cell differentiation in Arabidopsis. Curr. Biol. 21, 999-1008 https://doi.org/10.1016/j.cub.2011.04.041
  41. Sarojam, R., Sappl, P.G., Goldshmidt, A., Efroni, I., Floyd, S.K., Eshed, Y., and Bowman, J.L. (2010). Differentiating Arabidopsis shoots from leaves by combined YABBY activities. Plant Cell 22, 2113-2130. https://doi.org/10.1105/tpc.110.075853
  42. Shen, W.-H., and Xu, L. (2009). Chromatin remodeling in stem cell maintenance in Arabidopsis thaliana. Mol. Plant 2, 600-609 https://doi.org/10.1093/mp/ssp022
  43. Sherman, F. (1991). Getting started with yeast. Methods Enzymol. 194, 3-21. https://doi.org/10.1016/0076-6879(91)94004-V
  44. Siegfried, K.R., Eshed, Y., Baum, S.F., Otsuga, D., Drews, G.N., and Bowman, J.L. (1999). Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development 126, 4117-4128
  45. Sussex, I.M. (1954). Experiments on the cause of dorsiventrality in leaves. Nature 174, 352-353. https://doi.org/10.1038/174352a0
  46. Tsukaya, H. (2013). Leaf development, Arabidopsis Book, ed 2013, Vol. 11. American Society of Plant Biologists, MD, e0163.
  47. Ueda, T., Yamaguchi, M., Uchimiya, H., and Nakano, A. (2001). Ara6, a plant-unique novel type Rab GTPase, functions in the endocytic pathway of Arabidopsis thaliana. EMBO J. 20, 4730-4741. https://doi.org/10.1093/emboj/20.17.4730
  48. Winkler, G.S., Petrakis, T.G., Ethelberg, S., Tokunaga, M., Erdjument-Bromage, H., Tempst, P., and Svejstrup, J.Q. (2001). RNA polymerase II elongator holoenzyme is composed of two discrete subcomplexes. J. Biol. Chem. 276, 32743-32749 https://doi.org/10.1074/jbc.M105303200
  49. Wittschieben, B.O., Otero, G., de Bizemont, T., Fellows, J., Erdjument-Bromage, H., Ohba, R., Li, Y., Allis, C.D., Tempst, P., and Svejstrup, J.Q. (1999). A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme. Mol. Cell 4, 123-128 https://doi.org/10.1016/S1097-2765(00)80194-X
  50. Yao, Y., Ling, Q., Wang, H., and Huang, H. (2008). Ribosomal proteins promote leaf adaxial identity. Development 135, 1325-1334. https://doi.org/10.1242/dev.017913
  51. Zhou, X., Hua, D., Chen, Z., Zhou, Z., and Gong, Z. (2009). Elongator mediates ABA responses, oxidative stress resistance and anthocyanin biosynthesis in Arabidopsis. Plant J. 60, 79-90. https://doi.org/10.1111/j.1365-313X.2009.03931.x

Cited by

  1. The Elongator complex-associated protein DRL1 plays a positive role in immune responses against necrotrophic fungal pathogens in Arabidopsis 2017, https://doi.org/10.1111/mpp.12516
  2. Wobble uridine modifications–a reason to live, a reason to die?! 2017, https://doi.org/10.1080/15476286.2017.1295204
  3. Use of a Yeast tRNase Killer Toxin to Diagnose Kti12 Motifs Required for tRNA Modification by Elongator vol.9, pp.9, 2017, https://doi.org/10.3390/toxins9090272