Forces maintaining organellar genomes: Is any as strong as genetic code disparity or hydrophobicity?

BioEssays

Volumn 27, Issue 4, 2005, Pages 436-446

  De Grey, Aubrey D N J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CELL ORGANELLE; CHLOROPLAST; CYTOSOL; GENE FUNCTION; GENE LOCATION; GENE TRANSFER; GENETIC CODE; GENOME; HYDROPHOBICITY; MITOCHONDRION; NONHUMAN; NUCLEUS ACCUMBENS; OXIDATION REDUCTION REACTION; PROTEIN FUNCTION;

ANIMALS; DNA, CHLOROPLAST; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC CODE; GENOME; HUMANS; HYDROPHOBICITY; PROTEINS;

ANIMALIA; MAMMALIA;

EID: 17844382664     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20209     Document Type: Article

References (67)

1. Cavalier-Smith T. 1992. The number of symbiotic origins of organelles. Biosystems 28:91-106.
2. Embley TM, van der Giezen M, Horner DS, Dyal PL, Bell S, et al. 2003. Hydrogenosomes, mitochondria and early eukaryotic evolution. IUBMB Life 55:387-395.
3. Blanchard JL, Lynch M. 2003. Organellar genes: why do they end up in the nucleus? Trends Genet 16:315-320.
4. Lang BF, Gray MW, Burger G. 1999. Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 33:351-397.
5. Allen JF. 1993. Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J Theor Biol 165:609-631.
6. Allen JF. 2003. The function of genomes in bioenergetic organelles. Philos Trans R Soc Lond B Biol Sci 358:19-37.
7. Bender E, Kadenbach B. 2000. The allosteric ATP-inhibition of cytochrome c oxidase activity is reversibly switched on by cAMP-dependent phosphorylation. FEBS Lett 466:130-134.
8. Race HL, Herrmann RG, Martin W. 1999. Why have organelles retained genomes? Trends Genet 15:364-370.
9. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, et al. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
10. Andersson GE, Kurland CG. 1991. An extreme codon preference strategy: codon reassignment. Mol Biol Evol 8:530-544.
11. Jacobs HT. 1991. Structural similarities between a mitochondrially encoded polypeptide and a family of prokaryotic respiratory toxins involved in plasmid maintenance suggest a novel mechanism for the evolutionary maintenance of mitochondrial DNA. J Mol Evol 32:333-339.
12. de Grey ADNJ. 1999. Are those 13 proteins really unimportable? In: From Symbiosis to Eukaryotism - Endocytobiology VII (Wagner E, Normann J, Greppin H, Hackstein JHP, Herrmann RG, et al., eds.), Geneva: Geneva University Press, pp. 489-502.
13. Leblanc C, Richard O, Kloareg B, Viehmann S, Zetsche K, et al. 1997. Origin and evolution of mitochondria: what have we learnt from red algae? Curr Genet 31:193-207.
14. Pont-Kingdon G, Okada NA, Macfarlane JL, Beagley CT, Watkins-Sims CD, et al. 1998. Mitochondrial DNA of the coral Sarcophyton glaucum contains a gene for a homologue of bacterial MutS: a possible case of gene transfer from the nucleus to the mitochondrion. J Mol Evol 46:419-431.
15. Beagley CT, Okimoto R, Wolstenholme DR. 1998. The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code. Genetics 148:1091-1108.
16. Helfenbein KG, Fourcade HM, Vanjani RG, Boore JL. 2004. The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes. Proc Natl Acad Sci USA 101:10639-10643.
17. Papillon D, Perez Y, Caubit X, Le Parco Y. 2004. Identification of chaetognaths as protostomes is supported by the analysis of their mitochondrial genome. Mol Biol Evol 21:2122-2129.
18. McManus DP, Le TH, Blair D. 2004. Genomics of parasitic flatworms. Int J Parasitol 34:153-158.
19. Okimoto R, Macfarlane JL, Clary DO, Wolstenholme DR. 1992. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130:471-498.
20. Hoffmann RJ, Boore JL, Brown WM. 1992. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131:397-412.
21. Yokobori S, Ueda T, Feldmaier-Fuchs G, Paabo S, Ueshima R, et al. 1999. Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata). Genetics 153:1851-1862.
22. Gissi C, Iannelli F, Pesole G. 2004. Complete mtDNA of Ciona intestinalis reveals extensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians. J Mol Evol 58:376-389.
23. Altendorf K, Stalz W, Greie J, Deckers-Hebestreit G. 2000. Structure and function of the F(o) complex of the ATP synthase from Escherichia coli. J Exp Biol 203:19-28.
24. Dreyer H, Steiner G. 2004. The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca). Mol Phylogenet Evol 31:605-617.
25. Lavrov DV, Brown WM. 2001. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAs and has a gene arrangement relatable to those of coelomate metazoans. Genetics 157:621-637.
26. Chatterjee P, Brady KL, Solem A, Ho Y, Caprara MG. 2003. Functionally distinct nucleic acid binding sites for a group I intron encoded RNA maturase/DNA homing endonuclease. J Mol Biol 329:239-251.
27. Ridder R, Kunkele KP, Osiewacz HD. 1991. Sequence of the nuclear ATP synthase subunit 9 gene of Podospora anserina: lack of similarity to the mitochondrial genome. Curr Genet 20:349-351.
28. Gray RE, Law RH, Devenish RJ, Nagley P. 1996. Allotopic expression of mitochondrial ATP synthase genes in nucleus of Saccharomyces cerevisiae. Methods Enzymol 264:369-389.
29. Sanchirico M, Tzellas A, Fox TD, Conrad-Webb H, Periman PS, et al. 1995. Relocation of the unusual VAR1 gene from the mitochondrion to the nucleus. Biochem Cell Biol 73:987-995.
30. Neu R, Goffart S, Wolf K, Schafer B. 1998. Relocation of urf a from the mitochondrion to the nucleus cures the mitochondrial mutator phenotype in the fission yeast Schizosaccharomyces pombe. Mol Gen Genet 258:389-396.
31. Bullerwell CE, Leigh J, Forget L, Lang BF. 2003. A comparison of three fission yeast mitochondrial genomes. Nucleic Acids Res 31:759-768.
32. Bullerwell CE, Burger G, Lang BF. 2000. A novel motif for identifying rps3 homologs in fungal mitochondrial genomes. Trends Biochem Sci 25:363-365.
33. Burger G, Forget L, Zhu Y, Gray MW, Lang BF. 2003. Unique mitochondrial genome architecture in unicellular relatives of animals. Proc Natl Acad Sci USA 100:892-897.
34. Popot JL, de Vitry C. 1990. On the microassembly of integral membrane proteins. Annu Rev Biophys Biophys Chem 19:369-403.
35. Claros MG, Perea J, Shu Y, Samatey FA, Popot JL, et al. 1995. Limitations to in vivo import of hydrophobic proteins into yeast mitochondria. The case of a cytoplasmically synthesized apocytochrome b. Eur J Biochem 228:762-771.
36. Funes S, Davidson E, Reyes-Prieto A, Magallon S, Herion P, et al. 2002. A green algal apicoplast ancestor. Science 298:2155.
37. Nedelcu AM, Lee RW, Lemieux C, Gray MW, Burger G. 2000. The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome. Genome Res 10:819-831.
38. Michaelis G, Vahrenholz C, Pratje E. 1990. Mitochondrial DNA of Chlamydomonas reinhardtii: the gene for apocytochrome b and the complete functional map of the 15.8 kb DNA. Mol Gen Genet 223:211-216.
39. Pritchard AE, Seilhamer JJ, Mahalingam R, Sable CL, Venuti SE, et al. 1990. Nucleotide sequence of the mitochondrial genome of Paramecium. Nucleic Acids Res 18:173-180.
40. Brunk CF, Lee LC, Tran AB, Li J. 2003. Complete sequence of the mitochondrial genome of Tetrahymena thermophila and comparative methods for identifying highly divergent genes. Nucleic Acids Res 31:1673-1682.
41. Zara V, Palmieri F, Mahlke K, Pfanner N. 1992. The cleavable presequence is not essential for import and assembly of the phosphate carrier of mammalian mitochondria but enhances the specificity and efficiency of import. J Biol Chem 267:12077-12081.
42. Rehling P, Pfanner N, Meisinger C. 2003. Insertion of hydrophobic membrane proteins into the inner mitochondrial membrane - a guided tour. J Mol Biol 326:639-657.
43. Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S. 1999. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res 6:283-290.
44. Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, et al. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA 91:9794-9798.
45. Clark SA, Theg SM. 1997. A folded protein can be transported across the chloroplast envelope and thylakoid membranes. Mol Biol Cell 8:923-934.
46. Padan E, Schuldiner S. 1978. Energy transduction in the photosynthetic membranes of the cyanobacterium (blue-green alga) Plectonema boryanum. J Biol Chem 253:3281-3286.
47. Nicholls DG, Ferguson SJ. 2002. Bioenergetics 3. London: Academic Press.
48. Wu C, Seibert FS, Ko K. 1994. Identification of chloroplast envelope proteins in close physical proximity to a partially translocated chimeric precursor protein. J Biol Chem 269:32264-32271.
49. Ellis RJ. 1979. The most abundant protein in the world. Trends Biochem Sci 4:241-244.
50. Spreitzer RJ. 2003. Role of the small subunit in ribulose-1,5- bisphosphate carboxylase/oxygenase. Arch Biochem Biophys 414:141-149.
51. Kanevski I, Maliga P. 1994. Relocation of the plastid rbcL gene to the nucleus yields functional ribulose-1,5-bisphosphate carboxylase in tobacco chloroplasts. Proc Natl Acad Sci USA 91:1969-1973.
52. Cahoon AB, Cunningham KA, Stern DB. 2003. The plastid clpP gene may not be essential for plant cell viability. Plant Cell Physiol 44:93-95.
53. Wolfe KH, Morden CW, Palmer JD. 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc Natl Acad Sci USA 89:10648-10652.
54. Konishi T, Shinohara K, Yamada K, Sasaki Y. 1996. Acetyl-CoA carboxylase in higher plants: most plants other than Gramineae have both the prokaryotic and the eukaryotic forms of this enzyme. Plant Cell Physiol 37:117-122.
55. Bungard RA. 2004. Photosynthetic evolution in parasitic plants: insight from the chloroplast genome. BioEssays 26:235-247.
56. Lemire BD, Fankhauser C, Baker A, Schatz G. 1989. The mitochondrial targeting function of randomly generated peptide sequences correlates with predicted helical amphiphilicity. J Biol Chem 264:20206-20215.
57. Wallace DC, Ye JH, Neckelmann SN, Singh G, Webster KA, et al. 1987. Sequence analysis of cDNAs for the human and bovine ATP synthase beta subunit: mitochondrial DNA genes sustain seventeen times more mutations. Curr Genet 12:81-90.
58. de Grey ADNJ. 2000. Mitochondrial gene therapy: an arena for the biomedical use of inteins. Trends Biotechnol 18:394-399.
59. von Heijne G. 1986. Why mitochondria need a genome. FEBS Lett 198:1-4.
60. Hartl FU, Neupert W. 1990. Protein sorting to mitochondria: evolutionary conservations of folding and assembly. Science 247:930-938.
61. Manfredi G, Fu J, Ojaimi J, Sadlock JE, Kwong JQ, et al. 2002. Rescue of a deficiency in ATP synthesis by transfer of MTATP6, a mitochondrial DNA-encoded gene, to the nucleus. Nat Genet 30:394-399.
62. r ATPase 6 gene to the nuclear genome: a model system for mtDNA gene therapy. Rejuvenation Res 8 (in press).
63. Guy J, Qi X, Pallotti F, Schon EA, Manfredi G, et al. 2002. Rescue of a mitochondrial deficiency causing Leber Hereditary Optic Neuropathy. Ann Neurol 52:534-542.
64. Tsukihara T, Shimokata K, Katayama Y, Shimada H, Muramoto K, et al. 2003. The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process. Proc Natl Acad Sci USA 100:15304-15309.
65. Finsterer J. 2004. Mitochondriopathies. Eur J Neurol 11:163-186.
66. de Grey ADNJ. 2004. Mitochondrial mutations in mammalian aging: an over-hasty about-turn? Rejuvenation Res 7:171-174.
67. de Grey ADNJ. 2004. Inter-species therapeutic cloning: the looming problem of mitochondrial DNA and two possible solutions. Rejuvenation Res 7:95-98.