Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Marcet Houben, Marina ^a   Marceddu, Giuseppe ^a,b   Gabaldán, Toni ^a  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITY OF TURIN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; OXIDOREDUCTASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE (UBIQUINONE); SUCCINATE DEHYDROGENASE (UBIQUINONE); UBIQUINOL CYTOCHROME C REDUCTASE;

ADAPTATION; AMINO ACID SEQUENCE; ANAEROBIC METABOLISM; ARTICLE; FUNGAL GENE; GENE DUPLICATION; GENE LOSS; GENETIC VARIABILITY; KLUYVEROMYCES; MITOCHONDRION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; OXIDATIVE PHOSPHORYLATION; PARALOGY; PHYLOGENY; SACCHAROMYCES; SCHIZOSACCHAROMYCES; ARABIDOPSIS; CLASSIFICATION; ENZYMOLOGY; FUNGUS; GENETICS; HUMAN;

FUNGI; MICROSPORIDIA;

ARABIDOPSIS; EVOLUTION, MOLECULAR; FUNGI; GENE DUPLICATION; HUMANS; OXIDATIVE PHOSPHORYLATION; OXIDOREDUCTASES; PHYLOGENY;

EID: 74049101127     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-295     Document Type: Article

References (39)

1. Oxidative phosphorylation at the fin de siecle. M Saraste, Science 1999 283 5407 1488 1493 10.1126/science.283.5407.1488 10066163
2. Reconstruction of the proto-mitochondrial metabolism. T Gabaldán MA Huynen, Science 2003 301 5633 609 10.1126/science.1085463 12893934
3. Shaping the mitochondrial proteome. T Gabaldán MA Huynen, Biochim Biophys Acta 2004 1659 2-3 212 220 10.1016/j.bbabio.2004.07.011 15576054
4. Tracing the Evolution of a Large Protein Complex in the Eukaryotes, NADH:Ubiquinone Oxidoreductase (Complex I). T Gabaldán D Rainey MA Huynen, J Mol Biol 2005 348 4 857 870 10.1016/j.jmb.2005.02.067 15843018
5. A molecular chaperone for mitochondrial complex I assembly is mutated in a progressive encephalopathy. I Ogilvie NG Kennaway EA Shoubridge, J Clin Invest 2005 115 10 2784 2792 10.1172/JCI26020 16200211
6. Genomics of the fungal kingdom: insights into eukaryotic biology. JE Galagan MR Henn LJ Ma CA Cuomo B Birren, Genome Res 2005 15 12 1620 1631 10.1101/gr.3767105 16339359
7. The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome. M Marcet-Houben T Gabaldán, PLoS ONE 2009 4 2 4357 10.1371/journal.pone.0004357 19190756
8. Fungal evolution: the case of the vanishing mitochondrion. CE Bullerwell BF Lang, Curr Opin Microbiol 2005 8 4 362 369 10.1016/j.mib.2005.06.009 15993645
9. Comparative genomics of the oxidative phosphorylation system in fungi. JL Lavin JA Oguiza L Ramirez AG Pisabarro, Fungal Genet Biol 2008 45 9 1248 1256 10.1016/j.fgb.2008.06.005 18647654
10. Dosage sensitivity and the evolution of gene families in yeast. B Papp C Pal LD Hurst, Nature 2003 424 6945 194 197 10.1038/nature01771 12853957
11. KEGG Atlas mapping for global analysis of metabolic pathways. S Okuda T Yamada M Hamajima M Itoh T Katayama P Bork S Goto M Kanehisa, Nucleic Acids Res 2008 36 Web Server 423 426 10.1093/nar/gkn282 18477636
12. The human phylome. J Huerta-Cepas H Dopazo J Dopazo T Gabaldán, Genome Biol 2007 8 6 109 17567924
13. Distinguishing homologous from analogous proteins. WM Fitch, Syst Zool 1970 19 2 99 113 10.2307/2412448 5449325
14. Large-scale assignment of orthology: back to phylogenetics? T Gabaldán, Genome Biol 2008 9 10 235 10.1186/gb-2008-9-10-235 18983710
15. Evolution by gene duplication. S Ohno, London: Allen & Unwin 1970
16. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. M Kellis BW Birren ES Lander, Nature 2004 428 6983 617 624 10.1038/nature02424 15004568
17. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. LJ Ma AS Ibrahim C Skory MG Grabherr G Burger M Butler M Elias A Idnurm BF Lang T Sone, et al. PLoS Genet 2009 5 7 1000549 10.1371/journal.pgen.1000549 19578406
18. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. MD Katinka S Duprat E Cornillot G Metenier F Thomarat G Prensier V Barbe E Peyretaillade P Brottier P Wincker, et al. Nature 2001 414 6862 450 453 10.1038/35106579 11719806
19. Cyanide-resistant respiration, a very frequent metabolic pathway in yeasts. A Veiga JD Arrabaca MC Loureiro-Dias, FEMS Yeast Res 2003 3 3 239 245 10.1016/S1567-1356(03)00036-9 12689632
20. Cloning and functional expression of the mitochondrial alternative oxidase of Aspergillus fumigatus and its induction by oxidative stress. T Magnani FM Soriani VP Martins AM Nascimento VG Tudella C Curti SA Uyemura, FEMS Microbiol Lett 2007 271 2 230 238 10.1111/j.1574-6968.2007.00716.x 17425662
21. Characterization of an alternative oxidase activity of Histoplasma capsulatum. CH Johnson JT Prigge AD Warren JE McEwen, Yeast 2003 20 5 381 388 10.1002/yea.968 12673621
22. Capsule enlargement in Cryptococcus neoformans confers resistance to oxidative stress suggesting a mechanism for intracellular survival. O Zaragoza CJ Chrisman MV Castelli S Frases M Cuenca-Estrella JL Rodriguez-Tudela A Casadevall, Cell Microbiol 2008 10 10 2043 2057 10.1111/j.1462-5822.2008.01186.x 18554313
23. The altered evolutionary trajectories of gene duplicates. M Lynch V Katju, Trends Genet 2004 20 11 544 549 10.1016/j.tig.2004.09.001 15475113
24. Inverse regulation of the yeast COX5 genes by oxygen and heme. MR Hodge G Kim K Singh MG Cumsky, Mol Cell Biol 1989 9 5 1958 1964 2546055
25. Mitochondrial processing peptidases. O Gakh P Cavadini G Isaya, Biochim Biophys Acta 2002 1592 1 63 77 10.1016/S0167-4889(02)00265-3 12191769
26. Mitochondrial acyl carrier protein is involved in lipoic acid synthesis in Saccharomyces cerevisiae. S Brody C Oh U Hoja E Schweizer, FEBS Lett 1997 408 2 217 220 10.1016/S0014-5793(97)00428-6 9187370
27. Different respiratory-defective phenotypes of Neurospora crassa and Saccharomyces cerevisiae after inactivation of the gene encoding the mitochondrial acyl carrier protein. R Schneider M Massow T Lisowsky H Weiss, Curr Genet 1995 29 1 10 17 10.1007/BF00313188 8595652
28. Presence of an acyl carrier protein in NADH:ubiquinone oxidoreductase from bovine heart mitochondria. MJ Runswick IM Fearnley JM Skehel JE Walker, FEBS Lett 1991 286 1-2 121 124 10.1016/0014-5793(91)80955-3 1907568
29. Genome duplication and gene-family evolution: the case of three OXPHOS gene families. A De Grassi C Lanave C Saccone, Gene 2008 421 1-2 1 6 10.1016/j.gene.2008.05.011 18573316
30. Metazoan OXPHOS gene families: evolutionary forces at the level of mitochondrial and nuclear genomes. C Saccone C Lanave A De Grassi, Biochim Biophys Acta 2006 1757 9-10 1171 1178 10.1016/j.bbabio.2006.04.021 16781661
31. KEGG for linking genomes to life and the environment. M Kanehisa M Araki S Goto M Hattori M Hirakawa M Itoh T Katayama S Kawashima S Okuda T Tokimatsu, et al. Nucleic Acids Res 2008 36 Database 480 484 18077471
32. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 3 403 410 2231712
33. PhylomeDB: a database for genome-wide collections of gene phylogenies. J Huerta-Cepas A Bueno J Dopazo T Gabaldán, Nucleic Acids Res 2008 36 Database 491 496 17962297
34. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. RC Edgar, BMC Bioinformatics 2004 5 1 113 10.1186/1471-2105-5-113 15318951
35. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. S Capella-Gutíerrez JM Silla-Martínez T Gabaldán, Bioinformatics 2009 25 15 1972 3 10.1093/bioinformatics/btp348 19505945
36. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 5 696 704 10.1080/10635150390235520 14530136
37. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. M Anisimova O Gascuel, Syst Biol 2006 55 4 539 552 10.1080/10635150600755453 16785212
38. Information theory and extension of the maximum likelihood principle. H Akaike, Proceedings of the 2nd international symposium on information theory: 1973; Budapest, Hungary 1973 267 281
39. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. KR Christie S Weng R Balakrishnan MC Costanzo K Dolinski SS Dwight SR Engel B Feierbach DG Fisk JE Hirschman, et al. Nucleic Acids Res 2004 32 Database 311 314 10.1093/nar/gkh033 14681421