Phylogenetic relationships among hypotrichous ciliates determined with the macronuclear gene encoding the large, catalytic subunit of DNA polymerase α

Journal of Molecular Evolution

Volumn 45, Issue 3, 1997, Pages 301-310

  Hoffman, David C ^a   Prescott, David M ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

DNA polymerase gene; Hypotrichous ciliates; Macronuclear genes; Phylogenetics

Indexed keywords

DNA DIRECTED DNA POLYMERASE ALPHA;

AMINO ACID SEQUENCE; ARTICLE; CILIATE; MACRONUCLEUS; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; TAXONOMY;

AMINO ACID SEQUENCE; ANIMALS; CLONING, MOLECULAR; DNA POLYMERASE II; HYPOTRICHIDA; MOLECULAR SEQUENCE DATA; MUTAGENESIS; NUCLEAR PROTEINS; OXYTRICHA; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY, AMINO ACID;

CILIOPHORA; EUKARYOTA; HALTERIA GRANDINELLA; HOLOSTICHA; LANCEOLATA; MYTILUS; OXYTRICHA; PARAUROSTYLA VIRIDIS; PLEUROTRICHA LANCEOLATA; STERKIELLA NOVA; STYLONYCHIA LEMNAE; UROLEPTUS GALLINA; UROSTYLA GRANDIS;

EID: 0030833337     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006234     Document Type: Article

References (45)

1. Araki H, Ropp PA, Johnson AL, Johnston LH, Morrison A, Sugino A (1992) DNA polymerase II, the probable homolog of mammalian DNA polymerase ∈, replicated chromosomal DNA in the yeast Saccharomyces cerevisiae. EMBO J 11:733-740
2. Asai DJ, Criswell PG (1995) Identification of new dynein heavy-chain genes by RNA-directed polymerase chain reaction. Methods Cell Biol 47:579-585
3. Baroin-Tourancheau A, Delgado P, Perasso R, Adoutte A (1992) A broad molecular phylogeny of ciliates: identification of major evolutionary trends and radiations within the phylum. Proc Natl Acad Sci USA 89:9764-9768
4. Blow J (1989) Eukaryotic chromosome replication requires both α and δ DNA polymerases. Trends Genet 5:134-136
5. Braithwaite DK, Ito J (1993) Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucl Acids Res 21:787-802
6. Copeland WC, Wang TS-F (1993) Mutational analysis of the human DNA polymerase α: the most conserved region in α-like DNA polymerases is involved in metal-specific catalysis. J Biol Chem 268:11028-11040
7. Copeland WC, Lam NK, Wang TS-F (1993) Fidelity studies of the human DNA polymerase α: the most conserved region among α-like DNA polymerases is responsible for metal-induced infidelity in DNA synthesis. J Biol Chem 268:11041-11049
8. Corliss JO (1979) The ciliated protozoa - characterization, classification, and guide to the literature. Pergamon Press, New York, New York
9. Cotterill SM, Reyland ME, Loeb LA, Lehman IR (1987) A cryptic proofreading 3′-5′ exonuclease associated with the polymerase subunit of the DNA polymerase-primase from Drosophila melanogaster. Proc Natl Acad Sci USA 84:5635-5639
10. Damagnez V, Tillit J, de Recondo A-M, Baldacci G (1991) The POL1 gene from the fission yeast, Schizosaccharomyces pombe, shows conserved amino acid blocks specific for eukaryotic DNA polymerase α. Mol Gen Genet 226:182-189
11. Dayhoff MO (1979) Atlas of Protein Sequence and Structure, Volume 5, Supplement 3. National Biomedical Research Foundation, Washington, DC
12. Dong Q, Copeland WC, Wang TS-F (1993a) Mutational studies of human DNA polymerase α: identification of residues critical for deoxynucleotide binding and misinsertion fidelity. J Biol Chem 268:24163-24174
13. Dong Q, Copeland WC, Wang TS-F (1993b) Mutational studies of human DNA polymerase α: serine 867 in the second most conserved region among α-like DNA polymerases is involved in primer binding and mispair primer extension. J Biol Chem 268: 24175-24182
14. Dong Q, Wang TS-F (1995) Mutational studies of human DNA polymerase α: lysine 950 in the third most conserved region of α-like DNA polymerases is involved in binding the deoxynucleotide triphosphate. J Biol Chem 270:21563-21570
15. DuBois ML (1995) The unusual structure and evolution of the germline genome of hypotrichous ciliates. PhD thesis, University of Colorado, Boulder
16. Elwood HJ, Olsen GJ, Sogin ML (1985) The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol Biol Evol 2:399-410
17. Felsenstein J (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166
18. GCG (1994) Program manual for the Wisconsin package, 8th edition, Genetics Computer Group, Madison, Wisconsin
19. Gibbs JS, Chiou HC, Bastow KF, Cheng Y-C, Coen DM (1988) Identification of amino acids in herpes simplex virus DNA polymerase involved in substrate and drug recognition. Proc Natl Acad Sci USA 85:6672-6676
20. Hanahan D (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166:557-580
21. Hoffman DC (1996) The scrambled gene encoding the large, catalytic subunit of DNA polymerase α in the germline and somatic genomes of hypotrichous ciliates. PhD thesis, University of Colorado, Boulder
22. Hoffman DC, Anderson RC, DuBois ML, Prescott DM (1995) Macronuclear gene-sized molecules of hypotrichs. Nucl Acids Res 23: 1279-1283
23. Kaguni LS, Rossignol J-M, Conaway RC, Banks GR, Lehman IR (1983) Association of DNA primase with the β/γ subunits of DNA polymerase α from Drosophila melanogaster embryos. J Biol Chem 258:9037-9039
24. Kornberg A, Baker TA (1992) DNA replication. WH Freeman and Company, New York, New York, pp 197-223
25. Lehman IR, Kaguni LS (1989) DNA polymerase α. J Biol Chem 264: 4265-4268
26. Lucchini G, Francesconi S, Foiani M, Badaracco G, Plevani P (1987) Yeast DNA polymerase-DNA primase complex: cloning of PRI1, a single essential gene related to DNA primase activity. EMBO J 6:737-742
27. Lynn DH, Corliss JO (1991) Ciliophora. In: Harrison, FW (ed) Microscopic anatomy of invertebrates. John Wiley & Sons, New York, New York, pp 333-467
28. Lynn DH, Sogin ML (1988) Assessment of phylogenetic relationships among ciliated protists using partial ribosomal RNA sequences derived from reverse transcripts. Biosystems 21:249-254
29. Mansour SJ, Hoffman DC, Prescott DM (1994) A gene-sized molecule encoding the catalytic subunit of DNA polymerase α in the macronucleus of Oxytricha nova. Gene 144:155-161
30. Olins DE, Olins AL, Cacheiro LH, Tan EM (1989) Proliferating cell nuclear antigen/cyclin in the ciliate Euplotes eurystomus: localization in the replication band and in micronuclei. J Cell Biol 109: 1399-1410
31. Olins DE, Olins AL (1994) The replication band of ciliated protozoa. Int Rev Cytol 153:137-170
32. Page RDM (1996) TreeView: an application to display phylogenetic trees on personal computers. Comp Appl Biosc, in press
33. Pizzagalli A, Valsasnini P, Plevani P, Lucchini G (1988) DNA polymerase I gene of Saccharomyces cerevisiae: nucleotide sequence, mapping of a temperature-sensitive mutation, and protein homology with other DNA polymerases. Proc Natl Acad Sci USA 85: 3772-3776
34. Plevani P, Foiani M, Valsasnini P, Badaracco G, Cheriathundam E, Chang LMS (1985) Polypeptide structure of DNA primase from a yeast DNA polymerase-primase complex. J Biol Chem 260:7102-7107
35. Pope B, Kent HM (1996) High efficiency 5 minute transformation of Escherichia coli. Nucl Acids Res 24:536-537
36. Prescott DM, Greslin AF (1992) The scrambled actin 1 gene in the micronucleus of Oxytricha nova. Dev Genet 13:66-74
37. Preston GM (1993) Use of degenerate oligonucleotide primers and the polymerase chain reaction to clone gene family members. In: White, BA (ed) Methods in molecular biology, Vol 15: PCR protocols: current methods and applications. Humana Press, Totowa, New Jersey, pp 317-337
38. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
39. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning - a laboratory manual, 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
40. Schlegel M, Elwood HJ, Sogin ML (1991) Molecular evolution in hypotrichous ciliates: sequence of the small subunit ribosomal RNA genes from Onychodromus quadricornatus and Oxytricha granulifera. J Mol Evol 32:64-69
41. So AG, Downey KM (1988) Mammalian DNA polymerases α and δ: current status in DNA replication. Biochemistry 27:4591-4595
42. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
43. Wang TS-F, Wong SW, Korn D (1989) Human DNA polymerase α: predicted functional domains and relationships with viral DNA polymerases. FASEB J 3:14-21
44. White JH, Kilbey BJ, de Vries E, Goman M, Alano P, Cheesman S, McAleese S, Ridley RG (1993) The gene encoding DNA polymerase α from Plasmodium falciparum. Nucleic Acids Res 21:3643-3646
45. Wong SW, Wahl AF, Yuan P-M, Arai N, Pearson BE, Arai KI, Korn D, Hunkapiller MW, Wang TS-F (1988) Human DNA polymerase a gene expression is cell proliferation dependent and its primary structure is similar to both prokaryotic and eukaryotic replicative DNA polymerases. EMBO J 7:37-47