Introns Regulate Gene Expression in in a Pab2p Dependent Pathway

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Most Cryptococccus neoformans genes are interrupted by introns, and alternative splicing occurs very often. In this study, we examined the influence of introns on C. neoformans gene expression. For most tested genes, elimination of introns greatly reduces mRNA accumulation. Strikingly, the number and the position of introns modulate the gene expression level in a cumulative manner. A screen for mutant strains able to express functionally an intronless allele revealed that the nuclear poly(A) binding protein Pab2 modulates intron-dependent regulation of gene expression in C. neoformans. PAB2 deletion partially restored accumulation of intronless mRNA. In addition, our results demonstrated that the essential nucleases Rrp44p and Xrn2p are implicated in the degradation of mRNA transcribed from an intronless allele in C. neoformans. Double mutant constructions and over-expression experiments suggested that Pab2p and Xrn2p could act in the same pathway whereas Rrp44p appears to act independently. Finally, deletion of the RRP6 or the CID14 gene, encoding the nuclear exosome nuclease and the TRAMP complex associated poly(A) polymerase, respectively, has no effect on intronless allele expression.

Vyšlo v časopise: Introns Regulate Gene Expression in in a Pab2p Dependent Pathway. PLoS Genet 9(8): e32767. doi:10.1371/journal.pgen.1003686
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003686

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Zdroje

1. SambrookJ (1977) Adenovirus amazes at Cold Sring Harbour. Nature 268: 101–104.

2. WahlMC, WillCL, LührmannR (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136: 701–718.

3. MooreMJ, SilverPA (2008) Global analysis of mRNA splicing. RNA 14: 197–203.

4. Le HirH, NottA, MooreMJ (2003) How introns influence and enhance eukaryotic gene expression. Trends Biochem Sciences 28: 215–220.

5. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931–945.

6. HaasBJ, WortmanJR, RonningCM, HannickLI, et al. (2005) Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol 22: 3–7.

7. JuneauK, PalmC, MirandaM, DavisRW (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci USA 104: 1522–1527.

8. LuS, CullenBR (2003) Analysis of the stimulatory effect of splicing on mRNA production and utilization in mammalian cells. RNA 9: 618–630.

9. JonssonJJ, GoresmanMD, WilsonN, McIvorRS (1992) Intron requirement for expression of the human purine nucleoside phosphorylase gene. Nucleic Acids Res 20: 3191–3198.

10. BuchmanAR, BergP (1988) Comparison of intron-dependent and intron-independent gene expression. Mol Cell Biol 8: 4395–4405.

11. RyuWS, MertzJE (1989) Simian virus 40 late transcripts lacking exisable intervening sequences are defective in both stability in the nucleus and transport to the cystoplasm. J Virol 63: 4386–4394.

12. ValenciaP, DiasAPRR (2008) Splicing promotes rapid and efficient mRNA export in mammalian cells. Proc Natl Acad Sci USA 105: 3386–3391.

13. MascarenhasD, MettlerIJ, PierceDA, LoweHW (1990) Intronmediated enhancement of heterologous gene expression in maize. Plant Mol Biol 15: 913–920.

14. RoseAB, BeliakoffJA (2000) Intron-mediated enhancement of gene expression independent of unique intron sequences and splicing. Plant Physiology 122: 535–542.

15. KarveR, LiuW, WilletSG, TorriiKU, et al. (2011) The presence of multiple introns is essential for ERECTA expression in Arabidopsis. RNA 17: 1907–1921.

16. WangHF, FengL, NiuDK (2007) Relation between mRNA stability and intron presence. Biochem Biophys Res Com 354: 203–208.

17. ParenteauJ, DurandM, VéronneauS, LacombeAA, et al. (2008) Deletion of many yeast introns reveals a minority of genes that require splicing for function. Mol Biol Cell 19: 1932–1945.

18. JuneauK, MirandaM, HillenmeyerME, NislowC, et al. (2006) Introns regulate RNA and protein abundance in yeast. Genetics 174: 511–508.

19. GalyV, GadalO, Fromont-RacineM, RomanoA, et al. (2004) Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell 116: 63–73.

20. Cuenca-BonoB, Garcia-MolineroV, Pascual-GarciaP, DopazoH, et al. (2011) SUS1 introns are required for efficient mRNA nuclear export in yeast. Nucleic Acids Res 39: 8599–8611.

21. ParenteauJ, DurandM, MorinG, GagnonJ, et al. (2011) Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell 147: 320–331.

22. NeuvégliseC, MarckC, GaillardinC (2011) The intronome of budding yeasts. C R Biol 334: 662–670.

23. WoodV, GwilliamR, RajandreamMA, LyneM, et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415: 871–880.

24. Giga-HamaY, KumagaiH (1999) Expression system for foreign genes using the fission yeast Schizosaccharomyces pombe. Biotechnol Appl Biochem 30: 235–244.

25. LubertozziD, KeaslingJD (2009) Developing Aspergillus as a host for heterologous expression. Biotech Advances 27: 53–75.

26. ShellyJ, Rasmussen-WilsonJS, PalasVJ (1997) Expression of a Plant Protein by Neurospora crassa. Appl Environ Microbiol 63: 3488–3493.

27. AllgaierS, WeilandN, HamadI, KempkenF (2009) Expression of ribonuclease A and ribonuclease N1 in the filamentous fungus Neurospora crassa. Appl Microbiol Biotechnol 85: 1041–1049.

28. Dequard-ChablatM, RötigA (1997) Homologous and heterologous expression of a ribosomal protein gene in Podospora anserina requires an intron. Mol Gen Genet 253: 546–552.

29. XuJ, GongZZ (2003) Intron requirement for AFP gene expression in Trichoderma viride. Microbiology 149: 3093–3097.

30. StajichJE, DietrichFS, RoySW (2007) Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biol 8: R223.

31. LugonesLG, ScholtmeijerK, KlootwijkR, WesselsJGH (1999) Introns are necessary for mRNA accumulation in Schizophyllum commune. Mol Microbiol 32: 681–689.

32. YamazakiT, OkajimaY, KawashimaH, TsukamotoA, et al. (2006) Intron-dependent accumulation of mRNA in Coriolus hirsutus of lignin peroxidase gene the product of which is involved in conversion/degradation of polychlorinated aromatic hydrocarbons. Biosci Biotechnol Biochem 1293–1299.

33. KilaruS, CollinsCM, HartleyAJ, BurnsC, et al. (2009) Investigating dominant selection markers for Coprinopsis cinerea: a carboxin resistance system and re-evaluation of hygromycin and phleomycin resistance vectors. Curr Genet 55: 543–550.

34. BurnsC, GregoryKE, KirbyM, CheungMK, et al. (2005) Efficient GFP expression in the mushrooms Agaricus bisporus and Coprinus cinereus requires introns. Fungal Genet Biol 42: 191–199.

35. MaB, MayfieldMB, GoldMH (2001) The green fluorescent protein genefunctions as a reporter of gene expression in Phanerochaete chrysosporium. Appl Environ Microbiol 67: 948–955.

36. Casadevall A, Perfect JR (1998) Cryptococcus neoformans. Washington, D.C.: American Society for Microbiology Press.

37. IdnurmA, BahnYS, NielsenK, LinX, et al. (2005) Deciphering the model pathogenic fungus Cryptococcus neoformans. Nat Rev Microbiol 3: 753–764.

38. JanbonG (2004) Cryptococcus neoformans capsule biosynthesis and regulation. FEMS Yeast Res 4/8: 765–771.

39. D'SouzaCA, KronstadJW, TaylorG, WarrenR, et al. (2011) Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. mBio 2: e00342–10.

40. LoftusB, FungE, RoncagliaP, RowleyD, et al. (2005) The genome and transcriptome of Cryptococcus neoformans, a basidiomycetous fungal pathogen of humans. Science 307: 1321–1324.

41. KupferDM, DrabenstotSD, BuchananKL, LaiH, et al. (2004) Introns and splicing elements of five diverse fungi. Eukaryot Cell 3: 1088–1100.

42. McGuireAM, PearsonMD, NeafseyDE, GalaganJE (2008) Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol 9: R50.

43. WarneckeT, J.LP, HurstLD (2008) Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes. Genome Biol 9: R29.

44. PanepintoJ, LiuL, RamosJ, ZhuX, et al. (2005) The DEAD-box RNA helicase Vad1 regulates multiple virulence-associated genes in Cryptococcus neoformans. J Clin Invest 115: 632–641.

45. MoyrandF, ChangYC, HimmelreichU, Kwon-ChungKJ, et al. (2004) Cas3p belongs to a seven member family of capsule structure designer proteins. Eukaryot Cell 3: 1513–1524.

46. MoyrandF, JanbonG (2004) UGD1 encoding the Cryptococcus neoformans UDP-glucose dehydrogenase is essential for growth at 37°C and for capsule biosynthesis. Eukaryot Cell 3: 1601–1608.

47. SmaleST (2009) Nuclear Run-On Assay. Cold Spring Harb Protoc doi:10.1101/pdb.prot5329

48. PerreaultA, LemieuxC, BachandF (2007) Regulation of the nuclear poly(A) binding protein by arginine methylation in fission yeast. J Biol Chem 282: 7552–7562.

49. BraisB, BouchardJP, XieYG, RochefortDL, et al. (1998) Short GCG expansions in the PABP2 gene cause oculopharyngeal muscular dystrophy. Nat Genet 18: 164–167.

50. LemayJF, D'AmoursA, LemieuxC, LacknerDH, et al. (2010) The nuclear poly(A)-binding protein interacts with the exosome to promote synthesis of noncoding small nucleolar RNAs. Mol Cell 37: 34–45.

51. St-AndréO, LemieuxC, PerreaultA, LacknerDH, et al. (2010) Negative regulation of meiotic gene expression by the nuclear poly(A)-binding protein in fission yeast. J Biol Chem 285: 27859–27868.

52. YamanakaS, YamashitaA, HarigayaY, IwataR, et al. (2010) Importance of polyadenylation in the selective elimination of meiotic mRNA in growing S. pombe cells. EMBO J 29: 2173–2181.

53. KinoshitaN, GoeblM, YanagidaM (1991) The fission yeast dis3+ gene encodes a 110-kDa essential protein implicated in mitotic control. Mol Cell Biol 11: 5939–5947.

54. MitchellP, PetfalskiE, ShevchenkoA, MannM, et al. (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′→5′ exoribonucleases. Cell 91: 457–466.

55. WickesBL, EdmanJC (1995) The Cryptococcus neoformans GAL7 gene and its use as an inducible promoter. Mol Microbiol 16: 1099–1109.

56. AndersonJT, WangX (2009) Nuclear surveillance: no sign of substrates tailing off. Crit Rev Biochem Mol Biol 44: 16–24.

57. WinTZ, DraperS, ReadRL, PearceJ, et al. (2006) Requirement of fission yeast Cid14 in polyadenylation of rRNAs. Mol Cell Biol 26: 1710–1721.

58. KühnU, WahleE (2004) Structure and function of poly(A) binding proteins. Biochim Biophys Acta 1678: 67–84.

59. Bousquet-AntonelliC, PresuttiC, TollerveyD (2000) Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102: 765–775.

60. DavidsonL, KerrA, WestS (2012) Co-transcriptional degradation of aberrant pre-mRNA by Xrn2. EMBO J 31: 2566–2578.

61. Rose AB (2008) Intron-mediated regulation of gene expression, in Reddy A.S.N. and Golovkin M., Eds. Nuclear pre-mRNA processing in plants. Berlin Heidelberg: Springer-Verlag. p. 277–290.

62. MooreMJ, ProudfootNJ (2009) Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136: 688–700.

63. ZhaoC, HamiltonT (2007) Introns regulate the rate of unstable mRNA decay. J Biol Chem 282: 20230–20237.

64. HouseleyJ, TollerveyD (2009) The many pathways of RNA degradation. Cell 136: 763–776.

65. RoyWS, PennyD, NeafseyDE (2007) Evolutiannory concervation of UTR intron boundaries in Cryptococcus. Mol Biol Evol 24: 1140–1148.

66. DumesicPA, NatarajanP, ChenC, DrinnenbergIA, et al. (2013) Stalled Spliceosomes Are a Signal for RNAi-Mediated Genome Defense. Cell 152: 957–968.

67. McDadeHC, CoxGM (2001) A new dominant selectable marker for use in Cryptococcus neoformans. Med Mycol 39: 151–154.

68. CoxGM, ToffalettiDL, PerfectJR (1996) Dominant selection system for use in Cryptococcus neoformans. J Med Vet Mycol 34: 385–391.

69. WaltonFJ, IdnurmA, HeitmanJ (2005) Novel gene functions required for melanization of the human pathogen Cryptococcus neoformans. Mol Microbiol 57: 1381–1396.

70. BenoitB, MitouG, ChartierA, TemmeC, et al. (2005) An essential cytoplasmic function for the nuclear poly(A) binding protein, PABP2, in poly(A) tail length control and early development in Drosophila. Dev Cell 9: 511–522.

71. LemieuxC, BachandF (2009) Cotranscriptional recruitment of the nuclear poly(A)-binding protein Pab2 to nascent transcripts and association with translating mRNPs. Nucleic Acids Res 37: 3418–3430.

72. ChenHM, FutcherB, LeatherwoodJ (2011) The fission yeast RNA binding protein Mmi1 regulates meiotic genes controlling intron specific splicing and polyadenylation coupled RNA turnover. PloS One 6: e26804.

73. LemieuxC, MargueratS, LafontaineJ, BarbezierN, et al. (2011) A pre-RNA degradation pathway that selectively targets intron-containing genes requires the nuclear poly(A)-binding protein. Mol Cell 44: 108–119.

74. LibriD (2010) Nuclear poly(a)-binding proteins and nuclear degradation: take the mRNA and run? Mol Cell 37: 3–5.

75. XuJ, SaundersCW, HuP, GrantRA, et al. (2007) Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. Proc Natl Acad Sci USA 104: 18730–18735.

76. KämperJ, KahmannR, BölkerM, MaLJ, et al. (2006) Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444: 97–101.

77. Kwon-ChungKJ, BennettJE, RhodesJC (1982) Taxonomic studies of Fillobasidiella species and their anamorphs. Antonie van Leeuwenhoek 48: 25–38.

78. Sherman F (1992), Getting started with yeast. In: Guthrie C and Fink GR, Eds. Guide to Yeast Genetics and Molecular Biology. San Diego: Academic Press. p. 3–21.

79. JanbonG, HimmelreichU, MoyrandF, ImprovisiL, et al. (2001) Cas1p is a membrane protein necessary for the O-acetylation of the Cryptococcus neoformans capsular polysaccharide. Mol Microbiol 42: 453–469.

80. RobertsGD, HorstmeierCD, LandGA, FoxworthJH (1978) Rapid urea broth test for yeasts. J Clin Microbiol 7: 584–588.

81. IdnurnA, ReedyJL, NussbaumJC, HeitmanJ (2004) Cryptococcus neoformans virulence gene discovery through insertional mutagenesis. Eukaryot Cell 3: 420–429.

82. IkedaR, NishimuraS, NishikawaA, ShinodaT (1996) Production of agglutinating monoclonal antibody against antigen 8 specific for Cryptococcus neoformans serotype D. Clin Diagn Lab Immunol 3: 89–92.

83. MoyrandF, KlaprothB, HimmelreichU, DromerF, et al. (2002) Isolation and characterization of capsule structure mutant strains of Cryptococcus neoformans. Mol Microbiol 45: 837–849.

84. ToffalettiDL, RudeTH, JohnstonSA, DurackDT, et al. (1993) Gene transfer in Cryptococcus neoformans by use of biolistic delivery of DNA. J Bacteriol 175: 1405–1411.

85. VarmaA, Kwon-ChungKJ (1991) Rapid method to extract DNA from Cryptococcus neoformans. J Clin Microbiol 29: 810–812.

86. MoyrandF, FontaineT, JanbonG (2007) Systematic capsule gene disruption reveals the central role of galactose metabolism on Cryptococcus neoformans virulence. Mol Microbiol 64: 771–781.

87. JänickeA, VancuylenbergJ, BoagPR, TravenA, et al. (2012) ePAT: a simple method to tag adenylated RNA to measure poly(A)-tail length and other 3′ RACE applications. RNA 18: 1289–1295.