Why genes persist in organelle genomes

Genome Biology

Volumn 6, Issue 5, 2005, Pages

  Daley, Daniel O ^a   Whelan, James ^b  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; COMPLEMENTARY DNA;

ARABIDOPSIS; ARTICLE; CELL NUCLEUS; CELL ORGANELLE; CHLOROPLAST; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENE TRANSFER; GENETIC CODE; GENOME; HUMAN; HYDROPHOBICITY; MITOCHONDRION; PHYLOGENY; PLANT GENETICS; PLASTID;

CHLOROPLASTS; EVOLUTION, MOLECULAR; GENES, MITOCHONDRIAL; GENOME; HYDROPHOBICITY; MITOCHONDRIA; MODELS, GENETIC; PLASTIDS;

EID: 33744638372     PISSN: 14656906     EISSN: None     Source Type: Journal    
DOI: 10.1186/gb-2005-6-5-110     Document Type: Article

References (58)

1. Timmis JN, Ayliffe MA, Huang CY, Martin W: Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 2004, 5:123-135.
2. Martin W, Stoebe B, Goremykin V, Hapsmann S, Hasegawa M, Kowallik KV: Gene transfer to the nucleus and the evolution of chloroplasts. Nature 1998, 393:162-165.
3. Adams KL, Daley DO, Qiu YL, Whelan J, Palmer JD: Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 2000, 408:354-357.
4. Adams KL, Qiu YL, Stoutemyer M, Palmer JD: Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci USA 2002, 99:9905-9912.
5. Adams KL, Palmer JD: Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 2003, 29:380-395.
6. Martin W, Muller M: The hydrogen hypothesis for the first eukaryote. Nature 1998, 392:37-41.
7. Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, Meyer HE, Schonfisch B, Perschil I, Chacinska A, Guiard B, et al.: The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci USA 2003, 100:13207-13212.
8. Kleffmann T, Russenberger D, von Zychlinski A, Christopher W, Sjolander K, Gruissem W, Baginsky S: The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr Biol 2004, 14:354-362.
9. Heazlewood JL, Tonti-Filippini JS, Gout AM, Day DA, Whelan J, Millar AH: Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins. Plant Cell 2004, 16:241-256.
10. Baker A, Schatz G: Sequences from a prokaryotic genome or the mouse dihydrofolate reductase gene can restore the import of a truncated precursor protein into yeast mitochondria. Proc Natl Acad Sci USA 1987, 84:3117-3121.
11. Lucattini R, Likic VA, Lithgow T: Bacterial proteins predisposed for targeting to mitochondria. Mol Biol Evol 2004, 21:652-658.
12. Palmer JD: Organelle genomes: going, going, gone! Science 1997, 275:790-791.
13. Boore JL: Animal mitochondrial genomes. Nucleic Acids Res 1999, 27:1767-1780.
14. Koumandou VL, Nisbet RE, Barbrook AC, Howe CJ: Dinoflagellate chloroplasts - where have all the genes gone? Trends Genet 2004, 20:261-267.
15. von Heijne G: Why mitochondria need a genome. FEBS Lett 1986, 198:1-4.
16. Popot JL, de Vitry C: On the microassembly of integral membrane proteins. Annu Rev Biophys Biophys Chem 1990, 19:369-403.
17. Claros MG, Perea J, Shu Y, Samatey FA, Popot JL, Jacq C: Limitations to in vivo import of hydrophobic proteins into yeast mitochondria. The case of a cytoplasmically synthesized apocytochrome b. Eur J Biochem 1995, 228:762-771.
18. Wattenberg B, Lithgow T: Targeting of C-terminal (tail)-anchored proteins: understanding how cytoplasmic activities are anchored to intracellular membranes. Traffic 2001, 2:66-71.
19. Rapaport D: Finding the right organelle. Targeting signals in mitochondrial outer-membrane proteins. EMBO Reports 2003, 4:948-952.
20. Horie C, Suzuki H, Sakaguchi M, Mihara K: Targeting and assembly of mitochondrial tail-anchored protein Tom5 to the TOM complex depend on a signal distinct from that of tail-anchored proteins dispersed in the membrane. J Biol Chem 2003, 278:41462-41471.
21. Horie C, Suzuki H, Sakaguchi M, Mihara K: Characterization of signal that directs C-tail-anchored proteins to mammalian mitochondrial outer membrane. Mol Biol Cell 2002, 13:1615-1625.
22. Daley DO, Clifton R, Whelan J: Intracellular gene transfer: reduced hydrophobicity facilitates gene transfer for subunit 2 of cytochrome c oxidase. Proc Natl Acad Sci USA 2002, 99:10510-10515.
23. Perez-Martinez X, Vazquez-Acevedo M, Tolkunova E, Funes S, Claros MG, Davidson E, King MP, Gonzalez-Halphen D: Unusual location of a mitochondrial gene. Subunit III of cytochrome C oxidase is encoded in the nucleus of Chlamydomonad algae. J Biol Chem 2000, 275:30144-30152.
24. Perez-Martinez X, Antaramian A, Vazquez-Acevedo M, Funes S, Tolkunova E, d'Alayer J, Claros MG, Davidson E, King MP, Gonzalez-Halphen D: Subunit II of cytochrome c oxidase in Chlamydomonad algae is a heterodimer encoded by two independent nuclear genes. J Biol Chem 2001, 276:11302-11309.
25. Funes S, Davidson E, Claros MG, van Lis R, Perez-Martinez X, Vazquez-Acevedo M, King MP, Gonzalez-Halphen D: The typically mitochondrial DNA-encoded ATP6 subunit of the FIF0-ATPase is encoded by a nuclear gene in Chlamydomonas reinhardtii. J Biol Chem 2002, 277:6051-6058.
26. Santillan Torres JL, Atteia A, Claros MG, Gonzalez-Halphen D: Cytochrome f and subunit IV, two essential components of the photosynthetic bf complex typically encoded in the chloroplast genome, are nucleus-encoded in Euglena gracilis. Biochim Biophys Acta 2003, 1604:180-189.
27. van Dooren GG, Schwartzbach SD, Osafune T, McFadden GI: Translocation of proteins across the multiple membranes of complex plastids. Biochim Biophys Acta 2001, 1541:34-53.
28. Manfredi G, Fu J, Ojaimi J, Sadlock JE, Kwong JQ, Guy J, Schon EA: Rescue of a deficiency in ATP synthesis by transfer of MTATP6, a mitochondrial DNA-encoded gene, to the nucleus. Nat Genet 2002, 30:394-399.
29. Oca-Cossio J, Kenyon L, Hao H, Moraes CT: Limitations of allotopic expression of mitochondrial genes in mammalian cells. Genetics 2003, 165:707-720.
30. Allen JF: Protein phosphorylation in regulation of photosynthesis. Biochim Biophys Acta 1992, 1098:275-335.
31. Allen JF: Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J Theor Biol 1993, 165:609-631.
32. Race HL, Herrmann RG, Martin W: Why have organelles retained genomes? Trends Genet 1999, 15:364-370.
33. Rodermel S: Pathways of plastid-to-nucleus signaling. Trends Plant Sci 2001, 6:471-478.
34. Pfannschmidt T, Schutze K, Fey V, Sherameti I, Oelmuller R: Chloroplast redox control of nuclear gene expression - a new class of plastid signals in interorganellar communication. Antioxid Redox Signal 2003, 5:95-101.
35. Kanevski I, Maliga P: Relocation of the plastid rbcL gene to the nucleus yields functional ribulose-1,5-bisphosphate carboxylase in tobacco chloroplasts. Proc Natl Acad Sci USA 1994, 91:1969-1973.
36. John Andrews T, Whitney SM: Manipulating ribulose bisphosphate carboxylase/oxygenase in the chloroplasts of higher plants. Arch Biochem Biophys 2003, 414:159-169.
37. Zhao Q, Wang J, Levichkin IV, Stasinopoulos S, Ryan MT, Hoogenraad NJ: A mitochondrial specific stress response in mammalian cells. EMBO J 2002, 21:4411-4419.
38. Adam Z, Clarke AK: Cutting edge of chloroplast proteolysis. Trends Plant Sci 2002, 7:451-456.
39. Arnold I, Langer T: Membrane protein degradation by AAA proteases in mitochondria. Biochim Biophys Acta 2002, 1592:89-96.
40. Baena-Gonzalez E, Aro EM: Biogenesis, assembly and turnover of photosystem II units. Philos Trans R Soc Lond B Biol Sci 2002, 357:1451-1460.
41. Zhang L, Aro EM: Synthesis membrane insertion and assembly of the chloroplast-encoded D1 protein into photosystem II. FEBS Lett 2002, 512:13-18.
42. Ossenbuhl F, Hartmann K, Nickelsen J: A chloroplast RNA binding protein from stromal thylakoid membranes specifically binds to the 5′ untranslated region of the psbA mRNA. Eur J Biochem 2002, 269:3912-3919.
43. Cheung AY, Bogorad L, Van Montagu M, Schnell J: Relocating a gene for herbicide tolerance: A chloroplast gene is converted into a nuclear gene. Proc Nat Acad Sci USA 1988, 85:391-395.
44. Zerges W: Does complexity constrain organelle evolution? Trends Plant Sci 2002, 7:175-182.
45. Pfanner N, Geissler A: Versatility of the mitochondrial protein import machinery. Nat Rev Mol Cell Biol 2001, 2:339-349.
46. Palmieri L, Runswick MJ, Fiermonte G, Walker JE, Palmieri F: Yeast mitochondrial carriers: bacterial expression, biochemical identification and metabolic significance. J Bioenerg Biomembr 2000, 32:67-77.
47. Dolganov NA, Bhaya D, Grossman AR: Cyanobacterial protein with similarity to the chlorophyll a/b binding proteins of higher plants: evolution and regulation. Proc Natl Acad Sci USA 1995, 92:636-640.
48. Grossman AR, Bhaya D, Apt KE, Kehoe DM: Light-harvesting complexes in oxygenic photosynthesis: diversity, control, and evolution. Annu Rev Genet 1995, 29:231-288.
49. Strand A, Asami T, Alonso J, Ecker JR, Chory J: Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrin IX. Nature 2003, 421:79-83.
50. Larkin RM, Alonso JM, Ecker JR, Chory J: GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science 2003, 299:902-906.
51. Butow RA, Avadhani NG: Mitochondrial signaling, the retrograde response. Mol Cell 2004, 14:1-15.
52. Poyton RO, Dagsgaard CJ: Mitochondrial-nuclear crosstalk is involved in oxygen-regulated gene expression in yeast. Adv Exp Med Biol 2000, 475:177-184.
53. Dagsgaard C, Taylor LE, O'Brien KM, Poyton RO: Effects of anoxia and the mitochondrion on expression of aerobic nuclear COX genes in yeast: evidence for a signaling pathway from the mitochondrial genome to the nucleus. J Biol Chem 2001, 276:7593-7601.
54. Contamine V, Picard M: Maintenance and integrity of the mitochondrial genome: a plethora of nuclear genes in the budding yeast. Microbiol Mol Biol Rev 2000, 64:281-315.
55. Rasmussen AK, Chatterjee A, Rasmussen LJ, Singh KK: Mitochondria-mediated nuclear mutator phenotype in Saccharomyces cerevisiae. Nucleic Acids Res 2003, 31:3909-3917.
56. Linke B, Nothnagel T, Borner T: Flower development in carrot CMS plants: mitochondria affect the expression of MADS box genes homologous to GLOBOSA and DEFICIENS. Plant J 2003, 34:27-37.
57. Loeb LA: A mutator phenotype in cancer. Cancer Res 2001, 61:3230-3239.
58. Allen JF: The function of genomes in bioenergetic organelles. Philos Trans R Soc Lond B Biol Sci 2003, 358:19-37.