The mitochondrial view of Blastocladiella emersonii

Gene

Volumn 424, Issue 1-2, 2008, Pages 33-39

  Tambor, José Humberto M ^a   Ribichich, Karina F ^a   Gomes, Suely L ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Blastocladiella emersonii; Chytrid; Endonuclease; Mitochondria

Indexed keywords

MITOCHONDRIAL DNA; RIBOSOME RNA; TRANSFER RNA;

ARABIDOPSIS; ARTICLE; BLASTOCLADIELLA; BLASTOCLADIELLA EMERSONII; CODON; CONTROLLED STUDY; DATA BASE; GENE DUPLICATION; GENOME; HUMAN; INTRON; MITOCHONDRIAL GENE; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATIVE PHOSPHORYLATION; PRIORITY JOURNAL; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; ZYGOMYCETES;

ADENINE; ALLOMYCES; BLASTOCLADIELLA; CODON; DNA, FUNGAL; DNA, MITOCHONDRIAL; GENE LIBRARY; GENOME, FUNGAL; OPEN READING FRAMES; PHYLOGENY; THYMINE;

ALLOMYCES MACROGYNUS; ARABIDOPSIS THALIANA; BLASTOCLADIELLA EMERSONII; HOMO SAPIENS; SACCHAROMYCES CEREVISIAE; ZYGOMYCETES;

EID: 52949100206     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2008.07.031     Document Type: Article

References (51)

1. Abascal F., Zardoya R., and Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21 (2005) 2104-2105
2. Adam A.C., Bornhovd C., Prokisch H., Neupert W., and Hell K. The Nfs1 interacting protein Isd11 has an essential role in Fe/S cluster biogenesis in mitochondria. Embo J. 25 (2006) 174-183
3. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
4. Bullerwell C.E., Forget L., and Lang B.F. Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences. Nucleic Acids Res. 31 (2003) 1614-1623
5. Cao Y., Adachi J., Janke A., Paabo S., and Hasegawa M. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J. Mol. Evol. 39 (1994) 519-527
6. Duby G., Oufattole M., and Boutry M. Hydrophobic residues within the predicted N-terminal amphiphilic alpha-helix of a plant mitochondrial targeting presequence play a major role in in vivo import. Plant J. 27 (2001) 539-549
7. Emanuelsson O., Nielsen H., Brunak S., and von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300 (2000) 1005-1016
8. Emerson R. An experimental study of the life cycle and taxonomy of Allomyces. Lloydia 4 (1941) 77-144
9. Ewing B., and Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8 (1998) 186-194
10. Fitzpatrick D.A., Logue M.E., Stajich J.E., and Butler G. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol. Biol. 6 (2006) 99
11. 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
12. Gabriel K., and Pfanner N. The mitochondrial machinery for import of precursor proteins. Methods Mol. Biol. 390 (2007) 99-118
13. Garber R.C., and Yoder O.C. Isolation of DNA from filamentous fungi and separation into nuclear, mitochondrial, ribosomal, and plasmid components. Anal. Biochem. 135 (1983) 416-422
14. Gordon D., Abajian C., and Green P. Consed: a graphical tool for sequence finishing. Genome Res. 8 (1998) 195-202
15. Graeber M.B., and Muller U. Recent developments in the molecular genetics of mitochondrial disorders. J. Neurol. Sci. 153 (1998) 251-263
16. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
17. Hibbett D.S., et al. A higher-level phylogenetic classification of the Fungi. Mycol. Res. 111 (2007) 509-547
18. Huang X., and Madan A. CAP3: a DNA sequence assembly program. Genome Res. 9 (1999) 868-877
19. James T.Y., et al. A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98 (2006) 860-871
20. Karling J.S. A note on Blastocladiella (Blastocladiaceae). Mycopath. Mycol. App. 49 (1973) 169-172
21. Korab-Laskowska M., et al. The Organelle Genome Database Project (GOBASE). Nucleic Acids Res. 26 (1998) 138-144
22. Kouvelis V.N., Ghikas D.V., and Typas M.A. The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: phylogenetic implications. Fungal Genet. Biol. 41 (2004) 930-940
23. Kroemer G., Dallaporta B., and Resche-Rigon M. The mitochondrial death/life regulator in apoptosis and necrosis. Annu. Rev. Physiol. 60 (1998) 619-642
24. Kumar S., Tamura K., Jakobsen I.B., and Nei M. MEGA 2: molecular evolutionary genetics analysis software. Bioinformatics 17 (2001) 1244-1245
25. Lambert A.J., and Brand M.D. Research on mitochondria and aging, 2006-2007. Aging Cell 6 (2007) 417-420
26. Liu Y.J., Hodson M.C., and Hall B.D. Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes. BMC Evol. Biol. 6 (2006) 74
27. Lovett J.S. Growth and differentiation of the water mold Blastocladiella emersonii: cytodifferentiation and the role of ribonucleic acid and protein synthesis. Bacteriol. Rev. 39 (1975) 345-404
28. 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
29. Marques Mdo V., and Gomes S.L. Cloning and structural analysis of the gene for the regulatory subunit of cAMP-dependent protein kinase in Blastocladiella emersonii. J. Biol. Chem. 267 (1992) 17201-17207
30. Martin W., and Muller M. The hydrogen hypothesis for the first eukaryote. Nature 392 (1998) 37-41
31. Page R.D. TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12 (1996) 357-358
32. Paquin B., and Lang B.F. The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus. J. Mol. Biol. 255 (1996) 688-701
33. Paquin B., Laforest M.J., and Lang B.F. Interspecific transfer of mitochondrial genes in fungi and creation of a homologous hybrid gene. Proc. Natl. Acad. Sci. U. S. A. 91 (1994) 11807-11810
34. Paquin B., et al. The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Curr. Genet. 31 (1997) 380-395
35. Paquin B., Laforest M.J., and Lang B.F. Double-hairpin elements in the mitochondrial DNA of allomyces: evidence for mobility. Mol. Biol. Evol. 17 (2000) 1760-1768
36. Reeves J.H. Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. J. Mol. Evol. 35 (1992) 17-31
37. Ribichich K.F., Georg R.C., and Gomes S.L. Comparative EST analysis provides insights into the basal aquatic fungus Blastocladiella emersonii. BMC Genomics 7 (2006) 177
38. Robbertse B., Reeves J.B., Schoch C.L., and Spatafora J.W. A phylogenomic analysis of the Ascomycota. Fungal Genet. Biol. 43 (2006) 715-725
39. Rocha C.R., and Gomes S.L. Characterization and submitochondrial localization of the alpha subunit of the mitochondrial processing peptidase from the aquatic fungus Blastocladiella emersonii. J. Bacteriol. 181 (1999) 4257-4265
40. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
41. Saccone C., Gissi C., Reyes A., Larizza A., Sbisa E., and Pesole G. Mitochondrial DNA in metazoa: degree of freedom in a frozen event. Gene 286 (2002) 3-12
42. Seif E., Leigh J., Liu Y., Roewer I., Forget L., and Lang B.F. Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms. Nucleic Acids Res. 33 (2005) 734-744
43. Sugiyama Y., et al. The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Mol. Genet. Genomics 272 (2005) 603-615
44. Tanabe Y., Watanabe M.M., and Sugiyama J. Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics. J. Gen. Appl. Microbiol. 51 (2005) 267-276
45. 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
46. Whelan S., and Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18 (2001) 691-699
47. Woo P.C., et al. The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts. FEBS Lett. 555 (2003) 469-477
48. Yacobi K., Tsafriri A., and Gross A. Luteinizing hormone-induced caspase activation in rat preovulatory follicles is coupled to mitochondrial steroidogenesis. Endocrinology 148 (2007) 1717-1726
49. Yang J., Wang J., Yao Z.J., Jin Q., Shen Y., and Chen R. GenomeComp: a visualization tool for microbial genome comparison. J. Microbiol. Methods 54 (2003) 423-426
50. Yang Z. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10 (1993) 1396-1401
51. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555-556