Selective forces for the origin of spliceosomes

Journal of Molecular Evolution

Volumn 74, Issue 3-4, 2012, Pages 226-231

  Vesteg, Matej ^a   Šándorová, Zuzana ^a   Krajčovič, Juraj ^a  

^a Physics and Informatics   (Slovakia)

Author keywords

Constructive neutral evolution; Ribosome; RNA world; Selection; Trans splicing

Indexed keywords

ARTICLE; BACTERIAL GENE; GENETICS; INTRON; MOLECULAR EVOLUTION; RIBOSOME; RNA SPLICING; SPLICEOSOME;

EVOLUTION, MOLECULAR; GENES, BACTERIAL; INTRONS; RIBOSOMES; RNA SPLICING; SPLICEOSOMES;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 84861846286     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-012-9494-3     Document Type: Article

References (55)

1. SG Andersson C Alsmark B Canbäck W Davids C Frank O Karlberg L Klasson B Antoine-Legault A Mira I Tamas 2002 Comparative genomics of microbial pathogens and symbionts Bioinformatics 18 S17 12385978 10.1093/bioinformatics/ 18.suppl-2.S17
2. A Audibert D Weil F Dautry 2002 In vivo kinetics of mRNA splicing and transport in mammalian cells Mol Cell Biol 22 6706 6718 12215528 10.1128/MCB.22.19.6706-6718.2002 1:CAS:528:DC%2BD38XntFansbw%3D
3. G Baurén L Wieslander 1994 Splicing of balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription Cell 76 183 192 8287477 10.1016/0092-8674(94)90182-1
4. AL Beyer YN Osheim 1988 Splice site selection, rate of splicing and alternative splicing on nascent transcripts Genes Dev 2 754 765 3138163 10.1101/gad.2.6.754 1:CAS:528:DyaL1cXkvVOgs78%3D
5. CC Blake 1978 Do genes-in-pieces imply proteins-in-pieces? Nature 273 267 10.1038/273267a0
6. MC Boerlijst P Hogeweg 1991 Spiral wave structures in prebiotic evolution-hypercycles stable against parasites Phys D 48 17 28 10.1016/0167-2789(91)90049-F
7. Cech TR (2011) The RNA world in context. Cold Spring Harb Perspect Biol. doi: 10.1101/cshperspect.a006742
8. L Collins D Penny 2005 Complex spliceosomal organization ancestral to extant eukaryotes Mol Biol Evol 22 1053 1066 15659557 10.1093/molbev/msi091 1:CAS:528:DC%2BD2MXjtFOqtrY%3D
9. PS Covello MW Gray 1993 On the evolution of RNA editing Trends Genet 9 265 268 8379005 10.1016/0168-9525(93)90011-6 1:CAS:528:DyaK3sXmtF2lsbw%3D
10. R Derelle T Momose M Manuel C Da Silva P Wincker E Houliston 2010 Convergent origins and rapid evolution of spliced leader trans-splicing in metazoa: insights from the ctenophora and hydrozoa RNA 16 696 707 20142326 10.1261/rna.1975210 1:CAS:528:DC%2BC3cXktlOks7w%3D
11. WF Doolittle 1978 Genes in pieces: were they ever together? Nature 272 581 582 10.1038/272581a0
12. WF Doolittle J Lukeš JM Archibald PJ Keeling MW Gray 2011 Comment on "Does constructive neutral evolution play an important role in the origin of cellular complexity?" BioEssays 33 427 429 21538416 10.1002/bies.201100039
13. V Douris MJ Telford M Averof 2010 Evidence for multiple independent origins of trans-splicing in metazoa Mol Biol Evol 27 684 693 19942614 10.1093/molbev/msp286 1:CAS:528:DC%2BC3cXitlarsL0%3D
14. O Fedorova A Solem AM Pyle 2010 Protein-facilitated folding of group II intron ribozymes J Mol Biol 397 799 813 20138894 10.1016/j.jmb.2010.02.001 1:CAS:528:DC%2BC3cXjt1WgsrY%3D
15. P Flegontov MW Gray G Burger J Lukeš 2011 Gene fragmentation: a key to mitochondrial genome evolution in euglenozoa? Curr Genet 57 225 232 21544620 10.1007/s00294-011-0340-8 1:CAS:528:DC%2BC3MXptFGjtLc%3D
16. P Forterre 1995 Thermoreduction, a hypothesis for the origin of prokaryotes C R Acad Sci Paris Life Sci 318 414 422
17. P Forterre 2002 The origin of DNA genomes and DNA replication proteins Curr Opin Microbiol 5 525 532 12354562 10.1016/S1369-5274(02)00360-0 1:CAS:528:DC%2BD38Xnt1Ggu7o%3D
18. P Forterre 2005 Two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells Biochimie 87 793 803 16164990 10.1016/j.biochi.2005.03.015 1:CAS:528:DC%2BD2MXhtVSmt7rF
19. P Forterre 2006 Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain Proc Natl Acad Sci USA 103 3669 3674 16505372 10.1073/pnas.0510333103 1:CAS:528:DC%2BD28XivFWju7c%3D
20. W Gilbert 1978 Why genes in pieces? Nature 271 501 622185 10.1038/271501a0 1:STN:280:DyaE1c%2Fpt1Chtw%3D%3D
21. Gilbert W, de Souza SJ (1999) Introns and the RNA world. In: Gesteland RF, Cech TR, Atkins RF (eds) The RNA world, the nature of modern RNA suggests a prebiotic RNA World, vol. 37, 2nd edn. CSHL Press, New York, pp 221-231
22. MW Gray J Lukeš JM Archibald PJ Keeling WF Doolitle 2010 Cell biology. Irremediable complexity? Science 12 920 921 10.1126/science.1198594
23. KEM Hastings 2005 SL trans-splicing: easy come or easy go? Trends Genet 21 240 247 15797620 10.1016/j.tig.2005.02.005 1:CAS:528:DC%2BD2MXis1KjtLs%3D
24. DC Jeffares AM Poole D Penny 1998 Relics from RNA world J Mol Evol 46 18 36 9419222 10.1007/PL00006280 1:CAS:528:DyaK1cXks1aisw%3D%3D
25. O Kessler Y Jiang LA Chasin 1993 Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA Mol Cell Biol 13 6211 6222 8413221 1:CAS:528:DyaK3sXms1Ogs78%3D
26. CG Kurland B Canbäck OG Berg 2007 The origins of modern proteomes Biochimie 89 1454 1463 17949885 10.1016/j.biochi.2007.09.004 1:CAS:528:DC%2BD2sXhtlGjt7zF
27. KM Lang RA Spritz 1987 In vitro splicing pathways of pre-mRNAs containing multiple intervening sequences Mol Cell Biol 7 3428 3437 3500397 1:CAS:528:DyaL2sXlvFaiur8%3D
28. Lukeš J, Leander BS, Keeling PJ (2009) Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc Natl Acad Sci USA 106:9963-9970
29. J Lukeš JM Archibald PJ Keeling WF Doolittle MW Gray 2011 How a neutral evolutionary ratchet can build cellular complexity IUBMB Life 63 528 537 21698757 10.1002/iub.489
30. Lynch M (2007) The origins of genome architecture. Sinauer, Sunderland
31. S Martínez-Calvillo JC Vizuet-de-Rueda LE Florencio- Martínez RG Manning-Cela EE Figueroa-Angulo 2010 Gene expression in trypanosomatid parasites J Biomed Biotech 2010 525241 10.1155/2010/525241
32. M Marz N Vanzo PF Stadler 2010 Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history J Bioinform Comput Biol 8 1 17 20183871 10.1142/S0219720010004525 1:CAS:528:DC%2BC3cXisVCgtb0%3D
33. AK Panigrahi NL Ernst GJ Domingo M Fleck R Salavati KD Stuart 2006 Compositionally and functionally distinct editosomes in Trypanosoma brucei RNA 2 1038 1049 10.1261/rna.45506
34. D Penny MP Hoeppner AM Poole DC Jeffares 2009 An overview of the introns-first theory J Mol Evol 69 527 540 19777149 10.1007/s00239-009-9279-5 1:CAS:528:DC%2BD1MXhsFaqt77F
35. AM Poole DT Logan 2005 Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? Mol Biol Evol 22 1444 1455 15774424 10.1093/molbev/msi132 1:CAS:528:DC%2BD2MXksFGktbo%3D
36. AM Poole D Jeffares D Penny 1998 The path from RNA world J Mol Evol 46 1 17 9419221 10.1007/PL00006275 1:CAS:528:DyaK1cXks1WisA%3D%3D
37. AM Poole D Jeffares D Penny 1999 Prokaryotes, the new kids on the block BioEssays 21 880 889 10497339 10.1002/(SICI)1521-1878(199910)21:10<880::AID- BIES11>3.0.CO;2-P 1:STN:280:DyaK1MvivVartQ%3D%3D
38. AM Pyle O Fedorova C Waldsich 2007 Folding of group II introns: a model for large multidomain RNAs? Trends Biochem Sci 32 251 10.1016/j.tibs.2007.01.005
39. M Roitzsch AM Pyle 2009 The linear form of group II intron catalyzes efficient autocatalytic reverse splicing, establishing a potential for mobility RNA 15 473 482 19168748 10.1261/rna.1392009 1:CAS:528:DC%2BD1MXis1agtrs%3D
40. JL Sachs JJ Bull 2005 Experimental evolution of conflict mediation between genomes Proc Natl Acad Sci USA 102 390 395 15630098 10.1073/pnas. 0405738102 1:CAS:528:DC%2BD2MXptFSktw%3D%3D
41. U Schmidt M Podar U Stahl PS Perlman 1996 Mutations of the two-nucleotide bulge of D5 of a group II intron block splicing in vitro and in vivo: phenotypes and suppressor mutations RNA 2 1161 1172 8903346 1:CAS:528: DyaK28XmslKmsro%3D
42. J Singh RA Padgett 2009 Rates of in situ transcription and splicing in large human genes Nat Struct Mol Biol 16 1128 1133 19820712 10.1038/nsmb.1666 1:CAS:528:DC%2BD1MXht1Cmu77N
43. A Stoltzfus 1999 On the possibility of constructive neutral evolution J Mol Evol 49 169 181 10441669 10.1007/PL00006540 1:CAS:528:DyaK1MXltFSksbY%3D
44. S Valadkhan Y Jaladat 2010 The spliceosomal proteome: at the heart of the largest cellular ribonucleoprotein machine Proteomics 10 4128 4141 21080498 10.1002/pmic.201000354 1:CAS:528:DC%2BC3cXhsVaitrzN
45. DL Valentine 2007 Adaptations to energy stress dictate the ecology and evolution of the Archaea Nat Rev Microbiol 5 316 323 17334387 10.1038/nrmicro1619 1:CAS:528:DC%2BD2sXivVGltrk%3D
46. M Vesteg J Krajčovič 2008 Origin of eukaryotic cells as a symbiosis of parasitic α-proteobacteria in the periplasm of two-membrane-bounded sexual pre-karyotes Commun Integr Biol 1 104 113 19513207 10.4161/cib.1.1.6349 1:CAS:528:DC%2BD1MXht1Kms73I
47. M Vesteg J Krajčovič 2011 The falsifiability of the models for the origin of eukaryotes Curr Genet 57 367 390 22008946 10.1007/s00294-011- 0357-z 1:CAS:528:DC%2BC3MXhsVKht7%2FN
48. M Vesteg R Vacula S Burey W Löffelhardt H Drahovská W Martin J Krajčovič 2009 Expression of nucleus-encoded genes for chloroplast proteins in the flagellate Euglena gracilis J Eukaryot Microbiol 56 159 166 19457056 10.1111/j.1550-7408.2008.00383.x 1:CAS:528:DC%2BD1MXltlymtL4%3D
49. M Vesteg R Vacula JM Steiner B Mateášiková W Löffelhardt B Brejová J Krajčovič 2010 A possible role for short introns in the acquisition of stroma-targeting peptides in the flagellate Euglena gracilis DNA Res 17 223 231 20587589 10.1093/dnares/dsq015 1:CAS:528:DC%2BC3cXhtVanurfO
50. JJ Wernegreen 2005 For better or worse: genomic consequences of intracellular mutualism and parasitism Curr Opin Genet Dev 15 572 583 16230003 10.1016/j.gde.2005.09.013 1:CAS:528:DC%2BD2MXhtFyks7%2FO
51. CR Woese 1998 The universal ancestor Proc Natl Acad Sci USA 95 6854 6859 9618502 10.1073/pnas.95.12.6854 1:CAS:528:DyaK1cXjslynu7w%3D
52. CR Woese 2000 Interpreting the universal phylogenetic tree Proc Natl Acad Sci USA 97 8392 8396 10900003 10.1073/pnas.97.15.8392 1:CAS:528: DC%2BD3cXlt1Ggtbc%3D
53. CR Woese 2001 Translation: in retrospect and prospect RNA 7 1055 1067 11497425 10.1017/S1355838201010615 1:CAS:528:DC%2BD3MXlvVGmt7w%3D
54. CR Woese 2002 On the evolution of cells Proc Natl Acad Sci USA 99 8742 8747 12077305 10.1073/pnas.132266999 1:CAS:528:DC%2BD38XltF2hsbc%3D
55. M Woolfit L Bromham 2003 Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes Mol Biol Evol 20 1545 1555 12832648 10.1093/molbev/msg167 1:CAS:528:DC%2BD3sXntlantbg%3D