From endosymbiont to host-controlled organelle: The hijacking of mitochondrial protein synthesis and metabolism

PLoS Computational Biology

Volumn 3, Issue 11, 2007, Pages 2209-2218

  Gabaldón, Toni ^a,b   Huynen, Martijn A ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; CELL PROLIFERATION; ENERGY CONVERSION; METABOLISM; MITOCHONDRIA; PHYSIOLOGY; SIGNAL TRANSDUCTION;

ENDOSYMBIONT; ENDOSYMBIOSIS; EUKARYOTICS; FREE LIVINGS; GAIN INSIGHT; MITOCHONDRIAL PROTEIN; MITOCHONDRIAS; PROTEIN METABOLISM; PROTEIN SYNTHESIS; PROTEOBACTERIA;

PROTEINS;

MITOCHONDRIAL PROTEIN; PROTEOME; FUNGAL PROTEIN;

ARTICLE; CELL DIVISION; CELL ORGANELLE; CELL TRANSPORT; COMPARATIVE STUDY; ENDOSYMBIONT; ENERGY CONVERSION; EUKARYOTIC CELL; EVOLUTION; HOST; HUMAN; MITOCHONDRION; NONHUMAN; PROTEIN METABOLISM; PROTEIN SYNTHESIS; SIGNAL TRANSDUCTION; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETIC VARIABILITY; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; SYMBIOSIS;

ALPHAPROTEOBACTERIA; EUKARYOTA; PROTEOBACTERIA;

BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; DNA MUTATIONAL ANALYSIS; EVOLUTION, MOLECULAR; FUNGAL PROTEINS; GENETIC VARIATION; HUMANS; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; MODELS, GENETIC; ORGANELLES; PROTEIN BIOSYNTHESIS; SYMBIOSIS;

EID: 36949022294     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030219     Document Type: Article

References (45)

1. Scheffler IE (2001) Mitochondria make a comeback. Adv Drug Deliv Rev 49: 3-26.
2. Miller WL (1995) Mitochondrial specificity of the early steps in steroidogenesis. J Steroid Biochem Mol Biol 55: 607-616.
3. Lill R, Muhlenhoff U (2005) Iron-sulfur-protein biogenesis in eukaryotes. Trends Biochem Sci 30: 133-141.
4. Gray MW, Burger G, Lang BF (1999) Mitochondrial evolution. Science 283: 1476-1481.
5. Gabaldón T, Huynen MA (2004) Shaping the mitochondrial proteome. Biochim Biophys Acta 1659: 212-220.
6. Kurland CG, Andersson SG (2000) Origin and evolution of the mitochondrial proteome. Microbiol Mol Biol Rev 64: 786-820.
7. Gray MW, Burger G, Lang BF (2001) The origin and early evolution of mitochondria. Genome Biol 2: REVIEWS1018.1-1018.5. doi:10.1186/gb-2001-2-6- reviews1018
8. Heazlewood JL, Millar AH, Day DA, Whelan J (2003) What makes a mitochondrion? Genome Biol 4: 218. doi: 10.1186/gb-2003-4-6-218
9. Gabaldón T, Huynen MA (2003) Reconstruction of the proto-mitochondrial metabolism. Science 301: 609.
10. Berry S (2003) Endosymbiosis and the design of eukaryotic electron transport. Biochim Biophys Acta 1606: 57-72.
11. Gabaldón T, Rainey D, Huynen MA (2005) Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I). J Mol Biol 348: 857-870.
12. Lang BF, Burger G, O'Kelly CJ, Cedergren R, Golding GB, et al. (1997) An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387: 493-497.
13. Kiefel BR, Gilson PR, Beech PL (2004) Diverse eukaryotes have retained mitochondrial homologues of the bacterial division protein FtsZ. Protist 155: 105-115.
14. Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, et al. (1999) Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res 9: 608-628.
15. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28: 33-36.
16. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29: 22-28.
17. Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27-30.
18. Huynen MA, Dandekar T, Bork P (1999) Variation and evolution of the citric-acid cycle: a genomic perspective. Trends Microbiol 7: 281-291.
19. Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, et al. (2000) Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res 28: 1397-1406.
20. Schnarrenberger C, Martin W (2002) Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants. A case study of endosymbiotic gene transfer. Eur J Biochem 269: 868-883.
21. Canback B, Andersson SG, Kurland CG (2002) The global phylogeny of glycolytic enzymes. Proc Natl Acad Sci U S A 99: 6097-6102.
22. Warnock DE, Fahy E, Taylor SW (2004) Identification of protein associations in organelles, using mass spectrometry-based proteomics. Mass Spectrom Rev 23: 259-280.
23. Taylor SW, Fahy E, Ghosh SS (2003) Global organellar proteomics. Trends Biotechnol 21: 82-88.
24. Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, et al. (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100: 13207-13212.
25. Cotter D, Guda P, Fahy E, Subramaniam S (2004) MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res 32 (Database issue): D463-D467.
26. Taylor SW, Fahy E, Zhang B, Glenn GM, Warnock DE, et al. (2003) Characterization of the human heart mitochondrial proteome. Nat Biotechnol 21: 281-286.
27. Mootha VK, Bunkenborg J, Olsen JV, Hjerrild M, Wisniewski JR, et al. (2003) Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115: 629-640.
28. Tanaka N, Fujita M, Handa H, Murayama S, Uemura M, et al. (2004) Proteomics of the rice cell: systematic identification of the protein populations in subcellular compartments. Mol Genet Genomics 271: 566-576.
29. van Roermund CW, Waterham HR, Ijlst L, Wanders RJ (2003) Fatty acid metabolism in Saccharomyces cerevisiae. Cell Mol Life Sci 60: 1838-1851.
30. Kuwana T, Newmeyer DD (2003) Bcl-2-family proteins and the role of mitochondria in apoptosis. Curr Opin Cell Biol 15: 691-699.
31. Karlberg O, Canback B, Kurland CG, Andersson SG (2000) The dual origin of the yeast mitochondrial proteome. Yeast 17: 170-187.
32. Andersson SG, Karlberg O, Canback B, Kurland CG (2003) On the origin of mitochondria: a genomics perspective. Philos Trans R Soc Lond B Biol Sci 358: 165-177.
33. Wiedemann N, Frazier AE, Pfanner N (2004) The protein import machinery of mitochondria. J Biol Chem 279: 14473-14476.
34. Osteryoung KW, Nunnari J (2003) The division of endosymbiotic organelles. Science 302: 1698-1704.
35. Herrmann JM (2003) Converting bacteria to organelles: evolution of mitochondrial protein sorting. Trends Microbiol 11: 74-79.
36. Dolezal P, Likic V, Tachezy J, Lithgow T (2006) Evolution of the molecular machines for protein import into mitochondria. Science 313: 314-318.
37. Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, et al. (2002) Systematic screen for human disease genes in yeast. Nat Genet 31: 400-404.
38. Denis-Duphil M (1989) Pyrimidine biosynthesis in Saccharomyces cerevisiae: the ura2 cluster gene, its multifunctional enzyme product, and other structural or regulatory genes involved in de novo UMP synthesis. Biochem Cell Biol 67: 612-631.
39. Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, et al. (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res 32 (Database issue): D311-D314.
40. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113. doi: 10.1186/1471-2105-5- 113
41. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
42. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147: 195-197.
43. Thompson JD, Higgins DG, Gibson TJ (1994) 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: 4673-4680.
44. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41. doi: 10.1186/1471-2105-4-41
45. Al-Shahrour F, Minguez P, Tarraga J, Montaner D, Alloza E, et al. (2006) BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res 34: W472-W476.