Origin, evolution and genetic effects of nuclear insertions of organelle DNA

Trends in Genetics

Volumn 21, Issue 12, 2005, Pages 655-663

  Leister, Dario ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MITOCHONDRIAL DNA;

CELL ORGANELLE; DNA REPAIR; DNA SEQUENCE; DNA STRAND BREAKAGE; DNA TRANSFER; EUKARYOTE; GENE DELETION; GENE INSERTION; GENETIC ORGANIZATION; GENETIC VARIABILITY; GENOME; HUMAN; MITOCHONDRION; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PLANT GENETICS; PLASTID; POINT MUTATION; PRIORITY JOURNAL; REVIEW;

CELL NUCLEUS; CHLOROPLASTS; DNA; EVOLUTION, MOLECULAR; HUMANS; MITOCHONDRIA; PHYLOGENY; PLANTS;

EUKARYOTA;

EID: 27744526687     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2005.09.004     Document Type: Review

References (76)

1. Leister, D. and Schneider, A. (2004) Evolutionary contribution of plastid genes to plant nuclear genomes and its effects on composition of the proteomes of all cellular compartments. In Organelle, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics (The Systematics Association Special Volume Series 68) (Horner, D.S., ed.), pp. 237-255, CRC Press
2. J.N. Timmis Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes Nat. Rev. Genet. 5 2004 123 135
3. J.L. Boore Animal mitochondrial genomes Nucleic Acids Res. 27 1999 1767 1780
4. K.L. Adams Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution Genetics 158 2001 1289 1300
5. K.L. Adams Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants Nature 408 2000 354 357
6. E. Richly, and D. Leister NUMTs in sequenced eukaryotic genomes Mol. Biol. Evol. 21 2004 1081 1084
7. E. Richly, and D. Leister NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs Mol. Biol. Evol. 21 2004 1972 1980
8. S.L. Pereira, and A.J. Baker Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics BMC Evol. Biol. 4 2004 17
9. D. Bensasson Mitochondrial pseudogenes: evolution's misplaced witnesses Trends Ecol. Evol. 16 2001 314 321
10. J.V. Lopez Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat J. Mol. Evol. 39 1994 174 190
11. The Rice Chromosome 10 Sequencing Consortium In-depth view of structure, activity, and evolution of rice chromosome 10 Science 300 2003 1566 1569
12. R.M. Stupar Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats Proc. Natl. Acad. Sci. U. S. A. 98 2001 5099 5103
13. X. Lin Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana Nature 402 1999 761 768
14. M. Woischnik, and C.T. Moraes Pattern of organization of human mitochondrial pseudogenes in the nuclear genome Genome Res. 12 2002 885 893
15. T. Mourier The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus Mol. Biol. Evol. 18 2001 1833 1837
16. Y. Tourmen Structure and chromosomal distribution of human mitochondrial pseudogenes Genomics 80 2002 71 77
17. D. Bensasson Rates of DNA duplication and mitochondrial DNA insertion in the human genome J. Mol. Evol. 57 2003 343 354
18. J.L. Blanchard, and G.W. Schmidt Mitochondrial DNA migration events in yeast and humans: integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns Mol. Biol. Evol. 13 1996 537 548
19. M. Ricchetti Continued colonization of the human genome by mitochondrial DNA PLoS Biol. 2 2004 E273
20. D. Mishmar Mitochondrial DNA-like sequences in the nucleus (NUMTs): insights into our African origins and the mechanism of foreign DNA integration Hum. Mutat. 23 2004 125 133
21. E. Hazkani-Covo Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications J. Mol. Evol. 56 2003 169 174
22. C. Noutsos Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants Genome Res. 15 2005 616 628
23. M. Matsuo The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux Plant Cell 17 2005 665 675
24. J.M. Nugent, and J.D. Palmer RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution Cell 66 1991 473 481
25. K.S. Shafer Mechanisms of mitochondrial DNA escape to the nucleus in the yeast Saccharomyces cerevisiae Curr. Genet. 36 1999 183 194
26. C.Y. Huang Simple and complex nuclear loci created by newly transferred chloroplast DNA in tobacco Proc. Natl. Acad. Sci. U. S. A. 101 2004 9710 9715
27. P.E. Thorsness, and T.D. Fox Escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae Nature 346 1990 376 379
28. C.Y. Huang Direct measurement of the transfer rate of chloroplast DNA into the nucleus Nature 422 2003 72 76
29. S. Stegemann High-frequency gene transfer from the chloroplast genome to the nucleus Proc. Natl. Acad. Sci. U. S. A. 100 2003 8828 8833
30. X. Yu, and A. Gabriel Patching broken chromosomes with extranuclear cellular DNA Mol. Cell 4 1999 873 881
31. M. Ricchetti Mitochondrial DNA repairs double-strand breaks in yeast chromosomes Nature 402 1999 96 100
32. D.S. Shin Structure and function of the double-strand break repair machinery DNA Repair (Amst.) 3 2004 863 873
33. D.C. van Gent Chromosomal stability and the DNA double-stranded break connection Nat. Rev. Genet. 2 2001 196 206
34. H. Puchta The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution J. Exp. Bot. 56 2005 1 14
35. P. Karran DNA double strand break repair in mammalian cells Curr. Opin. Genet. Dev. 10 2000 144 150
36. S. Salomon, and H. Puchta Capture of genomic and T-DNA sequences during double-strand break repair in somatic plant cells EMBO J. 17 1998 6086 6095
37. A. Kirik Species-specific double-strand break repair and genome evolution in plants EMBO J. 19 2000 5562 5566
38. J.E. Willett-Brozick Germ line insertion of mtDNA at the breakpoint junction of a reciprocal constitutional translocation Hum. Genet. 109 2001 216 223
39. C. Turner Human genetic disease caused by de novo mitochondrial-nuclear DNA transfer Hum. Genet. 112 2003 303 309
40. K. Borensztajn Characterization of two novel splice site mutations in human factor VII gene causing severe plasma factor VII deficiency and bleeding diathesis Br. J. Haematol. 117 2002 168 171
41. S. Gonzalez-Barrera Transcription and double-strand breaks induce similar mitotic recombination events in Saccharomyces cerevisiae Genetics 162 2002 603 614
42. J.L. Blanchard, and G.W. Schmidt Pervasive migration of organellar DNA to the nucleus in plants J. Mol. Evol. 41 1995 397 406
43. C.L. Campbell, and P.E. Thorsness Escape of mitochondrial DNA to the nucleus in yme1 yeast is mediated by vacuolar-dependent turnover of abnormal mitochondrial compartments J. Cell Sci. 111 1998 2455 2464
44. P.E. Thorsness, and E.R. Weber Escape and migration of nucleic acids between chloroplasts, mitochondria, and the nucleus Int. Rev. Cytol. 165 1996 207 234
45. N.T. Perna, and T.D. Kocher Mitochondrial DNA: molecular fossils in the nucleus Curr. Biol. 6 1996 128 129
46. C.Y. Huang Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes Plant Physiol. 138 2005 1723 1733
47. R. Thomas Novel mitochondrial DNA insertion polymorphism and its usefulness for human population studies Hum. Biol. 68 1996 847 854
48. Y. Cho From the Cover: Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants Proc. Natl. Acad. Sci. U. S. A. 101 2004 17741 17746
49. K.H. Wolfe Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs Proc. Natl. Acad. Sci. U. S. A. 84 1987 9054 9058
50. J.D. Palmer, and L.A. Herbon Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence J. Mol. Evol. 28 1988 87 97
51. B.S. Gaut Molecular clocks and nucleotide substitution rates in higher plants Evol. Biol. 30 1998 93 120
52. J. Paszkowski, and S.A. Whitham Gene silencing and DNA methylation processes Curr. Opin. Plant Biol. 4 2001 123 129
53. J. Bender Chromatin-based silencing mechanisms Curr. Opin. Plant Biol. 7 2004 521 526
54. R. Holliday, and G.W. Grigg DNA methylation and mutation Mutat. Res. 285 1993 61 67
55. W. Martin Molecular evolution: Lateral gene transfer and other possibilities Heredity 94 2005 565 566
56. O. Thalmann Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes Mol. Ecol. 13 2004 321 335
57. O. Thalmann Nuclear insertions help and hinder inference of the evolutionary history of gorilla mtDNA Mol. Ecol. 14 2005 179 188
58. H.I. Hadler Comment: mitochondrial genes and cancer FEBS Lett. 256 1989 230 232
59. C. Richter Do mitochondrial DNA fragments promote cancer and aging? FEBS Lett. 241 1988 1 5
60. J.W. Shay, and H. Werbin New evidence for the insertion of mitochondrial DNA into the human genome: significance for cancer and aging Mutat. Res. 275 1992 227 235
61. Q. Zhang Examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species Plant Cell Physiol. 44 2003 941 951
62. C. Esser A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes Mol. Biol. Evol. 21 2004 1643 1660
63. W. Martin Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus Proc. Natl. Acad. Sci. U. S. A. 99 2002 12246 12251
64. M. Unseld The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides Nat. Genet. 15 1997 57 61
65. Y. Notsu The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants Mol. Genet. Genomics 268 2002 434 445
66. S.W. Clifton Sequence and comparative analysis of the maize NB mitochondrial genome Plant Physiol. 136 2004 3486 3503
67. Sodmergen Reduction in amounts of mitochondrial DNA in the sperm cells as a mechanism for maternal inheritance in Hordeum vulgare Planta 216 2002 235 244
68. S. Arimura Frequent fusion and fission of plant mitochondria with unequal nucleoid distribution Proc. Natl. Acad. Sci. U. S. A. 101 2004 7805 7808
69. B. Westermann Mitochondrial membrane fusion Biochim. Biophys. Acta 1641 2003 195 202
70. M. Mota Electron microscope study of relationship between nucleus and mitochondria in Chlorophytum capense (L.) Kuntze Cytologia (Tokyo) 28 1963 409 416
71. T. Ehara Interactions between the nucleus and cytoplasmic organelles during the cell cycle of Euglena gracilis in synchronized cultures. IV. An aggregate form of chloroplasts in association with the nucleus appearing prior to chloroplast division Exp. Cell Res. 190 1990 104 112
72. H.S. Yu, and S.D. Russell Occurrence of mitochondria in the nuclei of tobacco sperm cells Plant Cell 6 1994 1477 1484
73. H. Jensen Ultrastructure of mitochondria-containing nuclei in human myocardial cells Virchows Arch. B Cell Pathol. 21 1976 1 12
74. E.Y. Kwok, and M.R. Hanson Stromules and the dynamic nature of plastid morphology J. Microsc. 214 2004 124 137
75. Maiti, A.K. et al. (2001) Isolation, in silico characterization and chromosomal localization of a group of cDNAs from ciliated epithelial cells after in vitro ciliogenesis. Genome Biol. 2, DOI:10.1186/gb-2001-2-7-research (http://genomebiology.com/2001/2/7/research/0026 )
76. I.A. Shahmuradov Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis Plant Mol. Biol. 52 2003 923 934