Loss of the RNA trimethylguanosine cap is compatible with nuclear accumulation of spliceosomal snRNAs but not pre-mRNA splicing or snRNA processing during animal development


Autoři: Lin Cheng aff001;  Yu Zhang aff003;  Yi Zhang aff005;  Tao Chen aff001;  Yong-Zhen Xu aff004;  Yikang S. Rong aff002
Působiště autorů: School of Life Sciences, Sun Yat-sen University, Guangzhou, China aff001;  Hengyang College of Medicine, University of South China, Hengyang, China aff002;  Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China aff003;  College of Life Sciences, Wuhan University, Wuhan, China aff004;  Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States of America aff005
Vyšlo v časopise: Loss of the RNA trimethylguanosine cap is compatible with nuclear accumulation of spliceosomal snRNAs but not pre-mRNA splicing or snRNA processing during animal development. PLoS Genet 16(10): e32767. doi:10.1371/journal.pgen.1009098
Kategorie: Research Article
doi: 10.1371/journal.pgen.1009098

Souhrn

The 2,2,7-trimethylguanosine (TMG) cap is one of the first identified modifications on eukaryotic RNAs. TMG, synthesized by the conserved Tgs1 enzyme, is abundantly present on snRNAs essential for pre-mRNA splicing. Results from ex vivo experiments in vertebrate cells suggested that TMG ensures nuclear localization of snRNAs. Functional studies of TMG using tgs1 mutations in unicellular organisms yield results inconsistent with TMG being indispensable for either nuclear import or splicing. Utilizing a hypomorphic tgs1 mutation in Drosophila, we show that TMG reduction impairs germline development by disrupting the processing, particularly of introns with smaller sizes and weaker splice sites. Unexpectedly, loss of TMG does not disrupt snRNAs localization to the nucleus, disputing an essential role of TMG in snRNA transport. Tgs1 loss also leads to defective 3’ processing of snRNAs. Remarkably, stronger tgs1 mutations cause lethality without severely disrupting splicing, likely due to the preponderance of TMG-capped snRNPs. Tgs1, a predominantly nucleolar protein in Drosophila, likely carries out splicing-independent functions indispensable for animal development. Taken together, our results suggest that nuclear import is not a conserved function of TMG. As a distinctive structure on RNA, particularly non-coding RNA, we suggest that TMG prevents spurious interactions detrimental to the function of RNAs that it modifies.

Klíčová slova:

Drosophila melanogaster – Immunostaining – Introns – Larvae – Reverse transcriptase-polymerase chain reaction – RNA sequencing – Small nuclear RNA – Small nucleolar RNA


Zdroje

1. Saponara AG, Enger MD. Occurrence of N2, N2, 7-trimethylguanosine in minor RNA species of a mammalian cell line. Nature. 1969; 223(5213): 1365–1366. doi: 10.1038/2231365a0 5817758

2. Busch H, Reddy R, Rothblum L, Choi YC. SnRNAs, SnRNPs, and RNA processing. Annu Rev Biochem, 1982; 51: 617–654. doi: 10.1146/annurev.bi.51.070182.003153 6180681

3. Reddy R, Henning D, Busch H. Primary and secondary structure of U8 small nuclear RNA. J Biol Chem. 1985; 260(20): 10930–10935. 2411727

4. Matera AG, Terns RM, Terns MP. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol. 2007; 8(3): 209–220. doi: 10.1038/nrm2124 17318225

5. Fischer U, Englbrecht C, Chari A. Biogenesis of spliceosomal small nuclear ribonucleoproteins. Wiley Interdiscip Rev RNA. 2011; 2(5): 718–731. doi: 10.1002/wrna.87 21823231

6. Godfrey AC, Kupsco JM, Burch BD, Zimmerman RM, Dominski Z, Marzluff WF, et al. U7 snRNA mutations in Drosophila block histone pre-mRNA processing and disrupt oogenesis. Rna. 2006; 12(3): 396–409. doi: 10.1261/rna.2270406 16495235

7. Terns MP, Dahlberg JE. Retention and 5'cap trimethylation of U3 snRNA in the nucleus. Science. 1994; 264 (5161): 959–961. doi: 10.1126/science.8178154 8178154

8. Franke J, Gehlen J, Ehrenhofer-Murray AE. Hypermethylation of yeast telomerase RNA by the snRNA and snoRNA methyltransferase Tgs1. J Cell Sci. 2008; 121(21): 3553–3560.

9. Lasda EL, Blumenthal T. Trans-splicing. Wiley Interdiscip Rev RNA. 2011; 2(3): 417–434. doi: 10.1002/wrna.71 21957027

10. Krchňáková Z, Krajčovič J, Vesteg M. On the possibility of an early evolutionary origin for the spliced leader Trans-Splicing. J Mol Evol. 2017; 85(1–2): 37–45. doi: 10.1007/s00239-017-9803-y 28744787

11. Wurth L, Gribling-Burrer AS, Verheggen C, Leichter M, Takeuchi A, Baudrey S, et al. Hypermethylated-capped selenoprotein mRNAs in mammals. Nucleic Acids Res. 2014; 42(13): 8663–8677. doi: 10.1093/nar/gku580 25013170

12. Yedavalli VS, Jeang KT. Trimethylguanosine capping selectively promotes expression of Rev-dependent HIV-1 RNAs. Proc Natl Acad Sci U S A. 2010; 107(33): 14787–14792. doi: 10.1073/pnas.1009490107 20679221

13. Martinez I, Hayes KE, Barr JA, Harold AD, Xie M, Bukhari SI, et al. An Exportin-1-dependent microRNA biogenesis pathway during human cell quiescence. Proc Natl Acad Sci U S A. 2017; 114(25): E4961–E4970. doi: 10.1073/pnas.1618732114 28584122

14. Fischer U, Lührmann R. An essential signaling role for the m3G cap in the transport of U1 snRNP to the nucleus. Science. 1990; 249 (4970): 786–790. doi: 10.1126/science.2143847 2143847

15. Hamm J, Darzynkiewicz E, Tahara SM, Mattaj IW. The trimethylguanosine cap structure of U1 snRNA is a component of a bipartite nuclear targeting signal. Cell, 1990; 62(3): 569–577. doi: 10.1016/0092-8674(90)90021-6 2143105

16. Fischer U, Darzynkiewicz E, Tahara SM, Dathan NA, Lührmann R, Mattaj IW. Diversity in the signals required for nuclear accumulation of U snRNPs and variety in the pathways of nuclear transport. J Cell Biol. 1991; 113(4): 705–714. doi: 10.1083/jcb.113.4.705 1827444

17. Fischer U, Heinrich J, Van Zee K, Fanning E, Lührmann R. Nuclear transport of U1 snRNP in somatic cells: differences in signal requirement compared with Xenopus laevis oocytes. J Cell Biol. 1994; 125(5): 971–980 doi: 10.1083/jcb.125.5.971 8195300

18. Mouaikel J, Verheggen C, Bertrand E, Tazi J, Bordonné R. Hypermethylation of the cap structure of both yeast snRNAs and snoRNAs requires a conserved methyltransferase that is localized to the nucleolus. Mol Cell. 2002; 9(4): 891–901. doi: 10.1016/s1097-2765(02)00484-7 11983179

19. Hausmann S, Shuman S. Specificity and mechanism of RNA cap guanine-N2 methyltransferase (Tgs1). J Biol Chem, 2005; 280(6): 4021–4024. doi: 10.1074/jbc.C400554200 15590684

20. Hausmann S, Ramirez A, Schneider S, Schwer B, Shuman S. Biochemical and genetic analysis of RNA cap guanine-N2 methyltransferases from Giardia lamblia and Schizosaccharomyces pombe. Nucleic Acids Res. 2007; 35(5): 1411–1420. doi: 10.1093/nar/gkl1150 17284461

21. Hausmann S, Zheng S, Costanzo M, Brost RL, Garcin D, Boone C, et al. Genetic and biochemical analysis of yeast and human cap trimethylguanosine synthase: functional overlap of 2,2,7-trimethylguanosine caps, small nuclear ribonucleoprotein components, pre-mRNA splicing factors, and RNA decay pathways. J Biol Chem. 2008; 283(46): 31706–31718. doi: 10.1074/jbc.M806127200 18775984

22. Schwer B, Erdjument-Bromage H, Shuman S. Composition of yeast snRNPs and snoRNPs in the absence of trimethylguanosine caps reveals nuclear cap binding protein as a gained U1 component implicated in the cold-sensitivity of tgs1 Δ cells. Nucleic Acids Res. 2011; 39(15): 6715–6728. doi: 10.1093/nar/gkr279 21558325

23. Qiu ZR, Shuman S, Schwer B. An essential role for trimethylguanosine RNA caps in Saccharomyces cerevisiae meiosis and their requirement for splicing of SAE3 and PCH2 meiotic pre-mRNAs. Nucleic Acids Res. 2011; 39(13): 5633–5646. doi: 10.1093/nar/gkr083 21398639

24. Murphy MW, Olson BL, Siliciano PG. The yeast splicing factor Prp40p contains functional leucine-rich nuclear export signals that are essential for splicing. Genetics. 2004; 166(1): 53–65. doi: 10.1534/genetics.166.1.53 15020406

25. Boon KL, Grainger RJ, Ehsani P, Barrass JD, Auchynnikava T, Inglehearn CF, et al. prp8 mutations that cause human retinitis pigmentosa lead to a U5 snRNP maturation defect in yeast. Nat Struct Mol Biol. 2007; 14(11): 1077–1083. doi: 10.1038/nsmb1303 17934474

26. Tkacz ID, Lustig Y, Stern MZ, Biton M, Salmon-Divon M, Das A, et al. Identification of novel snRNA-specific Sm proteins that bind selectively to U2 and U4 snRNAs in Trypanosoma brucei. RNA. 2007; 13(1): 30–43. doi: 10.1261/rna.174307 17105994

27. Palfi Z, Jaé N, Preusser C, Kaminska KH, Bujnicki JM, Lee JH, et al. SMN-assisted assembly of snRNPspecific Sm cores in trypanosomes. Genes Dev. 2009. 23(14): 1650–1664. doi: 10.1101/gad.526109 19605687

28. Jaé N, Preusser C, Krüger T, Tkacz ID, Engstler M, Michaeli S, et al. snRNA-specific role of SMN in trypanosome snRNP biogenesis in vivo. RNA Biol. 2011; 8(1): 90–100. doi: 10.4161/rna.8.1.13985 21282982

29. Becker D, Hirsch AG, Bender L, Lingner T, Salinas G, Krebber H. Nuclear Pre-snRNA Export Is an Essential Quality Assurance Mechanism for Functional Spliceosomes. Cell Rep. 2019; 27(11): 3199–3214. doi: 10.1016/j.celrep.2019.05.031 31189105

30. Lemm I, Girard C, Kuhn AN, Watkins NJ, Schneider M, Bordonné R, et al. Ongoing U snRNP biogenesis is required for the integrity of Cajal bodies. Mol Biol Cell. 2006; 17(7): 3221–3231. doi: 10.1091/mbc.e06-03-0247 16687569

31. Jia Y, Viswakarma N, Crawford SE, Sarkar J, Rao MS, Karpus WJ, et al. Early embryonic lethality of mice with disrupted transcription cofactor PIMT/NCOA6IP/Tgs1 gene. Mech Dev. 2012; 129(9–12): 193–207. doi: 10.1016/j.mod.2012.08.002 22982455

32. Komonyi O, Pápai G, Enunlu I, Muratoglu S, Pankotai T, Kopitova D, et al. DTL, the Drosophila homolog of PIMT/Tgs1 nuclear receptor coactivator interacting protein/RNA methyltransferase, has an essential role in development. J Biol Chem. 2009; 280(13): 12397–12404.

33. Zhang Y, Zhang L, Tang X, Bhardwaj SR, Ji J, Rong YS. MTV, an ssDNA protecting complex essential for transposon-based telomere maintenance in Drosophila. PLoS Genet. 2016; 12(11): e1006435. doi: 10.1371/journal.pgen.1006435 27835648

34. Bischof J, Maeda RK, Hediger M, Karch F, Basler K. An optimized transgenesis system for Drosophila using germ-line-specific φC31 integrases. Proc Natl Acad Sci U S A. 2007; 104(9): 3312–3317. doi: 10.1073/pnas.0611511104 17360644

35. Port F, Chen HM, Lee T, Bullock SL. Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. Proc Natl Acad Sci U S A. 2014; 111(29): E2967–E2976. doi: 10.1073/pnas.1405500111 25002478

36. Nizami ZF, Liu JL, Gall JG. Fluorescent In Situ Hybridization of Nuclear Bodies in Drosophila melanogaster Ovaries. Methods Mol Biol. 2015; 1328: 137–149. doi: 10.1007/978-1-4939-2851-4_10 26324435

37. Ezzeddine N, Chen J, Waltenspiel B, Burch B, Albrecht T, Zhuo M, et al. A subset of Drosophila integrator proteins is essential for efficient U7 snRNA and spliceosomal snRNA 3′-end formation. Mol Cell Biol. 2011; 31(2): 328–341. doi: 10.1128/MCB.00943-10 21078872

38. Raffa GD, Siriaco G, Cugusi S, Ciapponi L, Cenci G, Wojcik E, et al. The Drosophila modigliani (moi) gene encodes a HOAP interacting protein required for telomere protection. Proc Natl Acad Sci U S A. 2009; 106(7): 2271–2276. doi: 10.1073/pnas.0812702106 19181850

39. Komonyi O, Schauer T, Papai G, Deak P, Boros IM. A product of the bicistronic Drosophila melanogaster gene CG31241, which also encodes a trimethylguanosine synthase, plays a role in telomere protection. J Cell Sci. 2009; 122(6): 769–774.

40. Fuller MT. Genetic control of cell proliferation and differentiation in Drosophila spermatogenesis. Semin Cell Dev Biol. 1998; 9(4): 433–444. doi: 10.1006/scdb.1998.0227 9813190

41. White-Cooper H. Molecular mechanisms of gene regulation during Drosophila spermatogenesis. Reproduction. 2010; 139(1): 11–21. doi: 10.1530/REP-09-0083 19755484

42. Cenci G, Bonaccorsi S, Pisano C, Verni F, Gatti M. Chromatin and microtubule organization during premeiotic, meiotic and early postmeiotic stages of Drosophila melanogaster spermatogenesis. J Cell Sci. 1994; 107(12): 3521–3534.

43. Hernandez N, Weiner AM. Formation of the 3' end of U1 snRNA requires compatible snRNA promoter elements. Cell. 1986; 47(2): 249–258. doi: 10.1016/0092-8674(86)90447-2 3768956

44. de Vegvar HE, Lund E, Dahlberg JE. 3' end formation of U1 snRNA precursors is coupled to transcription from snRNA promoters. Cell. 1986; 47(2): 259–266. doi: 10.1016/0092-8674(86)90448-4 3021336

45. Sauterer RA, Feeney RJ, Zieve GW. Cytoplasmic assembly of snRNP particles from stored proteins and newly transcribed snRNA's in L929 mouse fibroblasts. Exp Cell Res. 1988; 176(2): 344–359. doi: 10.1016/0014-4827(88)90336-9 2967772

46. Ruan JP, Ullu E, Tschudi C. Characterization of the Trypanosoma brucei cap hypermethylase Tgs1. Mol Biochem Parasitol. 2007; 155(1): 66–69. doi: 10.1016/j.molbiopara.2007.05.008 17610965

47. Babar PH, Dey V, Jaiswar P, Patankar S. An insertion in the methyltransferase domain of P. falciparum trimethylguanosine synthase harbors a classical nuclear localization signal. Mol Biochem Parasitol. 2016; 210(1–2): 58–70. doi: 10.1016/j.molbiopara.2016.08.007 27619053

48. Zhu Y, Qi C, Cao WQ, Yeldandi AV, Rao MS, Reddy JK. Cloning and characterization of PIMT, a protein with a methyltransferase domain, which interacts with and enhances nuclear receptor coactivator PRIP function. Proc Natl Acad Sci U S A. 2001; 98(18): 10380–10385. doi: 10.1073/pnas.181347498 11517327

49. Enünlü I, Pápai G, Cserpán I, Udvardy A, Jeang KT, Boros I. Different isoforms of PRIP-interacting protein with methyltransferase domain/trimethylguanosine synthase localizes to the cytoplasm and nucleus. Biochem Biophys Res Commun. 2003; 309(1): 44–51. doi: 10.1016/s0006-291x(03)01514-6 12943661

50. Mouaikel J, Narayanan U, Verheggen C, Matera AG, Bertrand E, Tazi J, et al. Interaction between the small-nuclear-RNA cap hypermethylase and the spinal muscular atrophy protein, survival of motor neuron. EMBO Rep. 2003; 4(6): 616–622. doi: 10.1038/sj.embor.embor863 12776181

51. Mouaikel J, Bujnicki JM, Tazi J, Bordonné R. Sequence–structure function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase. Nucleic Acids Res. 2003; 31(16): 4899–4909. doi: 10.1093/nar/gkg656 12907733

52. Patton JR, Patterson RJ, Pederson T. Reconstitution of the U1 small nuclear ribonucleoprotein particle. Mol Cell Biol. 1987; 7(11): 4030–4037. doi: 10.1128/mcb.7.11.4030 2963210

53. Siegall CB, Hla TT, Kumar A. Reconstituted U1 small nuclear ribonucleoprotein complex restores 5′splice site cleavage activity. Biochem Biophys Res Commun. 1988; 154(3): 1010–1017. doi: 10.1016/0006-291x(88)90240-9 2970258

54. McPheeters DS, Fabrizio P, Abelson J. In vitro reconstitution of functional yeast U2 snRNPs. Genes Dev. 1989; 3(12b): 2124–2136. doi: 10.1101/gad.3.12b.2124 2560754

55. Wersig C, Bindereif A. Reconstitution of functional mammalian U4 small nuclear ribonucleoprotein: Sm protein binding is not essential for splicing in vitro. Mol Cell Biol. 1992; 12(4): 1460–1468. doi: 10.1128/mcb.12.4.1460 1532228

56. Ségault V, Will CL, Sproat BS, Lührmann R. In vitro reconstitution of mammalian U2 and U5 snRNPs active in splicing: Sm proteins are functionally interchangeable and are essential for the formation of functional U2 and U5 snRNPs. EMBO J. 1995; 14(16): 4010–4021. 7664740

57. Dönmez G, Hartmuth K, Lührmann R. Modified nucleotides at the 5′ end of human U2 snRNA are required for spliceosomal E-complex formation. Rna, 2004; 10(12): 1925–1933. doi: 10.1261/rna.7186504 15525712

58. Natalizio AH, Matera AG. Identification and characterization of Drosophila Snurportin reveals a role for the import receptor Moleskin/importin 7 in snRNP biogenesis. Mol Biol Cell. 2013; 24(18): 2932–2942. doi: 10.1091/mbc.E13-03-0118 23885126

59. Herold N, Will CL, Wolf E, Kastner B, Urlaub H, Lührmann R. Conservation of the protein composition and electron microscopy structure of Drosophila melanogaster and human spliceosomal complexes. Mol Cell Biol. 2009; 29(1): 281–301. doi: 10.1128/MCB.01415-08 18981222

60. Liu W, Zhao R, McFarland C, Kieft J, Niedzwiecka A, Jankowska-Anyszka M, et al. Structural insights into parasite eIF4E binding specificity for m7G and m2,2,7G mRNA caps. J Biol Chem. 2009; 284(45): 31336–31349. doi: 10.1074/jbc.M109.049858 19710013

61. Liu W, Jankowska-Anyszka M, Piecyk K, Dickson L, Wallace A, Niedzwiecka A, et al. Structural basis for nematode eIF4E binding an m(2,2,7)G-Cap and its implications for translation initiation. Nucleic Acids Res. 2011; 39(20): 8820–8832. doi: 10.1093/nar/gkr650 21965542

62. Strasser A, Dickmanns A, Lührmann R, Ficner R. Structural basis for m3G-cap-mediated nuclear import of spliceosomal UsnRNPs by snurportin1. EMBO J. 2005; 24(13): 2235–2243. doi: 10.1038/sj.emboj.7600701 15920472

63. Liu Y, Li S, Chen Y, Kimberlin AN, Cahoon EB, Yu, B. snRNA 3' End Processing by a CPSF73-Containing Complex Essential for Development in Arabidopsis. PLoS Biol. 2016; 14(10): e1002571. doi: 10.1371/journal.pbio.1002571 27780203

64. Jia D, Cai L, He H, Skogerbø G, Li T, Aftab MN, et al. Systematic identification of non-coding RNA 2, 2, 7-trimethylguanosine cap structures in Caenorhabditis elegans. BMC Mol Biol. 2007; 8(1): 86.


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