Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase

Gene

Volumn 381, Issue 1-2, 2006, Pages 92-101

  Shao, Zhiyong ^a   Graf, Shannon ^b   Chaga, Oleg Y ^c   Lavrov, Dennis V ^a,d  

^a IOWA STATE UNIVERSITY   (United States)

^b GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

^c NORTHWESTERN UNIVERSITY   (United States)

^d Department of Ecology Evolution and Organismal Biology ^*  (United States)

Author keywords

dnaB; Gene order; Linear mtDNA; Mitochondrial evolution

Indexed keywords

DNA B; DNA DIRECTED DNA POLYMERASE; EXONUCLEASE; MITOCHONDRIAL DNA; RIBOSOME DNA;

AMINO ACID SEQUENCE; ARTICLE; COELENTERATE; CONTROLLED STUDY; DNA SEQUENCE; ENZYME KINETICS; GENETIC TRANSCRIPTION; GENOME; GENOME ANALYSIS; JELLYFISH; MITOCHONDRION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN DOMAIN; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TELOMERE;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CNIDARIA; DNA, MITOCHONDRIAL; DNA-DIRECTED DNA POLYMERASE; GENOME; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; RNA, TRANSFER, MET; RNA, TRANSFER, TRP; SEQUENCE HOMOLOGY, AMINO ACID;

ANIMALIA; AURELIA AURITA; CNIDARIA; METAZOA; SCYPHOZOA;

EID: 33748919994     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.06.021     Document Type: Article

References (70)

1. Arai M.N. Functional Biology of Scyphozoa (1996), Chapman & Hall, New York, NY
2. Armstrong M.R., Block V.C., and Phillips M.S. A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. Genetics 154 (2000) 181-192
3. Beagley C.T., Macfarlane J.L., Pont-Kingdon G.A., Okimoto R., Okada N.A., and Wolstenholme D.R. Mitochondrial genomes of Anthozoa (Cnidaria). In: Palmieri F., Pappa S., Saccone C., and Gadaleta N. (Eds). Progress in Cell Research-Symposium on Thirty Years of Progress in Mitochondrial Bioenergetics and Molecular Biology (1995), Elsevier, Amsterdam 149-153
4. Beagley C.T., Okada N.A., and Wolstenholme D.R. Two mitochondrial group I introns in a metazoan, the sea anemone Metridium senile: one intron contains genes for subunits 1 and 3 of NADH dehydrogenase. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 5619-5623
5. Beagley C.T., Okimoto R., and Wolstenholme D.R. The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a nearstandard genetic code. Genetics 148 (1998) 1091-1108
6. Beaton M.J., Roger A.J., and Cavalier-Smith T. Sequence analysis of the mitochondrial genome of Sarcophyton glaucum: conserved gene order among octocorals. J. Mol. Evol. 47 (1998) 697-708
7. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., and Wheeler D.L. GenBank. Nucleic Acids Res. 31 (2003) 23-27
8. Berntson E.A., France S.C., and Mullineaux L.S. Phylogenetic relationships within the class Anthozoa (phylum Cnidaria) based on nuclear 18S rDNA sequences. Mol. Phylogenet. Evol. 13 (1999) 417-433
9. Bois F., Barroso G., Gonzalez P., and Labarere J. Molecular cloning, sequence and expression of Aa-polB, a mitochondrial gene encoding a family B DNA polymerase from the edible basidiomycete Agrocybe aegerita. Mol. Gen. Genet. 261 (1999) 508-513
10. Boore J.L. Animal mitochondrial genomes. Nucleic Acids Res. 27 (1999) 1767-1780
11. Braithwaite D.K., and Ito J. Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res. 21 (1993) 787-802
12. Bridge D., Cunningham C.W., Schierwater B., DeSalle R., and Buss L.W. Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure. Proc. Natl. Acad. Sci. U. S. A. 89 (1992) 8750-8753
13. Bridge D., Cunningham C.W., DeSalle R., and Buss L.W. Class-level relationships in the phylum Cnidaria: molecular and morphological evidence. Mol. Biol. Evol. 12 (1995) 679-689
14. Brusca R.C., and Brusca G.J. Invertebrates (2002), Sinauer Associates, Sunderland, MA
15. Burger G., Saint-Louis D., Gray M.W., and Lang B.F. Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea. Cyanobacterial introns and shared ancestry of red and green algae. Plant Cell 11 (1999) 1675-1694
16. Burger G., et al. Complete sequence of the mitochondrial genome of Tetrahymena pyriformis and comparison with Paramecium aurelia mitochondrial DNA. J. Mol. Biol. 297 (2000) 365-380
17. Chevalier B.S., and Stoddard B.L. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res. 29 (2001) 3757-3774
18. Coleman A.W., Thompson W.F., and Goff L.J. Identification of the mitochondrial genome in the chrysophyte alga Ochromonas danica. J. Protozool. 38 (1991) 129-135
19. Collins A.G. Phylogeny of Medusozoa and the evolution of cnidarian life cycles. J. Evol. Biol. 15 (2002) 418-432
20. Collins A.G., and Daly M. A new deepwater species of Stauromedusae, Lucernaria janetae (Cnidaria, Staurozoa, Lucernariidae), and a preliminary investigation of stauromedusan phylogeny based on nuclear and mitochondrial rDNA data. Biol. Bull. 208 (2005) 221-230
21. Dawson M.N., and Jacobs D.K. Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa). Biol. Bull. 200 (2001) 92-96
22. De Rijk P., Wuyts J., and De Wachter R. RnaViz 2: an improved representation of RNA secondary structure. Bioinformatics 19 (2003) 299-300
23. Ender A., and Schierwater B. Placozoa are not derived cnidarians: evidence from molecular morphology. Mol. Biol. Evol. 20 (2003) 130-134
24. Folmer O., Black M., Hoeh W., Lutz R., and Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3 (1994) 294-299
25. Forget L., Ustinova J., Wang Z., Huss V.A., and Lang B.F. Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi. Mol. Biol. Evol. 19 (2002) 310-319
26. Freemont P.S., Ollis D.L., Steitz T.A., and Joyce C.M. A domain of the Klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity. Proteins 1 (1986) 66-73
27. Fukami H., and Knowlton N. Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia). Coral Reefs 24 (2005) 410-417
28. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
29. Helfenbein K.G., Fourcade H.M., Vanjani R.G., and Boore J.L. The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 10639-10643
30. Joyce C.M., and Steitz T.A. Function and structure relationships in DNA polymerases. Ann. Rev. Biochem. 63 (1994) 777-822
31. Lang B.F., Gray M.W., and Burger G. Mitochondrial genome evolution and the origin of eukaryotes. Annu. Rev. Genet. 33 (1999) 351-397
32. Lavrov D.V., Forget L., Kelly M., and Lang B.F. Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution. Mol. Biol. Evol. 22 (2005) 1231-1239
33. Lowe T.M., and Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (1997) 955-964
34. Löytynoja A., and Milinkovitch M.C. SOAP, cleaning multiple alignments from unstable blocks. Bioinformatics 17 (2001) 573-574
35. Marck C., and Grosjean H. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8 (2002) 1189-1232
36. Marques A.C., and Collins A.G. Cladistic analysis of Medusozoa and cnidarian evolution. Invertebr. Biol. 123 (2004) 23-42
37. Medina M., Collins A.G., Silberman J.D., and Sogin M.L. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 9707-9712
38. Meinhardt F., Kempken F., Kamper J., and Esser K. Linear plasmids among eukaryotes: fundamentals and application. Curr. Genet. 17 (1990) 89-95
39. Meinhardt F., Schaffrath R., and Larsen M. Microbial linear plasmids. Appl. Microbiol. Biotechnol. 47 (1997) 329-336
40. Mouhamadou B., Barroso G., and Labarere J. Molecular evolution of a mitochondrial polB gene, encoding a family B DNA polymerase, towards the elimination from Agrocybe mitochondrial genomes. Mol. Genet. Genomics 272 (2004) 257-263
41. Nosek J., and Tomaska L. Mitochondrial telomeres: alternative solutions to the endreplication problem. In: Krupp G., and Parwaresch R. (Eds). Telomeres, Telomerases and Cancer (2002), Kluwer Academic/Plenum Publishers, New York, NY 396-417
42. Nosek J., and Tomaska L. Mitochondrial genome diversity: evolution of the molecular architecture and replication strategy. Curr. Genet. 44 (2003) 73-84
43. Ohno S. Universal rule for coding sequence construction: TA/CG deficiency-TG/CT excess. Proc. Natl. Acad. Sci. U. S. A. 85 (1988) 9630-9634
44. Papillon D., Perez Y., Caubit X., and Le Parco Y. Identification of chaetognaths as protostomes is supported by the analysis of their mitochondrial genome. Mol. Biol. Evol. 21 (2004) 2122-2129
45. Pearson W.R. Using the FASTA program to search protein and DNA sequence databases. Methods Mol. Biol. 25 (1994) 365-389
46. Pont-Kingdon G.A., Beagley C.T., Okimoto R., and Wolstenholme D.R. Mitochondrial DNA of the sea anemone, Metridium senile (Cnidaria): prokaryote-like genes for tRNA(f-Met) and small-subunit ribosomal RNA, and standard genetic code specificities for AGR and ATA codons. J. Mol. Evol. 39 (1994) 387-399
47. Pont-Kingdon G.A., et al. A coral mitochondrial mutS gene. Nature 375 (1995) 109-111
48. Pont-Kingdon G., et al. Mitochondrial DNA of the coral Sarcophyton glaucum contains a gene for a homologue of bacterial MutS: a possible case of gene transfer from the nucleus to the mitochondrion. J. Mol. Evol. 46 (1998) 419-431
49. Pont-Kingdon G., Vassort C.G., Warrior R., Okimoto R., Beagley C.T., and Wolstenholme D.R. Mitochondrial DNA of Hydra attenuata (Cnidaria): a sequence that includes an end of one linear molecule and the genes for l-rRNA, tRNA(f-Met), tRNA(Trp), COII, and ATPase8. J. Mol. Evol. 51 (2000) 404-415
50. Rich A., and RajBhandary U.L. Transfer RNA: molecular structure, sequence, and properties. Ann. Rev. Biochem. 45 (1976) 805-860
51. Robertus J.D., Ladner J.E., Finch J.T., Rhodes D., Brown R.S., Clark B.F., and Klug A. Structure of yeast phenylalanine tRNA at 3 A resolution. Nature 250 (1974) 546-551
52. Robison M.M., and Horgen P.A. Plasmid RNA polymerase-like mitochondrial sequences in Agaricus bitorquis. Curr. Genet. 29 (1996) 370-376
53. Robison M.M., and Wolyn D.J. A mitochondrial plasmid and plasmid-like RNA and DNA polymerases encoded within the mitochondrial genome of carrot (Daucus carota L.). Curr. Genet. 47 (2005) 57-66
54. Robison M.M., Royer J.C., and Horgen P.A. Homology between mitochondrial DNA of Agaricus bisporus and an internal portion of a linear mitochondrial plasmid of Agaricus bitorquis. Curr. Genet. 19 (1991) 495-502
55. Rodriguez I., et al. A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 6407-6412
56. Rokas A., King N., Finnerty J., and Carroll S.B. Conflicting phylogenetic signals at the base of the metazoan tree. Evolut. Develop. 5 (2003) 346-359
57. Rokas A., Kruger D., and Carroll S.B. Animal evolution and the molecular signature of radiations compressed in time. Science 310 (2005) 1933-1938
58. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
59. Rousvoal S., Oudot M., Fontaine J., Kloareg B., and Goer S.L. Witnessing the evolution of transcription in mitochondria: the mitochondrial genome of the primitive brown alga Pylaiella littoralis (L.) Kjellm. encodes a T7-like RNA polymerase. J. Mol. Biol. 277 (1998) 1047-1057
60. Schroth W., Jarms G., Streit B., and Schierwater B. Speciation and phylogeography in the cosmopolitan marine moon jelly, Aurelia sp. BMC Evol. Biol. 2 (2002) 1
61. Smith A.E., and Marcker K.A. N-formylmethionyl transfer RNA in mitochondria from yeast and rat liver. J. Mol. Biol. 38 (1968) 241-243
62. Sprinzl M., Hartmann T., Weber J., Blank J., and Zeidler R. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 17 (1989) 1-172 (Suppl.)
63. Staden R. The Staden sequence analysis package. Mol. Biotechnol. 5 (1996) 233-241
64. Thompson J.D., Higgins D.G., and Gibson T.J. 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 (1994) 4673-4680
65. Truniger V., Lazaro J.M., Salas M., and Blanco L. Phi 29 DNA polymerase requires the N-terminal domain to bind terminal protein and DNA primer substrates. J. Mol. Biol. 278 (1998) 741-755
66. Vahrenholz C., Riemen G., Pratje E., Dujon B., and Michaelis G. Mitochondrial DNA of Chlamydomonas reinhardtii: the structure of the ends of the linear 15.8-kb genome suggests mechanisms for DNA replication. Curr. Genet. 24 (1993) 241-247
67. van Oppen M.J., Catmull J., McDonald B.J., Hislop N.R., Hagerman P.J., and Miller D.J. The mitochondrial genome of Acropora tenuis (Cnidaria; Scleractinia) contains a large group I intron and a candidate control region. J. Mol. Evol. 55 (2002) 1-13
68. Weber B., Borner T., and Weihe A. Remnants of a DNA polymerase gene in the mitochondrial DNA of Marchantia polymorpha. Curr. Genet. 27 (1995) 488-490
69. Wesley U.V., and Wesley C.S. Rapid directional walk within DNA clones by step-out PCR. Methods Mol. Biol. 67 (1997) 279-285
70. Wolstenholme D.R. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cyt. 141 (1992) 173-216