Origination of the split structure of spliceosomal genes from random genetic sequences

PLoS ONE

Volumn 3, Issue 10, 2008, Pages

  Regulapati, Rahul ^a   Bhasi, Ashwini ^b   Singh, Chandan Kumar ^c   Senapathy, Periannan ^b,c  

^a INDIAN INSTITUTE OF TECHNOLOGY MADRAS   (India)

^b Genome International Corporation   (United States)

^c International Center for Advanced Genomics and Proteomics   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DNA SEQUENCE; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; EXON; GENE STRUCTURE; GENOME SIZE; HUMAN; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMODIUM FALCIPARUM; RNA SEQUENCE; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SEQUENCE ANALYSIS; SPECIES COMPARISON; SPLICEOSOME; STOP CODON; STREPTOCOCCUS PNEUMONIAE; ANIMAL; BIOLOGICAL MODEL; EUKARYOTIC CELL; GENE; GENETICS; GENOME; PROKARYOTIC CELL;

EUKARYOTA;

ANIMALS; BASE SEQUENCE; EUKARYOTIC CELLS; EXONS; GENES; GENOME; HUMANS; INTRONS; MODELS, GENETIC; OPEN READING FRAMES; PROKARYOTIC CELLS; SPLICEOSOMES;

EID: 55149091552     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003456     Document Type: Article

References (41)

1. Roy SW, Gilbert W (2006) The evolution of spliceosomal introns: patterns, puzzels and progress. Nature Rev Genet 7: 211-221.
2. Roy SW, Gilbert W (2005) Complex early genes. Proc Natl Acad Sci U S A 102: 1986-1991.
3. Roy SW, Gilbert W (2005) Rates of intron loss and gain: implications for early eukaryotic evolution. Proc Natl Acad Sci U S A 102: 5773-5778.
4. Rogozin IB Wolf YI, Sorokin AV, Mirkin BG, Koonin EV (2003) Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 13: 1512-1517.
5. Roy SW, Fedorov A, Gilbert W (2003) Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci U S A 100: 7158-7162.
6. Gilbert W (1987) The exor, theory of genes. Cold Spring Harb Symp Quant Biol 52: 901-905.
7. de Souza SJ (2003) The emergence of a synthetic theory of intron evolution. Genetica 118: 117-121.
8. Roy SW (2003) Recent evidence for the exon theory of genes. Genetica 118: 251-266.
9. Logsdon JM Jr (2004) Worm genomes hold the smoking guns of intron gain. Proc Natl Acad Sci U S A 101: 11195-11196.
10. Qiu WG, Schisler N, Stoltzfus A (2004) The evolutionary gain of spliceosomal introns: sequence and phase preferences. Mol Biol Evol 21: 1252-1263.
11. Lynch M, Richardson AO (2002) The evolution of spliceosomal introns. Curr Opin Genet Dev 12: 701-710.
12. Lewin B (1994) Genes V. NY: Oxford University Press.
13. Nei M (1987) Molecular Evolutionary Genetics. NY: Columbia University Press.
14. McCullough AJ, Berget SM (1997) G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol Cell Biol 7: 4562-4571.
15. Sirand-Pugnet P, Durosay P, Brody E, Marie J (1995) An intronic (A/U)GGG repeat enhances the splicing of an alternative intron of the chicken beta-tropomyosin pre-mRNA. Nucleic Acids Res 23: 3501-3507.
16. Gilbert W (1978) Why genes in pieces? Nature 271: 501-516.
17. Doolittle WF (1978) Genes in pieces: were they ever together? Nature 272: 581-582.
18. Blake CCF (1978) Do Genes in pieces imply proteins in pieces. Nature 273: 267.
19. Cavalier-Smith T (1985) Selfish DNA and the origin of introns. Nature 315: 283-284.
20. Palmer JD, Logsdon JM Jr (1991) The recent origins of introns. Curr Opin Genet Dev 1: 470-477.
21. Lynch M (2002) Intron evolution as a population-genetic process. Proc Natl Acad Sci U S A 99: 6118-6123.
22. Long M, Rosenberg C (2000) Testing the "proto-splice sites" model of intron origin: evidence from analysis of intron phase correlations. Mol Biol Evol 17: 1789-1796.
23. de Souza SJ, Long M, Schoenbach L, Roy SW, Gilbert W (1996) Intron positions correlate with module boundaries in ancient proteins. Proc Natl Acad Sci U S A 93: 14632-14636.
24. Fedorova L, Fedorov A (2003) Introns in gene evolution. Genetica 118: 123-131.
25. de Souza SJ, Long M, Robert JK, Roy S, Lin S, et al. (1998) 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 U S A 95: 5094-5099.
26. Rodríguez-Trelles F, Tarrío R, Ayala FJ (2006) Origins and evolution of spliceosomal introns. Annu Rev Genet 40: 47-76.
27. Senapathy P (1986) Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications. Proc Natl Acad Sci U S A 83: 2133-2137.
28. Lu Y, Freeland S (2006) On the evolution of the standard amino-acid alphabet. Genome Biology 7: 102.
29. Subak-Sharpe H, Burk RR, Crawford LV, Morrison JM, Hay J, et al. (1966) An approach to evolutionary relationships of mammalian DNA viruses through analysis of the pattern of nearest neighbor base sequences. Cold Spring Harb Symp Quant Biol 31: 737-748.
30. Senapathy P (1995) Introns and the origin of protein-coding genes. Science 268: 1366-1367.
31. Senapathy P (1988) Possible evolution of splice-junction signals in eukaryotic genes from stop codons. Proc Natl Acad Sci U S A 85: 1129-1133.
32. Bhattacharya D, Friedl T, Damberger S (1996) Nuclear-encoded rDNA group I introns: origin and phylogenetic relationships of insertion site lineages in the green algae. Mol Biol Evol 13: 978-989.
33. Robart AR, Zimmerly S (2005) Group II intron retroelementts: function and diversity. Cytogenet. Genome Res 110: 589-597.
34. Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 1: R17-R29.
35. Collins L, Penny D (2005) Complex spliceosomal organization ancestral to extant eukaryotes. Molecular Biology and Evolution 22: 1053-1066.
36. Senapathy P (1994) Independent Birth of Organisms. Madison, Wisconsin: Genome Press.
37. Caetano-Anollés G, Caetano-Anollés D (2003) An Evolutionarily Structured Universe of Protein Architecture. Genome Res 13: 1563-1571.
38. Forterre P, Philippe H (1999) Where is the root of the universal tree of life? BioEssays 21: 871-879.
39. Labedan B, et al. (1999) The Evolutionary History of Carbamoyl transferases: A Complex Set of Paralogous Genes Was Already Present in the Last Universal Common Ancestor. J Mol Evol 49: 461-473.
40. Glansdorff N, Xu Y, Labedan B (2008) The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biology Direct 3: 29.
41. Bhasi A, Pandey RV, Utharasamy SP, Senapathy P (2007) EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes. Bioinformatics 23: 1815-23.