On the Possibility of an Early Evolutionary Origin for the Spliced Leader Trans-Splicing

  • Zuzana Krchňáková
  • Juraj Krajčovič
  • Matej Vesteg
Original Article
  • 91 Downloads

Abstract

Trans-splicing is a process by which 5′- and 3′-ends of two pre-RNA molecules transcribed from different sites of the genome can be joined together to form a single RNA molecule. The spliced leader (SL) trans-splicing is mediated by the spliceosome and it allows the replacement of 5′-end of pre-mRNA by 5′(SL)-end of SL-RNA. This form of splicing has been observed in many phylogenetically unrelated eukaryotes. Either the SL trans-splicing (SLTS) originated in the last eukaryotic common ancestor (LECA) (or even earlier) and it was lost in most eukaryotic lineages, or this mechanism of RNA processing evolved several times independently in various unrelated eukaryotic taxa. The bioinformatic comparisons of SL-RNAs from various eukaryotic taxonomic groups have revealed the similarities of secondary structures of most SL-RNAs and a relative conservation of their splice sites (SSs) and Sm-binding sites (SmBSs). We propose that such structural and functional similarities of SL-RNAs are unlikely to have evolved repeatedly many times. Hence, we favor the scenario of an early evolutionary origin for the SLTS and multiple losses of SL-RNAs in various eukaryotic lineages.

Keywords

Intron RNA secondary structure Sm-binding site SL-RNA Spliceosome 

Abbreviations

LECA

The last eukaryotic common ancestor

LUCA

The last universal common ancestor

Sm

“Smith antigen” proteins which bind to small nuclear RNAs (snRNAs), i.e., spliceosomal U (U-rich) or SL snRNAs

SmBS

Sm-binding site

SL

Capped spliced leader sequence which is transferred to 5′-end of pre-mRNA during SL trans-splicing

SL-RNA

Spliced leader (SL) snRNA which serves as donor of capped SL sequences for pre-mRNA

SLTS

Spliced leader trans-splicing

SS

Splice site

Supplementary material

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Supplementary material 12 (XLS 85 kb)

References

  1. Allen MA, Hillier LW, Waterston RH, Blumenthal T (2011) A global analysis of C. elegans trans-splicing. Genome Res 21:255–264CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bangs JD, Crain PF, Hashizume T, McCloskey JA, Boothroyd JC (1992) Mass spectrometry of mRNA cap 4 from trypanosomatids reveals two novel nucleosides. J Biol Chem 267:9805–9815PubMedGoogle Scholar
  3. Bartschat S, Samuelsson T (2010) U12 type introns were lost at multiple occasions during evolution. BMC Genom 11:106CrossRefGoogle Scholar
  4. Beauparlant MA, Drouin G (2014) Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species. Curr Genet 60:17–24CrossRefPubMedGoogle Scholar
  5. Berriman M, Ghedin E, Hertz-Fowler C et al (2005) The genome of the african trypanosome Trypanosoma brucei. Science 309:416–422CrossRefPubMedGoogle Scholar
  6. Bitar M, Boroni M, Macedo AM, Machado CR, Franco GR (2013) The spliced leader trans-splicing mechanism in different organisms: molecular details and possible biological roles. Front Genet 4:199CrossRefPubMedPubMedCentralGoogle Scholar
  7. Blaxter M, Liu L (1996) Nematode spliced leaders—ubiquity, evolution and utility. Int J Parasitol 26:1025–1033PubMedGoogle Scholar
  8. Blumenthal T (2004) Operons in eukaryotes. Brief Funct Genomic Proteom 3:199–211CrossRefGoogle Scholar
  9. Blumenthal T (2012) Trans-splicing and operons in C. elegans. WormBook. 2012 Nov 20:1–11. doi: 10.1895/wormbook.1.5.2
  10. Blumenthal T, Davis P,Garrido-Lecca A (2015) Operon and non-operon gene clusters in the C. elegans genome (April 28, 2015). WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.175.1, http://www.wormbook.org
  11. Brehm K, Jensen K, Frosch M (2000) mRNA trans-splicing in the human parasitic cestode Echinococcus multilocularis. J Biol Chem 275:38311–38318CrossRefPubMedGoogle Scholar
  12. Bruzik JP, Steitz JA (1990) Spliced leader RNA sequences can substitute for the essential 5′ end of U1 RNA during splicing in a mammalian in vitro system. Cell 62:889–899CrossRefPubMedGoogle Scholar
  13. Bruzik JP, Doren KV, Hirsh D, Steitz JA (1988) Trans splicing involves a novel form of small nuclear ribonucleoprotein particles. Nature 335:559–562CrossRefPubMedGoogle Scholar
  14. Campbell DA, Thomas S, Sturm NR (2003) Transcription in kinetoplastid protozoa: why be normal? Microbes Infect 5:1231–1240CrossRefPubMedGoogle Scholar
  15. Darty K, Denise A, Ponty Y (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25:1974–1975CrossRefPubMedPubMedCentralGoogle Scholar
  16. Davis RE (1996) Spliced leader RNA trans-splicing in metazoa. Parasitol Today 12:33–40CrossRefPubMedGoogle Scholar
  17. Davis RE (1997) Surprising diversity and distribution of spliced leader RNAs in flatworms. Mol Biochem Parasitol 87:29–48CrossRefPubMedGoogle Scholar
  18. Davis RE, Hardwick C, Tavernier P, Hodgson S, Singh H (1995) RNA Trans-splicing in flatworms. Analysis of trans-spliced mRNAs and genes in the human parasite Schistosoma mansoni. J Biol Chem 270:21813–21819CrossRefPubMedGoogle Scholar
  19. Denker JA, Zuckerman DM, Maroney PA, Nilsen TW (2002) New components of the spliced leader RNP required for nematode trans-splicing. Nature 417:667–670CrossRefPubMedGoogle Scholar
  20. Derelle R, Momose T, Manuel M, Da Silva C, Wincker P, Houliston E (2010) Convergent origins and rapid evolution of spliced leader trans-splicing in Metazoa: Insights from the Ctenophora and Hydrozoa. RNA 16:696–707CrossRefPubMedPubMedCentralGoogle Scholar
  21. Doren KV, Hirsh D (1988) Trans-spliced leader RNA exists as small nuclear ribonucleoprotein particles in Caenorhabditis elegans. Nature 335:556–559CrossRefPubMedGoogle Scholar
  22. Douris V, Telford MJ, Averof M (2010) Evidence for multiple independent origins of trans-splicing in Metazoa. Mol Biol Evol 27:684–693CrossRefPubMedGoogle Scholar
  23. Drouin G, Tsang C (2012) 5S rRNA gene arrangements in protists: a case of nonadaptive evolution. J Mol Evol 74:342–351CrossRefPubMedGoogle Scholar
  24. Ebel C, Frantz C, Paulus F, Imbault P (1999) Trans-splicing and cis-splicing in the colourless Euglenoid, Entosiphon sulcatum. Curr Genet 35:542–550CrossRefPubMedGoogle Scholar
  25. Evans D, Blumenthal T (2000) trans splicing of polycistronic Caenorhabditis elegans pre-mRNAs: analysis of the SL2 RNA. Mol Cell Biol 20:6659–6667CrossRefPubMedPubMedCentralGoogle Scholar
  26. Evans D, Zorio D, MacMorris M, Winter CE, Lea K, Blumenthal T (1997) Operons and SL2 trans-splicing exist in nematodes outside the genus Caenorhabditis. Proc Natl Acad Sci USA 94:9751–9756CrossRefPubMedPubMedCentralGoogle Scholar
  27. Ganot P, Kallesøe T, Reinhardt R, Chourrout D, Thompson EM (2004) Spliced-leader RNA trans splicing in a chordate, Oikopleura dioica, with a compact genome. Mol Cell Biol 24:7795–7805CrossRefPubMedPubMedCentralGoogle Scholar
  28. Gibson W, Bingle L, Blendeman W, Brown J, Wood J, Stevens J (2000) Structure and sequence variation of the trypanosome spliced leader transcript. Mol Biochem Parasitol 107:269–277CrossRefPubMedGoogle Scholar
  29. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98Google Scholar
  30. Hannon GJ, Maroney PA, Nilsen TW (1991) U small nuclear ribonucleoprotein requirements for nematode cis- and trans-splicing in vitro. J Biol Chem 266:22792–22795PubMedGoogle Scholar
  31. Harris KA, Crothers DM, Ullu E (1995) In vivo structural analysis of spliced leader RNAs in Trypanosoma brucei and Leptomonas collosoma: a flexible structure that is independent of cap4 methylations. RNA 1:351–362PubMedPubMedCentralGoogle Scholar
  32. Harrison N, Kalbfleisch A, Connolly B, Pettitt J, Müller B (2010) SL2-like spliced leader RNAs in the basal nematode Prionchulus punctatus: New insight into the evolution of nematode SL2 RNAs. RNA 16:1500–15007CrossRefPubMedPubMedCentralGoogle Scholar
  33. Hastings KEM (2005) SL trans-splicing: easy come or easy go? Trends Genet 21:240–247CrossRefPubMedGoogle Scholar
  34. Hofacker IL, Fekete M, Stadler PF (2002) Secondary structure prediction for aligned RNA sequences. J Mol Biol 319:1059–1066CrossRefPubMedGoogle Scholar
  35. Kim S, Bachvaroff TR, Handy SM, Delwiche CF (2011) Dynamics of actin evolution in dinoflagellates. Mol Biol Evol 28:1469–1480CrossRefPubMedGoogle Scholar
  36. Koehl P (2001) Protein structure similarities. Curr Opinion Struct Biol 11:348–353CrossRefGoogle Scholar
  37. Lasda EL, Blumenthal T (2011) Trans-splicing. Wiley Interdiscip Rev. RNA 2:417–434PubMedGoogle Scholar
  38. LeCuyer KA, Crothers DM (1993) The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms. Biochemistry 32:5301–5311CrossRefPubMedGoogle Scholar
  39. Liang XH, Haritan A, Uliel S, Michaeli S (2003) trans and cis splicing in trypanosomatids: mechanism, factors, and regulation. Eukaryot Cell 2:830–840CrossRefPubMedPubMedCentralGoogle Scholar
  40. Lidie KB, van Dolah FM (2007) Spliced leader RNA-mediated trans-splicing in a dinoflagellate, Karenia brevis. J Eukaryot Microbiol 54:427–435CrossRefPubMedGoogle Scholar
  41. Lin CF, Mount SM, Jarmołowski A, Makałowski W (2010) Evolutionary dynamics of U12-type spliceosomal introns. BMC Evol Biol 10:47CrossRefPubMedPubMedCentralGoogle Scholar
  42. Lorenz R, Bernhart S, Honer zu Siederdissen C, Tafer H, Flamm C, Stadler P, Hofacker I (2011) ViennaRNA Package 2.0. Algorithms Mol Biol 6:26Google Scholar
  43. Marlétaz F, Gilles A, Caubit X, Perez Y, Dossat C, Samain S, Gyapay G, Wincker P, Le Parco Y (2008) Chaetognath transcriptome reveals ancestral and unique features among bilaterians. Genome Biol 9:R94CrossRefPubMedPubMedCentralGoogle Scholar
  44. Maroney PA, Hannon GJ, Shambaugh JD, Nilsen TW (1991) Intramolecular base pairing between the nematode spliced leader and its 5′ splice site is not essential for trans-splicing in vitro. EMBO J 10:3869–3875PubMedPubMedCentralGoogle Scholar
  45. Maroney PA, Denker JA, Darzynkiewicz E, Laneve R, Nilsen TW (1995) Most mRNAs in the nematode Ascaris lumbricoides are trans-spliced: a role for spliced leader addition in translational efficiency. RNA 1:714–723PubMedPubMedCentralGoogle Scholar
  46. Maroney PA, Yu YT, Jankowska M, Nilsen TW (1996) Direct analysis of nematode cis- and trans-spliceosomes: a functional role for U5 snRNA in spliced leader addition trans-splicing and the identification of novel Sm snRNPs. RNA 2:735–745PubMedPubMedCentralGoogle Scholar
  47. Marz M, Vanzo N, Stadler PF (2010) Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history. J Bioinf Comput Biol 8:1–17CrossRefGoogle Scholar
  48. Mateášiková-Kováčová B, Vesteg M, Drahovská H, Záhonová K, Vacula R, Krajčovič J (2012) Nucleus-encoded mRNAs for chloroplast proteins GapA, PetA, and PsbO are trans-spliced in the flagellate Euglena gracilis irrespective of light and plastid function. J Eukaryot Microbiol 59:651–653CrossRefPubMedGoogle Scholar
  49. Matera AG, Wang Z (2014) A day in the life of the spliceosome. Nat Rev Mol Cell Biol 15:108–121CrossRefPubMedPubMedCentralGoogle Scholar
  50. Miller SI, Landfear SM, Wirth DF (1986) Cloning and characterization of a Leishmania gene encoding a RNA spliced leader sequence. Nucl Acids Res 14:7341–7360CrossRefPubMedPubMedCentralGoogle Scholar
  51. Muhich ML, Hughes DE, Simpson AM, Simpson L (1987) The monogenetic kinetoplastid protozoan, Crithidia fasciculata, contains a transcriptionally active, multicopy mini-exon sequence. Nucl Acids Res 15:3141–3153CrossRefPubMedPubMedCentralGoogle Scholar
  52. Nilsen TW (1993) Trans-splicing of nematode premessenger RNA. Annu Rev Microbiol 47:413–440CrossRefPubMedGoogle Scholar
  53. Nilsen TW (1995) trans-splicing: an update. Mol Biochem Parasitol 73:1–6CrossRefPubMedGoogle Scholar
  54. Nilsen TW (2001) Evolutionary origin of SL-addition trans-splicing: still an enigma. Trends Genet 17:678–680CrossRefPubMedGoogle Scholar
  55. Nowack ECM, Price DC, Bhattacharya D, Singer A, Melkonian M, Grossman AR (2016) Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora. Proc Natl Acad Sci USA 113:12214–12219CrossRefPubMedPubMedCentralGoogle Scholar
  56. Palfi Z, Schimanski B, Güntze A, Lücke S, Bindereif A (2005) U1 small nuclear RNP from Trypanosoma brucei: a minimal U1 snRNA with unusual protein components. Nucl Acids Res 8:2493–2503CrossRefGoogle Scholar
  57. Pouchkina-Stantcheva NN, Tunnacliffe A (2005) Spliced leader RNA-mediated trans-splicing in phylum Rotifera. Mol Biol Evol 22:1482–1489CrossRefPubMedGoogle Scholar
  58. Protasio AV, Tsai IJ, Babbage A et al (2012) A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. PLoS Negl Trop Dis 6:e1455CrossRefPubMedPubMedCentralGoogle Scholar
  59. Rajkovic A, Davis RE, Simonsen JN, Rottman FM (1990) A spliced leader is present on a subset of mRNAs from the human parasite Schistosoma mansoni. Proc Natl Acad Sci USA 87:8879–8883CrossRefPubMedPubMedCentralGoogle Scholar
  60. Rossi A, Ross EJ, Jack A, Sánchez Alvarado A (2014) Molecular cloning and characterization of SL3: a stem cell-specific SL RNA from the planarian Schmidtea mediterranea. Gene 533:156–167CrossRefPubMedGoogle Scholar
  61. Roy SW (2017) Genomic and transcriptomic analysis reveals spliced leader trans-splicing in cryptomonads. Genome Biol Evol 9:468–473CrossRefPubMedGoogle Scholar
  62. Russell AG, Charette JM, Spencer DF, Gray MW (2006) An early evolutionary origin for the minor spliceosome. Nature 443:863–866CrossRefPubMedGoogle Scholar
  63. Siebert S, Backofen R (2005) MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics 21:3352–3359CrossRefPubMedGoogle Scholar
  64. Siegel TN, Hekstra DR, Wang X, Dewell S, Cross GAM (2010) Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites. Nucl Acids Res 38:4946–4957CrossRefPubMedPubMedCentralGoogle Scholar
  65. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539CrossRefPubMedPubMedCentralGoogle Scholar
  66. Stover NA, Steele RE (2001) Trans-spliced leader addition to mRNAs in a cnidarian. Proc Natl Acad Sci USA 98:5693–5698CrossRefPubMedPubMedCentralGoogle Scholar
  67. Stover NA, Kaye MS, Cavalcanti ARO (2006) Spliced leader trans-splicing. Curr Biol 16:R8–R9CrossRefPubMedGoogle Scholar
  68. Sturm NR, Yu MC, Campbell DA (1999) Transcription termination and 3′-end processing of the spliced leader RNA in kinetoplastids. Mol Cell Biol 19:1595–1604CrossRefPubMedPubMedCentralGoogle Scholar
  69. Thomas JD, Conrad RC, Blumenthal T (1988) The C. elegans trans-spliced leader RNA is bound to Sm and has a trimethylguanosine cap. Cell 54:533–539CrossRefPubMedGoogle Scholar
  70. Torarinsson E, Lindgreen S (2008) WAR: Webserver for aligning structural RNAs. Nucleic Acids Res 36:W79–W84CrossRefPubMedPubMedCentralGoogle Scholar
  71. Van Doren K, Hirsh D (1990) mRNAs that mature through trans-splicing in Caenorhabditis elegans have a trimethylguanosine cap at their 5′ termini. Mol Cell Biol 10:1769–1772CrossRefPubMedPubMedCentralGoogle Scholar
  72. Vesteg M, Krajčovič J (2011) The falsifiability of the models for the origin of eukaryotes. Curr Genet 57:367–390CrossRefPubMedGoogle Scholar
  73. Vesteg M, Vacula R, Burey S, Löffelhardt W, Drahovská H, Martin W, Krajčovič J (2009) Expression of nucleus-encoded genes for chloroplast proteins in the flagellate Euglena gracilis. J Eukaryot Microbiol 56:159–166CrossRefPubMedGoogle Scholar
  74. Vesteg M, Vacula R, Steiner JM, Mateášiková B, Löffelhardt W, Brejová B, Krajčovič J (2010) A possible role for short introns in the acquisition of stroma-targeting peptides in the flagellate Euglena gracilis. DNA Res 17:223–231CrossRefPubMedPubMedCentralGoogle Scholar
  75. Vesteg M, Šándorová Z, Krajčovič J (2012) Selective forces for the origin of spliceosomes. J Mol Evol 74:226–231CrossRefPubMedGoogle Scholar
  76. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189–1191CrossRefPubMedPubMedCentralGoogle Scholar
  77. Yang F, Xu D, Zhuang Y et al (2015) Spliced leader RNA trans-splicing discovered in copepods. Sci Rep 5:17411CrossRefPubMedPubMedCentralGoogle Scholar
  78. Yeats B, Matsumoto J, Mortimer SI, Shoguchi E, Satoh N, Hastings KE (2010) SL RNA genes of the ascidian tunicates Ciona intestinalis and Ciona savignyi. Zool Sci 27:171–180CrossRefPubMedGoogle Scholar
  79. Yu YT, Maroney PA, Nilsen TW (1993) Functional reconstitution of U6 snRNA in nematode cis- and trans-splicing: u6 can serve as both a branch acceptor and a 5′ exon. Cell 75:1049–1059CrossRefPubMedGoogle Scholar
  80. Zayas RM, Bold TD, Newmark PA (2005) Spliced-leader trans-splicing in freshwater planarians. Mol Biol Evol 22:2048–2054CrossRefPubMedGoogle Scholar
  81. Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, Gaasterland T, Lin S (2007) Spliced leader RNA trans-splicing in dinoflagellates. Proc Nat Acad Sci USA 104:4618–4623CrossRefPubMedPubMedCentralGoogle Scholar
  82. Zhang H, Campbell DA, Sturm NR, Lin S (2009) Dinoflagellate spliced leader RNA genes display a variety of sequences and genomic arrangements. Mol Biol Evol 26:1757–1771CrossRefPubMedPubMedCentralGoogle Scholar
  83. Zhang H, Campbell DA, Sturm NR, Dungan CF, Lin S (2011) Spliced leader RNAs, mitochondrial gene frameshifts and multi-protein phylogeny expand support for the genus Perkinsus as a unique group of alveolates. PLoS ONE 6:e19933CrossRefPubMedPubMedCentralGoogle Scholar
  84. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucl Acids Res 31:3406–3415CrossRefPubMedPubMedCentralGoogle Scholar

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Authors and Affiliations

  1. 1.Department of RNA Biology, Institute of Molecular GeneticsAcademy of Sciences of the Czech RepublicPragueCzech Republic
  2. 2.Department of Biology, Faculty of Natural SciencesUniversity of ss. Cyril and MethodiusTrnavaSlovakia
  3. 3.Department of Biology and Ecology, Faculty of Natural SciencesMatej Bel UniversityBanská BystricaSlovakia

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