Mitochondrial genomes of yeasts of the Yarrowia clade

FEMS Yeast Research

Volumn 12, Issue 3, 2012, Pages 317-331

  Gaillardin, Claude ^a,b   Neuvéglise, Cécile ^a,b   Kerscher, Stefan ^c   Nicaud, Jean Marc ^a,b  

^a AGROPARISTECH   (France)

^b UMR1319 MICALIS   (France)

^c Heinrich von Gagern Gymnasium   (Germany)

Author keywords

Group I and II introns; Phylogeny; Synteny; TilS

Indexed keywords

ENDONUCLEASE; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; CANDIDA; CANDIDA ALIMENTARIA; CANDIDA DEFORMANS; CANDIDA GALLI; CANDIDA PHANGNGENSIS; CLADISTICS; CODON USAGE; DNA SEQUENCE; GENE STRUCTURE; GENETIC CODE; GENOME SIZE; INTRON; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; SYNTENY; YARROWIA LIPOLYTICA;

CANDIDA; DNA, MITOCHONDRIAL; GENE ORDER; GENOME SIZE; GENOME, MITOCHONDRIAL; INTRONS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SYNTENY; YARROWIA;

CANDIDA; CANDIDA DEFORMANS; CANDIDA GALLI; CANDIDA SALMANTICENSIS; YARROWIA; YARROWIA LIPOLYTICA;

EID: 84859622599     PISSN: 15671356     EISSN: 15671364     Source Type: Journal    
DOI: 10.1111/j.1567-1364.2011.00782.x     Document Type: Article

References (77)

1. Acker J, Ozanne C, Kachouri-Lafond R, Gaillardin C, Neuveglise C & Marck C (2008) Dicistronic tRNA-5S rRNA genes in Yarrowia lipolytica: an alternative TFIIIA-independent way for expression of 5S rRNA genes. Nucleic Acids Res 36: 5832-5844.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W & Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
3. Belfort M & Perlman PS (1995) Mechanisms of intron mobility. J Biol Chem 270: 30237-30240.
4. Bendich AJ (2007) The size and form of chromosomes are constant in the nucleus, but highly variable in bacteria, mitochondria and chloroplasts. Bioessays 29: 474-483.
5. Bigey F, Tuery K, Bougard D, Nicaud JM & Moulin G (2003) Identification of a triacylglycerol lipase gene family in Candida deformans: molecular cloning and functional expression. Yeast 20: 233-248.
6. Bullerwell CE & Lang BF (2005) Fungal evolution: the case of the vanishing mitochondrion. Curr Opin Microbiol 8: 362-369.
7. Bullerwell CE, Leigh J, Forget L & Lang BF (2003) A comparison of three fission yeast mitochondrial genomes. Nucleic Acids Res 31: 759-768.
8. Cannone JJ, Subramanian S, Schnare MN et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2.
9. Cardazzo B, Minuzzo S, Sartori G, Grapputo A & Carignani G (1998) Evolution of mitochondrial DNA in yeast: gene order and structural organization of the mitochondrial genome of Saccharomyces uvarum. Curr Genet 33: 52-59.
10. Casaregola S, Neuveglise C, Lepingle A, Bon E, Feynerol C, Artiguenave F, Wincker P & Gaillardin C (2000) Genomic exploration of the hemiascomycetous yeasts: 17. Yarrowia lipolytica. FEBS Lett 487: 95-100.
11. Clark-Walker GD & Weiller GF (1994) The structure of the small mitochondrial DNA of Kluyveromyces thermotolerans is likely to reflect the ancestral gene order in fungi. J Mol Evol 38: 593-601.
12. Dereeper A, Guignon V, Blanc G et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36: W465-W469.
13. Dujon B (2010) Yeast evolutionary genomics. Nat Rev Genet 11: 512-524.
14. Dujon B, Belfort M, Butow RA, Jacq C, Lemieux C, Perlman PS & Vogt VM (1989) Mobile introns: definition of terms and recommended nomenclature. Gene 82: 115-118.
15. Dujon B, Sherman D, Fischer G et al. (2004) Genome evolution in yeasts. Nature 430: 35-44.
16. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
17. Eldarov MA, Mardanov AV, Beletsky AV, Ravin NV & Skryabin KG (2011) Complete sequence and analysis of the mitochondrial genome of the methylotrophic yeast Hansenula polymorpha DL-1. FEMS Yeast Res 11: 464-472.
18. Ferandon C, Moukha S, Callac P, Benedetto JP, Castroviejo M & Barroso G (2010) The Agaricus bisporus cox1 gene: the longest mitochondrial gene and the largest reservoir of mitochondrial group I introns. PLoS ONE 5: e14048.
19. Gaillardin C, Duchateau-Nguyen G, Tekaia F et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes. FEBS Lett 487: 134-149.
20. Gascuel O (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14: 685-695.
21. Goloboff PA, Farris JS & Nixon KC (2008) TNT, a free program for phylogenetic analysis. Cladistics 24: 774-786.
22. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W & Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
23. Hellborg L & Piskur J (2009) Complex nature of the genome in a wine spoilage yeast, Dekkera bruxellensis. Eukaryot Cell 8: 1739-1749.
24. Huang H, Chopra R, Verdine GL & Harrison SC (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282: 1669-1675.
25. Huelsenbeck JP & Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
26. Huse SM, Huber JA, Morrison HG, Sogin ML & Welch DM (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
27. Ikeuchi Y, Soma A, Ote T, Kato J, Sekine Y & Suzuki T (2005) Molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. Mol Cell 19: 235-246.
28. Jung PP, Schacherer J, Souciet JL, Potier S, Wincker P & de Montigny J (2009) The complete mitochondrial genome of the yeast Pichia sorbitophila. FEMS Yeast Res 9: 903-910.
29. Jung PP, Friedrich A, Souciet JL, Louis V, Potier S, de Montigny J & Schacherer J (2010) Complete mitochondrial genome sequence of the yeast Pichia farinosa and comparative analysis of closely related species. Curr Genet 56: 507-515.
30. Kerscher S, Durstewitz G, Casaregola S, Gaillardin C & Brandt U (2001) The complete mitochondrial genome of Yarrowia lipolytica. Comp Funct Genomics 2: 80-90.
31. Kerscher S, Drose S, Zwicker K, Zickermann V & Brandt U (2002) Yarrowia lipolytica, a yeast genetic system to study mitochondrial complex I. Biochim Biophys Acta 1555: 83-91.
32. Knutsen AK, Robert V, Poot GA, Epping W, Figge M, Holst-Jensen A, Skaar I & Smith MT (2007) Polyphasic re-examination of Yarrowia lipolytica strains and the description of three novel Candida species: Candida oslonensis sp. nov., Candida alimentaria sp. nov. and Candida hollandica sp. nov. Int J Syst Evol Microbiol 57: 2426-2435.
33. Konings DA & Gutell RR (1995) A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. RNA 1: 559-574.
34. Kosa P, Valach M, Tomaska L, Wolfe KH & Nosek J (2006) Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants. Nucleic Acids Res 34: 2472-2481.
35. Koszul R, Malpertuy A, Frangeul L, Bouchier C, Wincker P, Thierry A, Duthoy S, Ferris S, Hennequin C & Dujon B (2003) The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata. FEBS Lett 534: 39-48.
36. Kuberl A, Schneider J, Thallinger GG et al. (2011) High-quality genome sequence of Pichia pastoris CBS7435. J Biotechnol 154: 312-320.
37. Kurtzman CP (2005) New species and a new combination in the Hyphopichia and Yarrowia yeast clades. Antonie Van Leeuwenhoek 88: 121-130.
38. Kurtzman CP (2011a) Candida Berhout (1923). The Yeasts A Taxonomic Study, Vol. 2 (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 987-1278. Elsevier, London.
39. Kurtzman CP (2011b) Discussion of teleomorphic and ascomycetous yeasts and yeast-like taxa. The Yeasts A Taxonomic Study, Vol. 2 (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 293-310. Elsevier, London.
40. Kurtzman CP (2011c) Starmerella Rosa & Lachance (1998). The Yeasts A Taxonomic Study, Vol. 2 (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 811-815. Elsevier, London.
41. Kurtzman CP (2011d) Yarrowia van der Walt & von Arx (1980). The Yeasts A Taxonomic Study, Vol. 2 (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 928-929. Elsevier, London.
42. Limtong S, Youngmanitchai W, Kawasaki H & Seki T (2008) Candida phangngensis sp. nov., an anamorphic yeast species in the Yarrowia clade, isolated from water in mangrove forests in Phang-Nga Province, Thailand. Int J Syst Evol Microbiol 58: 515-519.
43. Loeytynoja A & Goldman N (2010) webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 11: 579-585.
44. Loytynoja A & Goldman N (2005) An algorithm for progressive multiple alignment of sequences with insertions. P Natl Acad Sci USA 102: 10557-10562.
45. Marck C, Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B & Grosjean H (2006) The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res 34: 1816-1835.
46. Matsuoka M, Matsubara M, Inoue J, Kakehi M & Imanaka T (1994) Organization and transcription of the mitochondrial ATP synthase genes in the yeast Yarrowia lipolytica. Curr Genet 26: 382-389.
47. Mekouar M, Blanc-Lenfle I, Ozanne C, Da Silva C, Cruaud C, Wincker P, Gaillardin C & Neuveglise C (2010) Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts. Genome Biol 11: R65.
48. Michel F & Ferat JL (1995) Structure and activities of group II introns. Annu Rev Biochem 64: 435-461.
49. Michel F & Westhof E (1990) Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol 216: 585-610.
50. Nakao Y, Kanamori T, Itoh T, Kodama Y, Rainieri S, Nakamura N, Shimonaga T, Hattori M & Ashikari T (2009) Genome sequence of the lager brewing yeast, an interspecies hybrid. DNA Res 16: 115-129.
51. Neuveglise C, Chalvet F, Wincker P, Gaillardin C & Casaregola S (2005) Mutator-like element in the yeast Yarrowia lipolytica displays multiple alternative splicings. Eukaryot Cell 4: 615-624.
52. Nosek J, Novotna M, Hlavatovicova Z, Ussery DW, Fajkus J & Tomaska L (2004) Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis. Mol Genet Genomics 272: 173-180.
53. Novo M, Bigey F, Beyne E et al. (2009) Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. P Natl Acad Sci USA 106: 16333-16338.
54. Osinga KA, De Vries E, Van der Horst GT & Tabak HF (1984) Initiation of transcription in yeast mitochondria: analysis of origins of replication and of genes coding for a messenger RNA and a transfer RNA. Nucleic Acids Res 12: 1889-1900.
55. Pantou MP, Kouvelis VN & Typas MA (2008) The complete mitochondrial genome of Fusarium oxysporum: insights into fungal mitochondrial evolution. Gene 419: 7-15.
56. Paquin B, Laforest MJ, Forget L, Roewer I, Wang Z, Longcore J & Lang BF (1997) The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Curr Genet 31: 380-395.
57. Peter G, Dlauchy D, Vasdinyei R, Tornai-Lehoczki J & Deak T (2004) Candida galli sp. nov., a new yeast from poultry. Antonie Van Leeuwenhoek 86: 105-110.
58. Pramateftaki PV, Kouvelis VN, Lanaridis P & Typas MA (2008) Complete mitochondrial genome sequence of the wine yeast Candida zemplinina: intraspecies distribution of a novel group-IIB1 intron with eubacterial affiliations. FEMS Yeast Res 8: 311-327.
59. Prochazka E, Polakova S, Piskur J & Sulo P (2010) Mitochondrial genome from the facultative anaerobe and petite-positive yeast Dekkera bruxellensis contains the NADH dehydrogenase subunit genes. FEMS Yeast Res 10: 545-557.
60. Saccone C, De Giorgi C, Gissi C, Pesole G & Reyes A (1999) Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 238: 195-209.
61. Schattner P, Brooks AN & Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33: W686-W689.
62. Schnare MN, Damberger SH, Gray MW & Gutell RR (1996) Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA. J Mol Biol 256: 701-719.
63. Seif ER, Forget L, Martin NC & Lang BF (2003) Mitochondrial RNase P RNAs in ascomycete fungi: lineage-specific variations in RNA secondary structure. RNA 9: 1073-1083.
64. Sipiczki M (2003) Candida zemplinina sp. nov., an osmotolerant and psychrotolerant yeast that ferments sweet botrytized wines. Int J Syst Evol Microbiol 53: 2079-2083.
65. Solieri L (2010) Mitochondrial inheritance in budding yeasts: towards an integrated understanding. Trends Microbiol 18: 521-530.
66. Tamura K, Peterson D, Peterson N, Stecher G, Nei M & Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
67. Tateno Y, Takezaki N & Nei M (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol Biol Evol 11: 261-277.
68. Thi Nguyen MA, Gesell T & von Haeseler A (2011) ImOSM: intermittent evolution and robustness of phylogenetic methods. Mol Biol Evol. doi: 10.1093/molbev/msr220.
69. Toor N, Hausner G & Zimmerly S (2001) Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7: 1142-1152.
70. Valach M, Farkas Z, Fricova D et al. (2011) Evolution of linear chromosomes and multipartite genomes in yeast mitochondria. Nucleic Acids Res 39: 4202-4219.
71. Vernis L, Poljak L, Chasles M, Uchida K, Casaregola S, Kas E, Matsuoka M, Gaillardin C & Fournier P (2001) Only centromeres can supply the partition system required for ARS function in the yeast Yarrowia lipolytica. J Mol Biol 305: 203-217.
72. Weber F, Dietrich A, Weil JH & Marechaldrouard L (1990) A potato mitochondrial isoleucine transfer-RNA is coded for by a mitochondrial gene possessing a methionine anticodon. Nucleic Acids Res 18: 5027-5030.
73. Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B & Stein N (2006) 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7: 275.
74. Wu Q, James SA, Roberts IN, Moulton V & Huber KT (2008) Exploring contradictory phylogenetic relationships in yeasts. FEMS Yeast Res 8: 641-650.
75. Yokoyama S, Muramatsu T, Horie N, Nishikawa K, Matsuda A, Ueda T, Yamaizumi Z, Kuchino Y, Nishimura S & Miyazawa T (1989) A novel lysine-substituted nucleoside in the 1st position of the anticodon of minor isoleucine transfer-RNA from Escherichia coli. Pure Appl Chem 61: 573-576.
76. Zimmerly S, Guo H, Perlman PS & Lambowitz AM (1995a) Group II intron mobility occurs by target DNA-primed reverse transcription. Cell 82: 545-554.
77. Zimmerly S, Guo H, Eskes R, Yang J, Perlman PS & Lambowitz AM (1995b) A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell 83: 529-538.