Sequences of the largest subunit of RNA polymerase II from two red algae and their implications for rhodophyte evolution

Journal of Phycology

Volumn 34, Issue 5, 1998, Pages 857-864

  Stiller, John W ^a   Hall, Benjamin D ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Bonnemaisonia hamifera; Carboxyl terminal domain; Evolution; Molecular phylogeny; mRNA transcription; Multicellular development; Porphyra yezoensis; Rhodophyta; RNA polymerase II; RPB1

Indexed keywords

ALGA; BIODIVERSITY; GENE SEQUENCING; GENETICS; MESSENGER RNA; RNA POLYMERASE II; TRANSCRIPTION REGULATION;

EVOLUTION; GENETIC ANALYSIS; RED ALGA;

BONNEMAISONIA HAMIFERA; PORPHYRA YEZOENSIS;

EID: 0031760020     PISSN: 00223646     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1529-8817.1998.340857.x     Document Type: Article

References (48)

1. Adachi, J. & Hasegawa, M. 1993. MOLPHY. Computer Science Monograph 27. Institute of Statistical Mathematics, Tokyo.
2. Baldauf, S. L. & Doolittle, W. F. 1997. Origin and evolution of the slime molds (Mycetozoa). Proc. Natl. Acad. Sci. USA 94: 12007-12.
3. Bold, H. C. & Wynne, M. J. 1985. Introduction to the Algae, 2nd ed. Prentice-Hall Inc., Englewood Cliffs, New Jersey, 720 pp.
4. Bourqin, J. P., Stagljar, I., Meier, P., Moosman, P., Silke, J., Baechi, T., Georgiev, O. & Schaffner, W. 1997. A serine/arginine-rich nuclear matrix cyclophilin interacts with the C-terminal domain of RNA polymerase II. Nucleic Acids Res. 25: 2055-61.
5. Butterfield, N. J., Knoll, A. H. & Swett, K. 1990. A bangiophyte red alga from the proterozoic of arctic Canada. Science (Wash. D. C.) 250:104-7.
6. Chabot, B. 1996. Directing alternative splicing: cast and scenarios. Trends Genet. 12:472-8.
7. Coomans, R. J. & Hommersand, M. H. 1990. Vegetative growth and organization. In Cole, K. M & Sheath, R. G. [Eds.] Biology of the Red Algae. Cambridge University Press, New York, 517 pp.
8. Corden, J. L. 1990. Tails of polymerase II. TIBS 15:383-7.
9. Dixon, P. S. 1973. Biology of the Rhodophyta. Hafner Press, New York, 285 pp.
10. Evers, R., Hammer, A. & Cornelissen, A. W. C. A. 1989a. Unusual C-terminal domain of the largest subunit of RNA polymerase II of Crithidia fasciculata. Nucleic Acids. Res. 17:3403-13.
11. Evers, R., Hammer, A., Köck, J., Waldemar, J., Borst, P., Mémet, S. & Cornelissen, A. W. C. A. 1989b. Trypanosoma brucei contains two RNA polymerase II largest subunit genes with an altered C-terminal domain. Cell 56:585-97.
12. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using bootstrap. Evolution 39:783-91.
13. _ 1989. PHYLIP - phylogenetic inference package (version 3.2). Cladistics 5:164-5.
14. Giesecke, H., Barale, J. C., Langsley, G. & Cornelissen, A. W. 1991. The C-terminal domain of RNA polymerase II of the malaria parasite Plasmodium berghei. Biochem. Biophys. Res. Commun. 180:1350-5.
15. Higgins, D. G., Bleasby, A. J. & Fuchs, R. 1992. CLUSTAL V: improved software for multiple sequence alignment. CABIOS 8:189-91.
16. Jokerst, R. S., Weeks, J. R., Zehring, W. A. & Greenleaf, A. L. 1989. Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila. Mol. Gen. Genet. 215:266-75.
17. Kim, Y-J., Björklund, S., Li, Y., Sayre, M. H. & Kornberg, R. D. 1994. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77:599-608.
18. Klenk, H-P., Zillig, W., Lanzendörfer, M., Brampp, B. & Palm, P. 1995. Location of protist lineages in a phylogenetic tree inferred from sequences of DNA-dependent RNA polymerases. Arch. Protistenkd. 145:221-30.
19. Knoll, A. H. 1992. The early evolution of eukaryotes: a geological perspective. Science (Wash. D. C.) 256:622-7.
20. Kumar, S. & Rzhetsky, A. 1996. Evolutionary relationships of eukaryotic organisms. J. Mol. Evol. 42:183-93.
21. Lam, T. Y., Chan, L., Yip, P. & Siu, C. H. 1992. The largest subunit of RNA polymerase II in Dictyostelium: conservation of the unique tail domain and gene expression. Biochem. Cell Biol. 70:792-9.
22. Li, W-B., Bzik, D. J., Gu, H., Tanaka, M., Fox, B. A. & Inselburg, J. 1989. An enlarged largest subunit of Plasmodium falciparum RNA polymerase II defines conserved and variable RNA polymerase domains. Nucleic Acids Res. 17:9621-36.
23. Lüning, K. 1990. Seaweeds. Their Environment, Biogeography and Ecophysiology. J. Wiley, New York, 527 pp.
24. Maldonado, E., Shiekhatter, R., Sheldon, M., Cho, H., Drapkin, R., Rickert, P., Lees, E., Anderson, C. W., Linn, S. & Reinberg, D. 1996. A human, RNA polymerase II complex associated with SRB and DNA-repair proteins. Nature 381:86-9.
25. Marshall, N. F., Peng, J., Xie, Z. & Price, D. H. 1996. Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J. Biol. Chem. 271:27176-83.
26. McCrackin, S., Fong, N., Yankulov, K., Ballantyne, S., Pan, G., Greenblatt, J., Patterson, S. D., Wickens, M. & Bentley, D. L. 1997. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385:357-61.
27. Meisels, E., Gilieadi, O. & Corden, J. L. 1990. Partial truncation of the yeast RNA polymerase II carboxyl-terminal domain preferentially reduces expression of glycolytic genes. J. Biol. Chem. 270:31255-61.
28. Nonet, M. L. & Young, R. A. 1989. Intragenic and extragenic suppressors of mutations in the heptapeptide repeat domain of Saccharomyces cerevisiae RNA polymerase II. Genetics 123: 715-24.
29. Palumbi, S. & Baker, C. 1994. Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Mol. Biol. Evol. 11:426-35.
30. Pühler, G., Leffers, H., Gropp, F., Palm, P., Klenk, H-P., Lottspeich, F., Garret, R. A. & Zillig, W. 1989. Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. Proc. Natl. Acad. Sci. USA 86: 4569-73.
31. Quon, D. V. K., Delgadillo, M. G. & Johnson, P. J. 1996. Transcription in the early diverging eukaryotic Trichomonas vaginalis: an unusual RNA polymerase II and a-amanitin-resistant transcription of protein-coding genes. J. Mol. Evol. 43:253-62.
32. Ragan, M. A., Bird, C. J., Rice, E. L., Gutell, R. R., Murphy, C. A. & Singh, R. K. 1994. A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proc. Natl. Acad. Sci. USA 91:7276-80.
33. Ragan, M. & Gutell, R. 1995. Are red algae plants? Bot. J. Linn. Soc. 118:81-105.
34. Saunders, G. W. & Druehl, L. D. 1992. Nucleotide sequences of the small-subunit ribosomal RNA genes from selected Laminariales (Phaeophyta): implications for kelp evolution. J. Phycol. 28:544-9.
35. Scafe, C., Chao, D., Lopes, J., Hirsch, J. P., Henry, S. & Young, R. A. 1990. RNA polymerase II C-terminal repeat influences response to transcription enhancer signals. Nature 347:491-4.
36. Siebert, P. D., Chenchik, A., Kellogg, D. E., Lukyanov, K. A. & Lukyanov, S. A. 1995. An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res. 23:1087-8.
37. Smith, J. L., Levin, J. R., Ingles, C. J. & Agabian, N. 1989. In trypanosomes the homologue of the largest subunit of RNA polymerase II is encoded by two genes and has a highly unusual C-terminal domain structure. Cell 56:815-27.
38. Steinmetz, E. J. 1997. Pre-mRNA processing and the CTD of RNA polymerase II: the tail that wags the dog? Cell 89:491-4.
39. Stiller, J. W. & Hall, B. D. 1997. the origin of red algae: implications for plastid evolution. Proc. Natl. Acad. Sci. USA 94: 4520-5.
40. Stiller, J. W. & Waaland, J. R. 1993. Molecular analysis reveals cryptic diversity in Porphyra (Rhodophyta). J. Phycol. 29:506-17.
41. Svejstrup, J. Q., Li, Y., Fellows, J., Gnatt, A., Björklund, S. & Kornberg, R. D. 1997. Evidence for a mediator cycle at the initiation of transcription. Proc. Natl. Acad. Sci. USA 94:6075-8.
42. Swofford, D. L. 1993. PAUP 3.1.1. Illinois Natural History Survey, Champaign, Illinois.
43. Tanner, S., Stagljar, I., Georgiev, O., Schaffner, W. & Bourquin, J. P. 1997. A novel SR-related protein specifically interacts with the carboxyl-terminal domain (CTD) of RNA polymerase II through a conserved interaction domain. Biol. Chem. 378:565-671.
44. Van de Peer, Y., Rensing, S. A., Maier, U-G. & De Wachter, R. 1996. Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae. Proc. Natl. Acad. Sci. USA 93:7732-6.
45. West, M. L. & Corden, J. L. 1995. Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutants. Genetics 140:1223-33.
46. Yuryev, A. & Corden, J. L. 1996. Suppression analysis reveals a functional difference between the serines in positions two and five in the consensus sequence of the C-terminal domain of yeast RNA polymerase II. Genetics 143:661-71.
47. Yuryev, A., Patturajan, M., Litingtung, Y., Joshi, R. V., Gentile, C., Gebara, M. & Corden, J. L. 1996. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc. Natl. Acad. Sci. USA 93:6975-80.
48. Zhu, S. & Chen, H. 1995. Megascopic multicellular organisms form the 1700-million-year old Tuanshanzi formation in the Jixian area, north China. Science (Wash. D. C.) 279:620-2.