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The Arabidopsis RNA Binding Protein with K Homology Motifs, SHINY1, Interacts with the C-terminal Domain Phosphatase-like 1 (CPL1) to Repress Stress-Inducible Gene Expression


The phosphorylation state of the C-terminal domain (CTD) of the RNA polymerase II plays crucial roles in transcription and mRNA processing. Previous studies showed that the plant CTD phosphatase-like 1 (CPL1) dephosphorylates Ser-5-specific CTD and regulates abiotic stress response in Arabidopsis. Here, we report the identification of a K-homology domain-containing protein named SHINY1 (SHI1) that interacts with CPL1 to modulate gene expression. The shi1 mutant was isolated from a forward genetic screening for mutants showing elevated expression of the luciferase reporter gene driven by a salt-inducible promoter. The shi1 mutant is more sensitive to cold treatment during vegetative growth and insensitive to abscisic acid in seed germination, resembling the phenotypes of shi4 that is allelic to the cpl1 mutant. Both SHI1 and SHI4/CPL1 are nuclear-localized proteins. SHI1 interacts with SHI4/CPL1 in vitro and in vivo. Loss-of-function mutations in shi1 and shi4 resulted in similar changes in the expression of some stress-inducible genes. Moreover, both shi1 and shi4 mutants display higher mRNA capping efficiency and altered polyadenylation site selection for some of the stress-inducible genes, when compared with wild type. We propose that the SHI1-SHI4/CPL1 complex inhibits transcription by preventing mRNA capping and transition from transcription initiation to elongation.


Vyšlo v časopise: The Arabidopsis RNA Binding Protein with K Homology Motifs, SHINY1, Interacts with the C-terminal Domain Phosphatase-like 1 (CPL1) to Repress Stress-Inducible Gene Expression. PLoS Genet 9(7): e32767. doi:10.1371/journal.pgen.1003625
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003625

Souhrn

The phosphorylation state of the C-terminal domain (CTD) of the RNA polymerase II plays crucial roles in transcription and mRNA processing. Previous studies showed that the plant CTD phosphatase-like 1 (CPL1) dephosphorylates Ser-5-specific CTD and regulates abiotic stress response in Arabidopsis. Here, we report the identification of a K-homology domain-containing protein named SHINY1 (SHI1) that interacts with CPL1 to modulate gene expression. The shi1 mutant was isolated from a forward genetic screening for mutants showing elevated expression of the luciferase reporter gene driven by a salt-inducible promoter. The shi1 mutant is more sensitive to cold treatment during vegetative growth and insensitive to abscisic acid in seed germination, resembling the phenotypes of shi4 that is allelic to the cpl1 mutant. Both SHI1 and SHI4/CPL1 are nuclear-localized proteins. SHI1 interacts with SHI4/CPL1 in vitro and in vivo. Loss-of-function mutations in shi1 and shi4 resulted in similar changes in the expression of some stress-inducible genes. Moreover, both shi1 and shi4 mutants display higher mRNA capping efficiency and altered polyadenylation site selection for some of the stress-inducible genes, when compared with wild type. We propose that the SHI1-SHI4/CPL1 complex inhibits transcription by preventing mRNA capping and transition from transcription initiation to elongation.


Zdroje

1. KomarnitskyP, ChoEJ, BuratowskiS (2000) Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev 14: 2452–2460.

2. HiroseY, OhkumaY (2007) Phosphorylation of the C-terminal domain of RNA polymerase II plays central roles in the integrated events of eukaryotic gene expression. J Biochem 141: 601–608.

3. NiZ, SchwartzBE, WernerJ, SuarezJR, LisJT (2004) Coordination of transcription, RNA processing, and surveillance by P-TEFb kinase on heat shock genes. Mol Cell 13: 55–65.

4. YeoM, LinPS, DahmusME, GillGN (2003) A novel RNA polymerase II C-terminal domain phosphatase that preferentially dephosphorylates serine 5. J Biol Chem 278: 26078–26085.

5. ZhangY, KimY, GenoudN, GaoJ, KellyJW, et al. (2006) Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1. Mol Cell 24: 759–770.

6. KrishnamurthyS, HeX, Reyes-ReyesM, MooreC, HampseyM (2004) Ssu72 Is an RNA polymerase II CTD phosphatase. Mol Cell 14: 387–394.

7. HausmannS, ShumanS (2002) Characterization of the CTD phosphatase Fcp1 from fission yeast. Preferential dephosphorylation of serine 2 versus serine 5. J Biol Chem 277: 21213–21220.

8. HausmannS, SchwerB, ShumanS (2004) An encephalitozoon cuniculi ortholog of the RNA polymerase II carboxyl-terminal domain (CTD) serine phosphatase Fcp1. Biochemistry 43: 7111–7120.

9. KoiwaH, HausmannS, BangWY, UedaA, KondoN, et al. (2004) Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases. Proc Natl Acad Sci USA 101: 14539–14544.

10. HausmannS, KoiwaH, KrishnamurthyS, HampseyM, ShumanS (2005) Different strategies for carboxyl-terminal domain (CTD) recognition by serine 5-specific CTD phosphatases. J Biol Chem 280: 37681–37688.

11. XiongL, LeeH, IshitaniM, TanakaY, StevensonB, et al. (2002) Repression of stress-responsive genes by FIERY2, a novel transcriptional regulator in Arabidopsis. Proc Natl Acad Sci USA 99: 10899–10904.

12. KoiwaH, BarbAW, XiongL, LiF, McCullyMG, et al. (2002) C-terminal domain phosphatase-like family members (AtCPLs) differentially regulate Arabidopsis thaliana abiotic stress signaling, growth, and development. Proc Natl Acad Sci USA 99: 10893–10898.

13. AksoyE, JeongIS, KoiwaH (2013) Loss of function of Arabidopsis C-terminal domain phosphatase-like 1 activates iron deficiency responses at the transcriptional level. Plant Physiol 161: 330–345.

14. ManavellaPA, HagmannJ, OttF, LaubingerS, FranzM, MacekB, WeigelD (2012) Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell 151: 859–870.

15. DreyfussG, KimVN, KataokaN (2002) Messenger-RNA-binding proteins and the messages they carry. Nat Rev Mol Cell Biol 3: 195–205.

16. AguileraA (2005) Cotranscriptional mRNP assembly: from the DNA to the nuclear pore. Curr Opin Cell Biol 17: 242–250.

17. MooreMJ (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science 309: 1514–1518.

18. LorkovicZJ, BartaA (2002) Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana. Nucleic Acids Res 30: 623–635.

19. LorkovicZJ (2009) Role of plant RNA-binding proteins in development, stress response and genome organization. Trends Plant Sci 14: 229–236.

20. SiomiH, MatunisMJ, MichaelWM, DreyfussG (1993) The pre-mRNA binding K protein contains a novel evolutionarily conserved motif. Nucleic Acids Res 21: 1193–1198.

21. ValverdeR, EdwardsL, ReganL (2008) Structure and function of KH domains. FEBS J 275: 2712–2726.

22. De BoulleK, VerkerkAJ, ReyniersE, VitsL, HendrickxJ, et al. (1993) A point mutation in the FMR-1 gene associated with fragile X mental retardation. Nat Genet 3: 31–35.

23. FengY, AbsherD, EberhartDE, BrownV, MalterHE, et al. (1997) FMRP associates with polyribosomes as an mRNP, and the I304N mutation of severe fragile X syndrome abolishes this association. Mol Cell 1: 109–118.

24. Garcia-MayoralMF, HollingworthD, MasinoL, Diaz-MorenoI, KellyG, et al. (2007) The structure of the C-terminal KH domains of KSRP reveals a noncanonical motif important for mRNA degradation. Structure 15: 485–498.

25. ChengY, KatoN, WangW, LiJ, ChenX (2003) Two RNA binding proteins, HEN4 and HUA1, act in the processing of AGAMOUS pre-mRNA in Arabidopsis thaliana. Dev Cell 4: 53–66.

26. MocklerTC, YuX, ShalitinD, ParikhD, MichaelTP, et al. (2004) Regulation of flowering time in Arabidopsis by K homology domain proteins. Proc Natl Acad Sci USA 101: 12759–12764.

27. RipollJJ, FerrandizC, Martinez-LabordaA, VeraA (2006) PEPPER, a novel K-homology domain gene, regulates vegetative and gynoecium development in Arabidopsis. Dev Biol 289: 346–359.

28. BaekD, PathangeP, ChungJS, JiangJ, GaoL, et al. (2010) A stress-inducible sulphotransferase sulphonates salicylic acid and confers pathogen resistance in Arabidopsis. Plant Cell Environ 33: 1383–1392.

29. KrepsJA, WuY, ChangH-S, ZhuT, WangX, HarperJF (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130: 2129–2141.

30. CloughSJ, BentAF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735–743.

31. FujikawaY, KatoN (2007) Split luciferase complementation assay to study protein-protein interactions in Arabidopsis protoplasts. Plant J 52: 185–195.

32. MatsudaO, SakamotoH, NakaoY, OdaK, IbaK (2009) CTD phosphatases in the attenuation of wound-induced transcription of jasmonic acid biosynthetic genes in Arabidopsis. Plant J 57: 96–108.

33. MandalSS, ChuC, WadaT, HandaH, ShatkinAJ, ReinbergD (2004) Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc Natl Acad Sci USA 101: 7572–7577.

34. OhtakeH, OhtokoK, IshimaruY, KatoS (2004) Determination of the capped site sequence of mRNA based on the detection of cap-dependent nucleotide addition using an anchor ligation method. DNA Res 11: 305–309.

35. ChoiYH, HagedornCH (2003) Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3′ poly(A) end phenotype. Proc Natl Acad Sci USA 100: 7033–7038.

36. HirayamaT, ShinozakiK (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J 61: 1041–1052.

37. Yamaguchi-ShinozakiK, ShinozakiK (1994) A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6: 251–264.

38. StockingerEJ, GilmourSJ, ThomashowMF (1997) Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci USA 94: 1035–1040.

39. LiuQ, KasugaM, SakumaY, AbeH, MiuraS, et al. (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10: 1391–1406.

40. GuanQ, WenC, ZengH, ZhuJ (2013) A KH domain-containing putative RNA-binding protein is critical for heat stress-responsive gene regulation and thermotolerance in Arabidopsis. Mol Plant 6: 386–395.

41. XiongL, DavidL, StevensonB, ZhuJK (1999) Luminescence imaging in the isolation of plant signal transduction mutants. Plant Mol Biol Rep 17: 159–170.

42. AlonsoJM, StepanovaAN, LeisseTJ, KimCJ, ChenH, et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653–657.

43. CurtisMD, GrossniklausU (2003) A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol 133: 462–469.

44. EarleyKW, HaagJR, PontesO, OpperK, JuehneT, et al. (2006) Gateway-compatible vectors for plant functional genomics and proteomics. Plant J 45: 616–629.

45. ChungJS, ZhuJK, BressanRA, HasegawaPM, ShiH (2008) Reactive oxygen species mediate Na+-induced SOS1 mRNA stability in Arabidopsis. Plant J 53: 554–565.

46. GietzRD, WoodsRA (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol 350: 87–96.

47. FanHY, HuY, TudorM, MaH (1997) Specific interactions between the K domains of AG and AGLs, members of the MADS domain family of DNA binding proteins. Plant J 12: 999–1010.

48. RossignolP, CollierS, BushM, ShawP, DoonanJH (2007) Arabidopsis POT1A interacts with TERT-V(I8), an N-terminal splicing variant of telomerase. J Cell Sci 120: 3678–3687.

49. CitovskyV, LeeLY, VyasS, GlickE, ChenMH, et al. (2006) Subcellular localization of interacting proteins by bimolecular fluorescence complementation in planta. J Mol Biol 362: 1120–1131.

50. YooSD, ChoYH, SheenJ (2007) Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat Protoc 2: 1565–1572.

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Genetika Reprodukčná medicína

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PLOS Genetics


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