Evolutionary diversity and taxon-specific modifications of the RNA polymerase II C-terminal domain

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 16, 2014, Pages 5920-5925

  Yang, Chunlin ^a   Stiller, John W ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

Author keywords

Development; Parasitism; Splicing; Transcription

Indexed keywords

RNA POLYMERASE II;

APICOMPLEXA; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONSENSUS SEQUENCE; EUKARYOTE; FUNGUS; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTIST; RED ALGA; TANDEM REPEAT; TAXONOMY;

DEVELOPMENT; PARASITISM; SPLICING; TRANSCRIPTION;

ANIMALS; EVOLUTION, MOLECULAR; FUNGI; GENETIC VARIATION; PHYLOGENY; PLANTS; PROTEIN STRUCTURE, TERTIARY; REPETITIVE SEQUENCES, AMINO ACID; RHODOPHYTA; RNA POLYMERASE II;

EID: 84899086064     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1323616111     Document Type: Article

References (42)

1. Allison LA, MoyleM, Shales M, Ingles CJ (1985) Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell 42(2):599-610.
2. West ML, Corden JL (1995) Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics 140(4):1223-1233.
3. Liu P, Kenney JM, Stiller JW, Greenleaf AL (2010) Genetic organization, length conservation, and evolution of RNA polymerase II carboxyl-terminal domain. Mol Biol Evol 27(11):2628-2641.
4. Buratowski S (2009) Progression through the RNA polymerase II CTD cycle. Mol Cell 36(4):541-546.
5. Bartkowiak B, Mackellar AL, Greenleaf AL (2011) Updating the CTD story: From tail to epic. Genet Res Int 2011:623718.
6. Hsin JP, Manley JL (2012) The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev 26(19):2119-2137.
7. Corden JL (2013) RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 113(11):8423-8455.
8. Eick D, Geyer M (2013) The RNA polymerase II carboxy-terminal domain (CTD) code. Chem Rev 113(11):8456-8490.
9. Egloff S, Murphy S (2008) Cracking the RNA polymerase II CTD code. Trends Genet 24(6):280-288.
10. Jasnovidova O, Stefl R (2013) The CTD code of RNA polymerase II: A structural view. Wiley Interdiscip Rev RNA 4(1):1-16.
11. Zhang DW, Rodríguez-Molina JB, Tietjen JR, Nemec CM, Ansari AZ (2012) Emerging views on the CTD code. Genet Res Int 2012:347214.
12. Heidemann M, Hintermair C, Voß K, Eick D (2013) Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription. Biochim Biophys Acta 1829(1):55-62.
13. Bartkowiak B, Greenleaf AL (2011) Phosphorylation of RNAPII: To P-TEFb or not to P-TEFb? Transcription 2(3):115-119.
14. Mayer A, et al. (2012) CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science 336(6089):1723-1725.
15. Chapman RD, et al. (2007) Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7. Science 318(5857):1780-1782. (Pubitemid 350274389)
16. Hsin JP, Sheth A, Manley JL (2011) RNAP II CTD phosphorylated on threonine-4 is required for histone mRNA 3? end processing. Science 334(6056):683-686.
17. Hintermair C, et al. (2012) Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation. EMBO J 31(12):2784-2797.
18. Werner-Allen JW, et al. (2011) cis-Proline-mediated Ser(P)5 dephosphorylation by the RNA polymerase II C-terminal domain phosphatase Ssu72. J Biol Chem 286(7):5717-5726.
19. Stiller JW, Hall BD (2002) Evolution of the RNA polymerase II C-terminal domain. Proc Natl Acad Sci USA 99(9):6091-6096. (Pubitemid 34493270)
20. Chapman RD, Heidemann M, Hintermair C, Eick D (2008) Molecular evolution of the RNA polymerase II CTD. Trends Genet 24(6):289-296.
21. Stump AD, Ostrozhynska K (2013) Selective constraint and the evolution of the RNA polymerase II C-Terminal Domain. Transcription 4(2):77-86.
22. Stechmann A, Cavalier-Smith T (2003) The root of the eukaryote tree pinpointed. Curr Biol 13(17):R665-R666. (Pubitemid 37078393)
23. Stiller JW, Hall BD (1998) Sequences of the largest subunit of RNA polymerase II from two red algae and their implications for rhodophyte evolution. J Phycol 34(5):857-864. (Pubitemid 28494394)
24. Lang BF, O'Kelly C, Nerad T, Gray MW, Burger G (2002) The closest unicellular relatives of animals. Curr Biol 12(20):1773-1778. (Pubitemid 35169794)
25. Guo Z, Stiller JW (2005) Comparative genomics and evolution of proteins associated with RNA polymerase II C-terminal domain. Mol Biol Evol 22(11):2166-2178. (Pubitemid 41437798)
26. James TY, et al. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443(7113):818-822. (Pubitemid 44622687)
27. Sutherland JE, et al. (2011) A new look at an ancient order: Generic revision of the Bangiales (Rhodophyta). J Phycol 47(5):1131-1151.
28. Riisberg I, et al. (2009) Seven gene phylogeny of heterokonts. Protist 160(2):191-204.
29. Kishore SP, Perkins SL, Templeton TJ, Deitsch KW (2009) An unusual recent expansion of the C-terminal domain of RNA polymerase II in primate malaria parasites features a motif otherwise found only in mammalian polymerases. J Mol Evol 68(6):706-714.
30. Jain R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96(7):3801-3806. (Pubitemid 29168991)
31. Koonin EV (2009) Intron-dominated genomes of early ancestors of eukaryotes. J Hered 100(5):618-623.
32. Rogozin IB, Carmel L, Csuros M, Koonin EV (2012) Origin and evolution of spliceosomal introns. Biol Direct 7:11.
33. Hirose Y, Tacke R, Manley JL (1999) Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev 13(10):1234-1239. (Pubitemid 29250190)
34. Schwer B, Shuman S (2011) Deciphering the RNA polymerase II CTD code in fission yeast. Mol Cell 43(2):311-318.
35. Stiller JW, McConaughy BL, Hall BD (2000) Evolutionary complementation for polymerase II CTD function. Yeast 16(1):57-64. (Pubitemid 30066096)
36. Kishore SP, Stiller JW, Deitsch KW (2013) Horizontal gene transfer of epigenetic machinery and evolution of parasitism in the malaria parasite Plasmodium falciparum and other apicomplexans. BMC Evol Biol 13:37.
37. Chapman RD, Conrad M, Eick D (2005) Role of the mammalian RNA polymerase II C-terminal domain (CTD) nonconsensus repeats in CTD stability and cell proliferation. Mol Cell Biol 25(17):7665-7674. (Pubitemid 41170128)
38. Litingtung Y, et al. (1999) Growth retardation and neonatal lethality in mice with a homozygous deletion in the C-terminal domain of RNA polymerase II. Mol Gen Genet 261(1):100-105. (Pubitemid 29137363)
39. Sims RJ, 3rd, et al. (2011) The C-terminal domain of RNA polymerase II is modified by site-specific methylation. Science 332(6025):99-103.
40. Charrier B, et al. (2008) Development and physiology of the brown alga Ectocarpus siliculosus: Two centuries of research. New Phytol 177(2):319-332. (Pubitemid 350295788)
41. Ghosh A, Shuman S, Lima CD (2011) Structural insights to how mammalian capping enzyme reads the CTD code. Mol Cell 43(2):299-310.
42. Schwer B, Sanchez AM, Shuman S (2012) Punctuation and syntax of the RNA polymerase II CTD code in fission yeast. Proc Natl Acad Sci USA 109(44):18024-18029.