Imported sequences in the mitochondrial yeast genome identified by nucleotide linguistics

Anziano, 1982, Functional domains in introns: trans-acting and cis-acting regions of intron 4 of the cob gene, Cell, 30, 925, 10.1016/0092-8674(82)90297-5 Belfort, 1990, Phage T4 introns: self-splicing and mobility, Annu. Rev. Genet., 24, 363, 10.1146/annurev.ge.24.120190.002051 Blaisdell, 1986, A measure of the similarity of sets of sequences not requiring sequence alignment, 83, 5155 Bonitz, 1980, Assembly of the mitochondrial membrane system. Structure and nucleotide sequence of the gene coding for subunit I of yeast cytochrome oxidase, J. Biol. Chem., 255, 11927, 10.1016/S0021-9258(19)70224-5 Boulet, 1990, The absence of introns in yeast mitochondria does not abolish mitochondrial recombination, Curr. Genet., 17, 537, 10.1007/BF00313085 Brendel, 1986, Linguistics of nucleotide sequences: morphology and comparison of vocabularies, J. Biomol. Struct. Dyn., 4, 11, 10.1080/07391102.1986.10507643 Burke, 1984, Cytochrome b gene of Neurospora crussa mitochondria: partial sequence and location of introns at sites different from those in Saccharomyces cerevisiae and Aspergillus nidulans, J. Biol. Chem., 259, 504, 10.1016/S0021-9258(17)43690-8 Burks, 1990, GenBank: current status and future directions, Methods Enzymol., 183, 3, 10.1016/0076-6879(90)83003-R Chomyn, 1987, Mitochondrial gene products, Curr. Topics Bioenerg., 15, 295, 10.1016/B978-0-12-152515-6.50014-X Colin, 1985, A new putative gene in the mitochondrial genome of Saccharomyces cerevisiae, Gene, 36, 1, 10.1016/0378-1119(85)90064-2 Colleaux, 1986, Universal code equivalent of a yeast mitochondrial intron reading frame is expressed into E.coli as a specific double strand endonuclease, Cell, 44, 521, 10.1016/0092-8674(86)90262-X Coruzzi, 1979, Assembly of the mitochondrial membrane system. DNA sequence of subunit 2 of yeast cytochrome oxidase, J. Biol. Chem., 254, 9324, 10.1016/S0021-9258(19)86848-5 Coruzzi, 1981, Assembly of the mitochondrial membrane system. Analysis of the nucleotide sequence and transcripts in the oxil region of yeast mitochondrial DNA, J. Biol. Chem., 256, 12780, 10.1016/S0021-9258(18)42963-8 Cummings, 1990, The complete DNA sequence of the mitochondrial genome of Podospora aiiserina, Curr. Genet., 17, 375, 10.1007/BF00334517 De Jong, 1983, The structure of the gene for subunit I of cytochrome c oxidase in Neurospora crassa mitochondria, Curr. Genet., 7, 21, 10.1007/BF00365676 de Zamaroczy, 1985, Sequence organization of the mitochondrial genome of yeast—a review, Gene, 37, 1, 10.1016/0378-1119(85)90252-5 de Zamaroczy, 1986, The primary structure of the mitochondrial genome of Saccharomyces cerevisiae—a review, Gene, 47, 155, 10.1016/0378-1119(86)90060-0 de Zamaroczy, 1987, The AT spacers and the varl genes from the mitochondrial genomes of Saccharomyces cerevisiae and Tomlopsis glabrata: evolutionary origin and mechanism of formation, Gene, 54, 1, 10.1016/0378-1119(87)90342-8 Devereux, 1984, A comprehensive set of sequence analysis programs for the VAX, Nucleic Acids Res., 12, 387, 10.1093/nar/12.1Part1.387 Doolittle, 1989, Origins and evolutionary relationships of retroviruses, Q. Rev. Biol., 64, 1, 10.1086/416128 Dujardin, 1982, Single base substitution in an intron of oxidase gene compensates splicing defects of the cytochrome b gene, Nature, 298, 628, 10.1038/298628a0 Dujon, 1989, Group I introns as mobile genetic elements: facts and mechanistic speculations—a review, Gene, 82, 91, 10.1016/0378-1119(89)90034-6 Fox, 1979, Five TGA ‘stop’ codons occur within the translated sequence of the yeast mitochondrial gene for cytochrome c oxidase subunit II, 76, 6534 Granero-Porati, 1988, Informational parameters and randomness of mitochondrial DNA, J. Mol. Evol., 27, 109, 10.1007/BF02138369 Hamm, 1986, The EMBL data library, Nucleic Acids Res., 14, 5, 10.1093/nar/14.1.5 Hengsens, 1983, Two intron sequences in yeast mitochondrial cox1 gene: homology among URF-containing introns and strain-dependent variation in flanking exons, Cell, 32, 379, 10.1016/0092-8674(83)90457-9 Jacquier, 1983, The intron of the mitochondrial 21S rRNA gene: distribution in different yeast species and sequence comparison between Kluyveromyces thermotolerans and Saccharomyces cerevisiae, Mol. Gen. Genet., 192, 487, 10.1007/BF00392195 Jacquier, 1985, An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene, Cell, 41, 383, 10.1016/S0092-8674(85)80011-8 Lambowitz, 1990, Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splining, Trends Biochem. Sci., 15, 440, 10.1016/0968-0004(90)90283-H Lang, 1984, The mitochondrial genome of the fission yeast Schizosaccharomyces pombe: highly homologous introns are inserted at the same position of the otherwise less conserved coxI genes in Schizosaccharomyces pombe and Aspergillus nidulans, EMBO J., 3, 2129, 10.1002/j.1460-2075.1984.tb02102.x Lazowska, 1980, Sequence of introns and flanking exons in wildtype and box3 mutants of cytochrome b reveals an interlaced splicing protein encoded by an intron, Cell, 22, 333, 10.1016/0092-8674(80)90344-X Levings, 1989, Molecular biology of plant mitochondria, Cell, 56, 171, 10.1016/0092-8674(89)90890-8 Macino, 1980, Assembly of the mitochondrial membrane system: sequence analysis of a yeast mitochondrial ATPase gene containing the oli-2 and oli-4 loci, Cell, 20, 507, 10.1016/0092-8674(80)90637-6 Michel, 1984, A maturase-like coding sequence downstream from the oxi2 gene of yeast mitochondrial DNA is interrupted by two GC clusters and a putative end-of-messenger signal, Curr. Genet., 8, 307, 10.1007/BF00419729 Michel, 1985, Analysis of class I introns in a mitochondrial plasmid associated with senescence of Podospora anserina reveals extraordinary resemblance to the Tetrahymena ribosomal intron, Curr. Genet., 10, 69, 10.1007/BF00418495 Michel, 1986, Genetic exchange between bacteriophage T4 and filamentous fungi?, Cell, 46, 323, 10.1016/0092-8674(86)90651-3 Michel, 1985, Mitochondrial class II introns encode proteins related to the reverse transcriptases ofretroviruses, Nature, 316, 641, 10.1038/316641a0 Netter, 1989, The differential overamplification of short sequences in the mitochondrial DNA of rho-petites in Saccharomyces cerevisiae stimulates recombination, Gene, 83, 25, 10.1016/0378-1119(89)90400-9 Nobrega, 1980, Assembly of the mitochondrial membrane system. DNA sequence and organization of the cytochrome b gene in Saccharomyces cerevisiae D273-10B, J. Biol. Chem., 255, 9828, 10.1016/S0021-9258(18)43467-9 Nussinov, 1984, Doublet frequencies in evolutionary distinct groups, Nucleic Acids Res., 12, 1749, 10.1093/nar/12.3.1749 Oliver, 1992, The complete DNA sequence of yeast chromosome III, Nature, 357, 38, 10.1038/357038a0 Perlman, 1989, Mobile introns and intron-encoded proteins, Science, 246, 1106, 10.1126/science.2479980 Pietrokovski, 1990, Linguistic measure of taxonomic and functional relatedness of nucleotide sequences, J. Biomol. Struct. Dyn., 7, 1251, 10.1080/07391102.1990.10508563 Russel, 1977, Similarity of the general designs of protochordates and invertebrates, Nature, 266, 533, 10.1038/266533a0 Seraphin, 1985, A mitochondrial reading frame which may code for a maturase-like protein in Saccharomyces cerevisiae, Nucleic Acids Res., 13, 3005, 10.1093/nar/13.8.3005 Seraphin, 1987, The mitochondrial reading frame RF3 is a functional gene in Saccharomyces uvarum, J. Biol. Chem., 262, 10146, 10.1016/S0021-9258(18)61090-7 Seraphin, 1987, Construction of ayeast strain devoid of mitochondrial introns and its use to screen nuclear genes involved in mitochondrial splicing, 84, 6810 Skelly, 1991, Distribution of mitochondrial intron sequences among 21 yeast species, Curr. Genet., 19, 89, 10.1007/BF00326288 Sor, 1983, Complete DNA sequence coding for the large ribosomal RNA of yeast mitochondria, Nucleic Acids Res., 11, 339, 10.1093/nar/11.2.339 Syvanen, 1987, Molecular clocks and evolutionary relationships: possible distortions due to horizontal gene flow, Mol. Evol., 26, 16, 10.1007/BF02111278 Thalenfeld, 1980, Assembly of mitochondrial membrane system: sequence of the oxi2 gene of yeast mitochondrial DNA, J. Biol. Chem., 255, 6173, 10.1016/S0021-9258(18)43718-0 Trinkl, 1986, The mosaic coxI gene in the mitochondrial genome of Schizosaccharomyces pombe: minimal structural requirements and evolution of group I introns, Gene, 45, 289, 10.1016/0378-1119(86)90027-2 Xiong, 1988, Similarity of reverse transcriptase-like sequences of viruses, transposable elements and mitochondrial introns, Mol. Biol. Evol., 5, 675 Zimmer, 1987, Distribution of mitochondrial introns in the species Schizosaccharomyces pombe and the origin of the group II intron in the gene encoding apocytochrome b, Curr. Genet., 12, 329, 10.1007/BF00405755