The largest subunit of RNA polymerase II from the Glaucocystophyta: Functional constraint and short-branch exclusion in deep eukaryotic phylogeny

BMC Evolutionary Biology

Volumn 5, Issue , 2005, Pages

  Stiller, John W ^a   Harrell, Leslie ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; RNA POLYMERASE II;

BAYES THEOREM; CHEMISTRY; EVOLUTION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; PLANT; PLANT GENE; PROTEIN TERTIARY STRUCTURE; RED ALGA; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STATISTICAL MODEL; TIME;

BAYES THEOREM; BIOLOGICAL EVOLUTION; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; GENES, PLANT; MODELS, STATISTICAL; PHYLOGENY; PLANTS; PROTEIN STRUCTURE, TERTIARY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RHODOPHYTA; RNA POLYMERASE II; TIME FACTORS;

EID: 30744433373     PISSN: 14712148     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2148-5-71     Document Type: Article

References (87)

1. Klenk HP, Palm P, Lottspeich F, Zillig W: Component-H of the DNA-Dependent RNA Polymerases of Archaea Is Homologous to a Subunit Shared by the 3 Eucaryal Nuclear-RNA Polymerases. P Natl Acad Sci USA 1992, 89(1):407-410.
2. Leffers H, Gropp F, Lottspeich F, Zillig W, Garrett RA: Sequence, Organization, Transcription and Evolution of RNA Polymerase Subunit Genes from the Archaebacterial Extreme Halophiles Halobacterium halobium and Halococcus morrhuae. J Mol Biol 1989, 206(1):1-17.
3. Hirt RP, Logsdon JM, Healy B, Dorey MW, Doolittle WF, Embley TM: Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins. P Natl Acad Sci USA 1999, 96(2):580-585.
4. Stiller JW, Hall BD: Evolution of the RNA polymerase II C-terminal domain. Proc Natl Acad Sci USA 2002, 99(9):6091-6096.
5. Stiller JW, Hall BD: The origin of red algae: Implications for plastid evolution. Proc Natl Acad Sci USA 1997, 94(9):4520-4525.
6. Stiller JW, Riley J, Hall BD: Are red algae plants? A critical evaluation of three key molecular data sets. J Mol Evol 2001, 52(6):527-539.
7. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF: A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 2000, 290(5493):972-977.
8. Arisue N, Hasegawa M, Hashimoto T: Root of the eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data. Mol Biol Evol 2005, 22(3):409-420.
9. Dacks JB, Marinets A, Doolittle WF, Cavalier-Smith T, Logsdon JM: Analyses of RNA polymerase II genes from free-living protists: Phylogeny, long branch attraction, and the eukaryotic big bang. Mol Biol Evol 2002, 19(6):830-840.
10. Baldauf SL: The deep roots of eukaryotes. Science 2003, 300(5626):1703-1706.
11. Bhattacharya D, Medlin L: The Phylogeny of Plastids - a Review Based on Comparisons of Small-Subunit Ribosomal-RNA Coding Regions. J Phycol 1995, 31(4):489-498.
12. Ragan MA, Gutell RR: Are Red Algae Plants? Bot J Linn Soc 1995, 118(2):81-105.
13. Delwiche CF, Palmer JD: The origin of plastids and their spread via secondary symbiosis. Plant Syst Evol 1997:53-86.
14. Stiller JW, Reel DC, Johnson JC: A single origin of plastids revisited: Convergent evolution in organellar genome content. J Phycol 2003, 39(1):95-105.
15. Stiller JW: Weighing the evidence for a single origin of plastids. J Phycol 2003, 39(6):1283-1285.
16. Moreira D, Le Guyader H, Philippe H: The origin of red algae and the evolution of chloroplasts. Nature 2000, 405(6782):69-72.
17. Nozaki H, Matsuzaki M, Takahara M, Misumi O, Kuroiwa H, Hasegawa M, Shin-i T, Kohara Y, Ogasawara N, Kuroiwa T: The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids. J Mol Evol 2003, 56(4):485-497.
18. McFadden GI: Primary and secondary endosymbiosis and the origin of plastids. J Phycol 2001, 37(6):951-959.
19. Palmer JD: The symbiotic birth and spread of plastids: How many times and whodunit? J Phycol 2003, 39(1):4-11.
20. Keeling P: A brief history of plastids and their hosts. Protist 2004, 155(1):3-7.
21. Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, Loffelhardt W, Bohnert HJ, Philippe H, Lang BF: Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr Biol 2005, 15(14):1325-1330.
22. Campbell NA, Reece JB: Biology. 7th edition. San Francisco , Pearson Education; 2005:1231.
23. Raven PH, Johnson GB, Losos JB, Singer SR: Biology. 7th edition. New York City, McGraw-Hill.
24. Freeman S: Biological Science. 2nd edition. Upper Saddle River, NJ, Pearson Education; 2005:1283.
25. Bhattacharya D, Schmidt HA: Division Glaucocystophyta. Plant Syst Evol 1997:139-148.
26. Loffelhardt W, Bohnert HJ, Bryant DA: The cyanelles of Cyanophora paradoxa. Crit Rev Plant Sci 1997, 16(4):393-413.
27. Loffelhardt W, Bohnert HJ, Bryant DA: The complete sequence of the Cyanophora paradoxa cyanelle genome (Glaucocystophyceae). Plant Syst Evol 1997:149-162.
28. Hoffmann L, Kostikov I: New record of Glaucocystis nostochinearum (Glaucophyta) in Belgium. Belg J Bot 2004, 137(2):205-208.
29. Kies L, Kremer BP: Phylum Glaucocystophyta. In Handbook of Protoctista Edited by: Margulis M, Corliss JO, Melkonian M, Chapman DJ. Boston , Jones and Bartlett Publishers; 1990:914.
30. Jokerst RS, Weeks JR, Zehring WA, Greenleaf AL: Analysis of the Gene Encoding the Largest Subunit of Rna Polymerase II in Drosophila. Mol Gen Genet 1989, 215(2):266-275.
31. Corden JL: Tails of RNA Polymerase II. Trends Biochem Sci 1990, 15(10):383-387.
32. Carty SM, Greenleaf AL: Hyperphosphorylated C-terminal repeat domain-associating proteins in the nuclear proteome link transcription to DNA/chromatin modification and RNA processing. Mol Cell Proteomics 2002, 1(8):598-610.
33. Schramke V, Sheedy DM, Denli AM, Bonila C, Ekwall K, Hannon GJ, Allshire RC: RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription. Nature 2005, 435(7046):1275-1279.
34. Hirose Y, Manley JL: RNA polymerase II and the integration of nuclear events. Genes Devel 2000, 14(12):1415-1429.
35. Kornblihtt AR, de la Mata M, Fededa JP, Munoz MJ, Nogues G: Multiple links between transcription and splicing. RNA 2004, 10(10):1489-1498.
36. Stiller JW, Cook MS: Functional unit of the RNA polymerase II C-terminal domain lies within heptapeptide pairs. Euk Cell 2004, 3(3):735-740.
37. Guo Z, Stiller JW: Comparative Genomics and Evolution of Proteins Associated with RNA Polymerase II C-Terminal Domain. Mol Biol Evol 2005, 22(11):2166-2178.
38. Stiller JW, Hall BD: Sequences of the largest subunit of RNA polymerase II from two red algae and their implications for rhodophyte evolution. J Phycol 1998, 34(5):857-864.
39. Lockhart P, Steel M: A tale of two processes. Syst Biol in press.
40. Bapteste E, Brinkmann H, Lee JA, Moore DV, Sensen CW, Gordon P, Durufle L, Gaasterland T, Lopez P, Muller M, Philippe H: The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci USA 2002, 99(3):1414-1419.
41. Baldauf SL, Doolittle WF: Origin and evolution of the slime molds (Mycetozoa). Proc Natl Acad Sci USA 1997, 94(22):12007-12012.
42. Harper JT, Keeling PJ: Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol 2003, 20(10):1730-1735.
43. Harper JT, Waanders E, Keeling PJ: On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int J Syst Evol Microbiol 2005, 55(Pt 1):487-496.
44. Sakurai H, Miyao T, Ishihama A: Subunit composition of RNA polymerase II from the fission yeast Schizosaccharomyces pombe. Gene 1996, 180(1-2):63-67.
45. Woychik NA, Young RA: RNA polymerase II: subunit structure and function. Trends Biochem Sci 1990, 15(9):347-351.
46. Kadonaga JT: Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 2004, 116(2):247-257.
47. Hampsey M: Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 1998, 62(2):465-503.
48. Stiller JW, Hall BD: Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol Biol Evol 1999, 16(9):1270-1279.
49. Susko E, Spencer M, Roger AJ: Biases in phylogenetic estimation can be caused by random sequence segments. J Mol Evol 2005, 61(3):351-359.
50. Gray MW, Cedergren R, Abel Y, Sankoff D: On the Evolutionary Origin of the Plant Mitochondrion and Its Genome. Proc Natl Acad Sci USA 1989, 86(7):2267-2271.
51. Bergsten J: A review of long-branch attraction. Cladistics 2005, 21(2):163-193.
52. Lockhart P, Novis P, Milligan BG, Riden J, Rambaut A, Larkem T: Heterotachy and tree building: a case study with plastids and eubacteria. Mol Biol Evol 2006, 23(1):40-45.
53. Lockhart PJ, Huson D, Maier U, Fraunholz MJ, Van de Peer Y, Barbrook AC, Howe CJ, Steel MA: How molecules evolve in eubacteria. Mol Biol Evol 2000, 17(5):835-838.
54. Guo Z, Stiller JW: Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs. BMC Genomics 2004, 5(1):69.
55. Naylor GJ, Brown WM: Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst Biol 1998, 47(1):61-76.
56. Germot A, Philippe H: Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family. J Euk Microbiol 1999, 46(2):116-124.
57. Inagaki Y, Simpson A, Dacks J, Roger A: Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study. Syst Biol 2004, 53(4):582-593.
58. Inagaki Y, Susko E, Fast NM, Roger AJ: Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies. Mol Biol Evol 2004, 21(7):1340-1349.
59. Moreira D, Kervestin S, Jean-Jean O, Philippe H: Evolution of eukaryotic translation elongation and termination factors: variations of evolutionary rate and genetic code deviations. Mol Biol Evol 2002, 19(2):189-200.
60. Rokas A, King N, Finnerty J, Carroll SB: Conflicting phylogenetic signals at the base of the metazoan tree. Evol Dev 2003, 5(4):346-359.
61. Philippe H, Lopez P, Brinkmann H, Budin K, Germot A, Laurent J, Moreira D, Muller M, Le Guyader H: Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proc Biol Sci 2000, 267(1449):1213-1221.
62. Philippe H, Forterre P: The rooting of the universal tree of life is not reliable. J Mol Evol 1999, 49(4):509-523.
63. Kumar S, Rzhetsky A: Evolutionary relationships of eukaryotic kingdoms. J Mol Evol 1996, 42(2):183-193.
64. Embley TM, Hirt RP: Early branching eukaryotes? Curr Opin Genet Dev 1998, 8(6):624-629.
65. Penny D, McComish BJ, Charleston MA, Hendy MD: Mathematical elegance with biochemical realism: The covarion model of molecular evolution. J Mol Evol 2001, 53(6):711-723.
66. Felsenstein J: Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 1978, 25:401-410.
67. Hendy MD, Penny D: A Framework for the Quantitative Study of Evolutionary Trees. Syst Zool 1989, 38(4):297-309.
68. Kolaczkowski B, Thornton JW: Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004, 431(7011):980-984.
69. Bodyl A: Do plastid-related characters support the chromalveolate hypothesis? J Phycol 2005, 41(3):712-719.
70. Nozaki H, Matsuzaki M, Misumi O, Kuroiwa H, Higashiyama T, Kuroiwa T: Phylogenetic implications of the CAD complex from the primitive red alga Cyanidioschyzon merolae (Cyanidiales, Rhodophyta). J Phycol 2005, 41(3):652-657.
71. Stiller JW: Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms. Genomics Proteomics Bioinformatics 2004, 2(2):70-76.
72. Hausmann S, Altura MA, Witmer M, Singer SM, Elmendorf HG, Shuman S: Yeast-like mRNA capping apparatus in Giardia lamblia. J Biol Chem 2005, 280(13):12077-12086.
73. Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF: Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol 2005, 5:33.
74. Stiller JW, Waaland JR: Molecular Analysis Reveals Cryptic Diversity in Porphyra (Rhodophyta). J Phycol 1993, 29(4):506-517.
75. Palumbi SR, Baker CS: Contrasting Population-Structure from Nuclear Intron Sequences and mtDNA of Humpback Whales. Mol Biol Evol 1994, 11(3):426-435.
76. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ: Multiple sequence alignment with Clustal X. Trends Biochem Sci 1998, 23(10):403-405.
77. Schmidt H, Strimmer K, Vingron M, von Haeseler A: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18(3):502-504.
78. Jones DT, Taylor WR, Thornton JM: The Rapid Generation of Mutation Data Matrices from Protein Sequences. Comput Appl Biosci 1992, 8(3):275-282.
79. Felsenstein J: PHYLIP-phylogenetic inference package (version 3.2). Cladistics 1989, 5:164-165.
80. Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19(12):1572-1574.
81. Swofford DL: PAUP - a Computer-Program for Phylogenetic Inference Using Maximum Parsimony. J Gen Physiol 1993, 102(6):A9-a9.
82. Kishino H, Hasegawa M: Evaluation of the Maximum-Likelihood Estimate of the Evolutionary Tree Topologies from DNA-Sequence Data, and the Branching Order in Hominoidea. J Mol Evol 1989, 29(2):170-179.
83. Shimodaira H, Hasegawa M: Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999, 16(8):1114-1116.
84. Maddison W: Phylogenetic Interpretations of Character Evolution Using the Computer-Program MacClade. J Gen Physiol 1993, 102(6):A9-a10.
85. Cavalier-Smith T: The phagotrophic origin of eukaryotes and phylogenetic classification of protozoa. Int J Syst Evol Micr 2002, 52:297-354.
86. West ML, Corden JL: Construction and Analysis of Yeast RNA Polymerase II CTD Deletion and Substitution Mutations. Genetics 1995, 140(4):1223-1233.
87. Stiller JW, McConaughy BL, Hall BD: Evolutionary complementation for polymerase II CTD function. Yeast 2000, 16(1):57-64.