Conserved intron positions in ancient protein modules

Biology Direct

Volumn 2, Issue , 2007, Pages

  de Roos, Albert D G ^a  

^a Syncyte BioIntelligence   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA; PROKARYOTA;

EID: 34248149860     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-2-7     Document Type: Review

References (49)

1. Mattick JS Introns: Evolution and function Curr Opin Genet Dev 1994 4 823-31 10.1016/0959-437X(94)90066-3 7888751
2. Logsdon JM The recent origins of spliceosomal introns revisited Curr Opin Genet Dev 1998 8 637-648 10.1016/S0959-437X(98)80031-2 9914210
3. Rzhetsky A Ayala FJ The enigma of intron origins Cell Mol Life Sci 1999 55 3-6 10.1007/s000180050264
4. Fedorova L Fedorov A Introns in gene evolution Genetica 2003 118 123-31 10.1023/A:1024145407467 12868603
5. Doolittle WF Genes in pieces: Were they ever together? Nature 1987 272 581-582 10.1038/272581a0
6. Gilbert W The exon theory of genes Cold Spring Harb Symp Quant Biol 1987 52 901-5 2456887
7. Rogers JH The role of introns in evolution FEBS Lett 1990 268 339-43 10.1016/0014-5793(90)81282-S 2200714
8. Patthy L Exons-original building blocks of proteins? Bioessays 1991 13 187-92 10.1002/bies.950130408 1859398
9. Palmer JD Logsdon JM Jr The recent origins of introns Curr Opin Genet Dev 1991 1 470-7 10.1016/S0959-437X(05)80194-7 1822279
10. Cavalier-Smith T Intron phylogeny: A new hypothesis Trends Genet 1991 7 145-8 2068786
11. Cho G Doolittle RF Intron distribution in ancient paralogs supports random insertion and not random loss J Mol Evol 1997 44 573-584 10.1007/ PL00006180 9169549
12. De Souza SJ Long M Klein RJ Roy S Lin S Gilbert W Toward a resolution of the introns early/late debate: Only phase zero introns are correlated with the structure of ancient proteins Proc Natl Acad Sci USA 1998 95 5094-9 20219 9560234 10.1073/pnas.95.9.5094
13. De Souza SJ The emergence of a synthetic theory of intron evolution Genetica 2003 118 117-121 10.1023/A:1024193323397 12868602
14. Roy SW Recent evidence for Exon Theory of Genes Genetica 2003 118 251-266 10.1023/A:1024190617462 12868614
15. Rodriguez-Trelles F Tarrio R Ayala FJ Origins and evolution of spliceosomal introns Annu Rev Genet 2006 40 47-76 10.1146/ annurev.genet.40.110405.090625 17094737
16. Reanney D RNA splicing and polynucleotide evolution Nature 1979 277 598-600 10.1038/277598b0 423958
17. Poole AM Jeffares DC Penny D The path from the RNA world J Mol Evol 1998 46 1-17 10.1007/PL00006275 9419221
18. De Roos ADG Origins of introns based on the definition of exon modules and their conserved interfaces Bioinformatics 2005 21 2-9 10.1093/ bioinformatics/bth475 15308547
19. Roy SW Gilbert W The evolution of spliceosomal introns: Patterns, puzzles and progress Nat Rev Genet 2006 7 211-21 16485020
20. Kersanach R Brinkmann H Liaud MF Zhang DX Martin W Cerff R Five identical intron positions in ancient duplicated genes of eubacterial origin Nature 1994 367 387-9 10.1038/367387a0 8114942
21. Fedorov A Cao X Saxonov S de Souza SJ Roy SW Gilbert W Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns Proc Natl Acad Sci USA 2001 98 13177-82 60844 11687643 10.1073/pnas.231491498
22. Fedorov A Merican AF Gilbert W Large-scale comparison of intron positions among animal, plant, and fungal genes Proc Natl Acad Sci USA 2002 99 16128-33 138576 12444254 10.1073/pnas.242624899
23. Rogozin IB Wolf YI Sorokin AV Mirkin BG Koonin EV Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution Curr Biol 2003 13 1512-7 10.1016/S0960-9822(03)00558-X 12956953
24. Coghlan A Wolfe KH Origins of recently gained introns in Caenorhabditis Proc Natl Acad Sci USA 2004 101 11362-7 509176 15243155 10.1073/ pnas.0308192101
25. Babenko VN Rogozin IB Mekhedov SL Koonin EV Prevalence of intron gain over intron loss in the evolution of paralogous gene families Nucleic Acids Res 2004 14 3724-33 10.1093/nar/gkh686
26. Roy SW Penny D Smoke without fire: Most reported cases of intron gain in nematodes instead reflect intron losses Mol Biol Evol 2006 23 2259-62 10.1093/molbev/msl098 16943250
27. Jeffares DC Mourier T Penny D The biology of intron gain and loss Trends Genet 2006 22 16-22 10.1016/j.tig.2005.10.006 16290250
28. Koonin EV The origin of introns and their role in eukaryogenesis: A compromise solution to the introns-early versus introns-late debate? Biol Direct 2006 1 22 1570339 16907971 10.1186/1745-6150-1-22
29. Blake CC Exons encode protein functional units Nature 1979 277 598 10.1038/277598a0 423957
30. Darnell JE Doolittle WF Speculations on the early course of evolution Proc Natl Acad Sci USA 1986 83 1271-5 323057 2419905 10.1073/ pnas.83.5.1271
31. Gilbert W Marchionni M McKnight G On the antiquity of introns Cell 1986 46 151-3 10.1016/0092-8674(86)90730-0 2424613
32. Dorit RL Schoenbach L Gilbert W How big is the universe of exons? Science 1990 250 1377-82 10.1126/science.2255907 2255907
33. Long M Rosenberg C Gilbert W Intron phase correlations and the evolution of the intron/exon structure of genes Proc Natl Acad Sci USA 1995 92 12495-9 40384 8618928 10.1073/pnas.92.26.12495
34. Go M Protein structures and split genes Adv Biophys 1985 19 91-131 10.1016/0065-227X(85)90052-8 3915183
35. De Souza SJ Long M Schoenbach L Roy SW Gilbert W Intron positions correlate with module boundaries in ancient proteins Proc Natl Acad Sci USA 1996 93 14632-6 26186 8962105 10.1073/pnas.93.25.14632
36. Roy SW Nosaka M de Souza SJ Gilbert W Centripetal modules and ancient introns Gene 1999 238 85-91 10.1016/S0378-1119(99)00292-9 10570987
37. Sakharkar M Passetti F de Souza JE Long M de Souza SJ ExInt: An Exon Intron Database Nucleic Acids Res 2002 30 191-4 99089 11752290 10.1093/ nar/30.1.191
38. Roy SW Gilbert W Resolution of a deep animal divergence by the pattern of intron conservation Proc Natl Acad Sci USA 2005 102 4403-8 555513 15769859 10.1073/pnas.0409891102
39. Sakharkar MK Chow VT Kangueane P Distributions of exons and introns in the human genome In Silico Biol 4 387-93 15217358
40. Endo T Fedorov A de Souza SJ Gilbert W Do introns favor or avoid regions of amino acid conservation? Mol Biol Evol 2002 19 521-5 11919293
41. Nguyen HD Yoshihama M Kenmochi N Phase distribution of spliceosomal introns: Implications for intron origin BMC Evol Biol 2006 6 69 1574350 16959043 10.1186/1471-2148-6-69
42. Roy SW Gilbert W Complex early genes Proc Natl Acad Sci USA 2005 102 1986-91 548548 15687506 10.1073/pnas.0408355101
43. Slamovits CH Keeling PJ A high density of ancient spliceosomal introns in oxymonad excavates BMC Evol Biol 2006 6 34 1501061 16638131 10.1186/ 1471-2148-6-34
44. Archibald JM O'Kelly CJ Doolittle WF The chaperonin genes of jakobid and jakobid-like flagellates: Implications for eukaryotic evolution Mol Biol Evol 2002 19 422-31 11919283
45. Gilbert W Glynias M On the ancient nature of introns Gene 1993 135 137-44 10.1016/0378-1119(93)90058-B 8276250
46. De Roos ADG The origin of the eukaryotic cell based on conservation of existing interfaces Artif Life 2006 12 513-23 10.1162/artl.2006.12.4.513 16953783
47. Poole A Jeffares D Penny D Early evolution: Prokaryotes, the new kids on the block Bioessays 1999 21 880-9 10.1002/ (SICI)1521-1878(199910)21:10<880::AID-BIES11>3.0.CO;2-P 10497339
48. Marchler-Bauer A Anderson JB DeWeese-Scott C Fedorova ND Geer LY He S Hurwitz DI Jackson JD Jacobs AR Lanczycki CJ Liebert CA Liu C Madej T Marchler GH Mazumder R Nikolskaya AN Panchenko AR Rao BS Shoemaker BA Simonyan V Song JS Thiessen PA Vasudevan S Wang Y Yamashita RA Yin JJ Bryant SH CDD: A curated Entrez database of conserved domain alignments Nucleic Acids Res 2003 31 383-387 165534 12520028 10.1093/nar/gkg087
49. Dibb NJ Newman AJ Evidence that introns arose at proto-splice sites EMBO J 1989 8 2015-21 401080 2792080