Two co-existing mechanisms account for the large-scale deletions of mitochondrial DNA in Podospora anserina that involve the 5' border of a group-II intron

Current Genetics

Volumn 34, Issue 4, 1998, Pages 326-335

  Sainsard Chanet, Annie ^a   Begel, Odile ^a   D'Aubenton Carafa, Yves ^a  

^a CNRS   (France)

Author keywords

Double strand breaks; Group II intron; Mitochondrial deletions; Stem loop structures

Indexed keywords

DOUBLE STRANDED DNA; MITOCHONDRIAL DNA; REPETITIVE DNA;

ARTICLE; DEGENERATION; DELETION MUTANT; DNA RECOMBINATION; FUNGUS; INTRON; NONHUMAN; PRIORITY JOURNAL; SPHAERIALES;

BASE SEQUENCE; BLOTTING, SOUTHERN; CLONING, MOLECULAR; DNA, MITOCHONDRIAL; GENES, FUNGAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; POLYMERASE CHAIN REACTION; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION;

EID: 0031725368     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002940050403     Document Type: Article

References (63)

1. Ahne A, Muller-Derlich J, Merlos-Lange AM, Kanbay F, Wolf K, Lang BF (1988) Two distinct mechanisms for deletion in mitochondrial DNA of Schizosaccharomyces pombe mutator strains. Slipped mispairing mediated by direct repeats and erroneous intron splicing. J Mol Biol 202:725-734
2. Akins RA, Lambowitz AM (1990) Analysis of large deletions in the Mauriceville and Varkud mitochondrial plasmids of Neurospora. Curr Genet 18:365-369
3. Akins RA, Kelley RL, Lambowitz AM (1986) Mitochondrial plasmids of Neurospora: integration into mitochondrial DNA and evidence for reverse transcription in mitochondria. Cell 47:505-516
4. Akins RA, Kelley RL, Lambowitz AM (1989) Characterization of mutant mitochondrial plasmids of Neurospora spp. that have incorporated tRNAs by reverse transcription. Mol Cell Biol 9:678-691
5. Almasan A, Mishra NC (1991) Recombination by sequence repeats with formation of suppressive or residual mitochondrial DNA in Neurospora. Proc Natl Acad Sci USA 88:7684-7688
6. Belcour L, Begel O, Picard M (1991) A site-specific deletion in the mitochondrial DNA of Podospora is under the control of nuclear genes. Proc Natl Acad Sci USA 88:3579-3583
7. Belmaaza A, Chartrand P (1994) One-sided invasion events in homologous recombination at double-strand breaks. Mutat Res DNA Repair 314:199-208
8. Bertrand B, Wu Q, Seidel-Rogol BL (1993) Hyperactive recombination in the mitochondrial DNA of the natural-death nuclear mutant of Neurospora crassa. Mol Cell Biol 13:6778-6788
9. Breslauer KJ, Frank R, Blöcker H, Marky LA (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 83:3746-3750
10. Chakrabarti S, Seidman MM (1986) Intramolecular recombination between transfected repeated sequences in mammalian cells is nonconservative. Mol Cell Biol 6:2520-2526
11. Chen B, Lambowitz AM (1997) De novo and DNA primer-mediated initiation of cDNA synthesis by the Mauricevill retroplasmid reverse transcriptase involve recognition of a 3′ CCA sequence. J Mol Biol 271:311-332
12. Chiang CC, Kennell JC, Wanner LA, Lambowitz AM (1994) A mitochondrial retroplasmid integrates into mitochondrial DNA by a novel mechanism involving the synthesis of a hybrid cDNA and homologous recombination. Mol Cell Biol 14:6419-6432
13. Clayton DA (1982) Replication of animal mitochodrial DNA. Cell 28:693-705
14. Contamine V, Picard M (1998) Escape from premature death due to nuclear mutations in Podospora anserina: repeal versus respite. Fungal Genet Biol 23:223-236
15. Contamine V, Lecellier G, Belcour L, Picard M (1996) Premature death in Podospora anserina: sporadic accumulation of the deleted mitochondrial genome, translational parameters and innocuity of the mating types. Genetics 44:541-555
16. Cummings DJ, Belcour L, Grandchamp C (1979) Mitochondrial DNA from Podospora anserina. II. Properties of mutant DNA and multimeric circular DNA from senescent cultures. Mol Gen Genet 171:239-250
17. Cummings DJ, Macneil IA, Domenico J, Matsuura ET (1985) Excison-amplification of mitochondrial DNA during senescence in Podospora anserina. J Mol Biol 185:659-680
18. Cummings DJ, McNally KL, Domenico JM, Matsuura ET (1990) The complete DNA sequence of the mitochondrial genome of Podospora anserina. Curr Genet 17:375-402
19. Dequard-Chablat M (1986) Genetics of translational fidelity in Podospora anserina: are all the genes involved in this ribosomal function identified? Curr Genet 10:531-536
20. Desautels L, Brouillette S, Wallenburg J, Belmaaza A, Gusew N, Trudel P, Chartrand P (1990) Characterization of nonconservative homologous junctions in mammalian cells. Mol Cell Biol 10:6613-6618
21. Dujon B, Belcour L (1989) Mitochondrial DNA instabilities and rearrangements in yeasts and fungi. In: Berg DE, Howe EE (eds) Mobile DNA, pp 861-878. American Society for Microbiology
22. Dürrenberger F, Thompson AJ, Herrin DL, Rochaix JD (1996) Double strand break-induced recombination in Chlamydomonas reinardtii chloroplasts. Nucleic Acids Res 24:3223-3331
23. Eskes R, Yang J, Lambowitz AM, Perlman PS (1997) Mobility of yeast mitochondrial group-II introns: engineering a new site-specificity and retrohoming via full reverse splicing. Cell 88:865-874
24. Fishman-Lobell J, Rudin N, Haber JE (1992) Two alternative pathways of double-strand break, repair that are kinetically separable and independently modulated. Mol Cell Biol 12:1292-1303
25. Foury F, van Dyck E (1985) A PIF-dependent recombinogenic signal in the mitochondrial DNA of yeast. EMBO J 4:3525-3530
26. George JA, Burke WD, Eickbush TH (1996) Analysis of the 5′ junctions of R2 insertions with the 28 S gene : implications for non-LTR retrotransposition. Genetics 142:853-863
27. Grossman LI, Shoubridge EA (1996) Mitochondrial genetics and human disease. BioEssays 18:983-991
28. Gudikote J, Van Tuyle G (1996) Rearrangements in the shorter arc of rat mitochondrial DNA involving the region of the heavy and light strand promoters. Mutat Res 356:275-286
29. Guo H, Zimmerly S, Perlman PS, Lambowitz AM (1997) Group-II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA. EMBO J 16:6835-6848
30. Haber JE (1992) Exploring the pathways of homologous recombination. Curr Opin Cell Biol 4:401-412
31. Jamet-Vierny C, Contamine V, Boulay j, Zickler D, Picard M (1997 a) Mutations in genes encoding the mitochondrial outer-membrane proteins Tom70 and Mdm10 of Podospora anserina modify the spectrum of mitochondrial DNA rearrangements associated with cellular death. Mol Cell Biol 17:6359-6366
32. Jamet-Vierny C, Boulay J, Briand JF (1997b) Intramolecular crossovers generate deleted mitochondrial DNA molecules in Podospora anserina. Curr Genet 31:162-170
33. Koll F, Begel O, Belcour L (1987) Insertion of short poly d(A)d(T) sequences at recombination junctions in mitochondrial DNA of Podospora. Mol Gen Genet 209:630-632
34. Landau NR, Schatz G, Rosa M, Baltimore D (1987) Increased frequency of N-region insertion in a murine pre-B-cell line infected with a terminal deoxynucleotidyl transferase retroviral expression vector. Mol Cell Biol 7:3237-3243
35. Larsson N-G, Clayton DA (1995) Molecular genetic aspects of human mitochondrial disorders. Annu Rev Genet 29:151-178
36. Lecellier G, Silar P (1994) Rapid methods for nucleic acids extraction from Petri dish-grown mycelia. Curr Genet 25:122-123
37. Lin FM, Sperle K, Sternberg N (1990) Intermolecular recombination between DNAs introduced into mouse L cells is mediated by a nonconservative pathway that leads to crossover products. Mol Cell Biol 10:103-112
38. Mita S, Rizzuto R, Moraes CT, Shanske S, Arnaudo E, Fabrizi GM, Koga Y, DiMauro S, Schon EA (1990) Recombination via flanking direct repeats is a major cause of large-scale deletions of human mitochondrial DNA. Nucleic Acids Res 18:561-567
39. Mueller M, Allmaier W, Eskes M, Schweyen R (1993) Transposition of group-II intron ai1 in yeast and invasion of mitochondrial genes at new locations. Nature 366:174-176
40. Nakagawa K, Morishima N, Shibata T (1992) An endonuclease with multiple cutting sites, Endo.SceI, initiates genetic recombination at its cutting site in yeast mitochondria. EMBO J 11:2707-2715
41. Nalbantoglu J, Hartley D, Phear G, Tear G, Meuth M (1986) Spontaneous deletion formation at the aprt locus of hamster cells: the presence of short sequence homologies and dyad symmetries at deletion termini. EMBO J 5:1199-1204
42. Ohta K, Nicolas A, Keszenman-Pereyra D, Shibata T (1996) Endo.SKI: an inducible site-specific endonuclease from yeast mitochondria. Mol Gen Genet 250:395-404
43. Osiewacz HD, Esser K (1984) The mitochondrial plasmid of Podospora anserina: a mobile intron of a mitochondrial gene. Curr Genet 8:299-305
44. Picard-Bennoun M (1976) Genetic evidence for ribosomal anti-suppressors in Podospora anserina. Mol Gen Genet 147:299-306
45. Rizet G, Engelmann C (1949) Contribution à l'étude génétique d'un ascomycète tétrasporé: Podospora anserina (Ces) Rehm. Rev Cytol Biol Veg 11:201-304
46. Roth DB, Porter TN, Wilson JH (1985) Mechanisms of nonhomologous recombination in mammalian cells. Mol Cell Biol 5:2599-2607
47. Sainsard-Chanet A, Begel O (1990) Insertion of an LrDN A gene fragment and of filler DNA at a mitochondrial exon-intron junction in Podospora. Nucleic Acids Res 18:779-783
48. Sainsard-Chanet A, Begel O, Belcour L (1993) DNA deletion of mitochondrial introns is correlated with the process of senescence in Podospora. J Mol Biol 234:1-7
49. Sainsard-Chanet A, Begel O, Belcour L (1994) DNA double-strand break in vivo at the 3′ extremity of exons located upstream of group-II introns. Senescence and circular DNA introns in Podospora mitochondria. J Mol Biol 242:630-643
50. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467
51. Schmidt WM, Schweyen RJ, Wolf K, Mueller MW (1994) Transposable group-II introns in fission and budding yeast. Site-specific genomic instabilities and formation of group-II IVS plDNAs. J Mol Biol 243:157-166
52. Schon EA, Rizzuto R, Moraes CT, Nakase H, Zeviani M, DiMauro S (1989) A direct repeat is a hotspot for large-scale deletion of human mitochondrial DNA. Science 244:346-349
53. Sellem CH, Lecellier G, Belcour L (1993) Transposition of a group-II intron. Nature 366:176-178
54. Turker MS, Domenico JM, Cummings DJ (1987) Excision-amplification of mitochondrial DNA during senescence in Podospora anserina. A potential role for an 11 base-pair consensus sequence in the excision process. J Mol Biol 198:171-185
55. Van Tuyle GC, Gudikote JP, Hurt VR, Miller BB, Moore CA (1996) Multiple, large deletions in rat mitochondrial DNA: evidence for a major hot spot. Mutat Res 349:95-107
56. Wallace DC (1994) Mitochondrial DNA mutations in human disease and aging. In: Esser K, Martin GH (eds) Molecular aspects of aging, pp 163-177. Wiley
57. Wessler S, Tarpley A, Purugganan M, Spell M, Okagaki R (1990) Filler DNA is associated with spontaneous deletions in maize. Proc Natl Acad Sci USA 87:8731-8735
58. Wu WM, Blumberg BM, Fay PJ, Bambara RA (1995) Strand transfer mediated by human immunodeficiency virus reverse transcriptase in vitro is promoted by pausing and results in misincorporation. J Biol Chem 270:325-332
59. Yang J, Zimmerly S, Perlman PS, Lambowitz AM (1996) Efficient integration of an intron RNA into double-stranded DNA by reverse splicing. Nature 381:332-335
60. Zamaroczy M de, Faugeron-Fonty G, Baldacci G, Coursot R, Bernardi G (1984) The ori sequences of the mitochondrial genome of a wild-type yeast strain: number, location, orientation and structure. Gene 32:439-457
61. Zeviani M, Servidei S, Gellera C, Bertini E, diMauro S, diDonato S (1989) An autosomal dominant disorder with multiple deletions of mitochondrial DNA starting at the D-loop region. Nature 339:309-311
62. Zhang J, Temin HM (1994) Retroviral recombination depends on the length of sequence identity and is not error prone. J Virol 68:2409-2414
63. Zimmerly S, Guo H, Eskes R, Yang J, Perlman PS, Lambowitz AM (1995) A group-II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell 83:529-538