#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

A Rolling Circle Replication Mechanism Produces Multimeric Lariats of Mitochondrial DNA in


Defects in the mitochondrial DNA (mtDNA) that encodes protein subunits of the respiratory complexes may cause severe metabolic disease in humans. Such defects are often caused by errors during mtDNA synthesis, motivating ongoing studies of this process. The nematode Caenorhabditis elegans has been proposed as a model for the study of mtDNA replication defects. Here we analyze the mechanism of mtDNA synthesis in the C. elegans gonad and demonstrate that it is unique among animals. Nascent worm mtDNA forms branched-circular lariat structures with concatemeric tails that we suggest would ultimately resolve into monomeric circles, the predominant molecular form identified by both transmission electron microscopy and two-dimensional gel electrophoresis. Our discovery that mtDNA replication in C. elegans does not faithfully model that in mammals is significant, because it demonstrates the breadth and evolutionary plasticity of the mechanisms that maintain this critical DNA among animals. Interestingly, the mtDNA replication mechanism within C. elegans is highly similar to that of bacteriophages, from which components of the mitochondrial DNA replisome are thought to be derived. Thus C. elegans may serve as a model for mtDNA synthesis as it occurred within ancient eukaryotes.


Vyšlo v časopise: A Rolling Circle Replication Mechanism Produces Multimeric Lariats of Mitochondrial DNA in. PLoS Genet 11(2): e32767. doi:10.1371/journal.pgen.1004985
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004985

Souhrn

Defects in the mitochondrial DNA (mtDNA) that encodes protein subunits of the respiratory complexes may cause severe metabolic disease in humans. Such defects are often caused by errors during mtDNA synthesis, motivating ongoing studies of this process. The nematode Caenorhabditis elegans has been proposed as a model for the study of mtDNA replication defects. Here we analyze the mechanism of mtDNA synthesis in the C. elegans gonad and demonstrate that it is unique among animals. Nascent worm mtDNA forms branched-circular lariat structures with concatemeric tails that we suggest would ultimately resolve into monomeric circles, the predominant molecular form identified by both transmission electron microscopy and two-dimensional gel electrophoresis. Our discovery that mtDNA replication in C. elegans does not faithfully model that in mammals is significant, because it demonstrates the breadth and evolutionary plasticity of the mechanisms that maintain this critical DNA among animals. Interestingly, the mtDNA replication mechanism within C. elegans is highly similar to that of bacteriophages, from which components of the mitochondrial DNA replisome are thought to be derived. Thus C. elegans may serve as a model for mtDNA synthesis as it occurred within ancient eukaryotes.


Zdroje

1. Bratic I, Hench J, Trifunovic A (2010) Caenorhabditis elegans as a model system for mtDNA replication defects. Methods 51: 437–443. doi: 10.1016/j.ymeth.2010.03.003 20230897

2. Bratic I, Trifunovic A (2010) Mitochondrial energy metabolism and ageing. Biochim Biophys Acta 1797: 961–967. doi: 10.1016/j.bbabio.2010.01.004 20064485

3. Falkenberg M, Larsson N-G, Gustafsson CM (2007) DNA Replication and Transcription in Mammalian Mitochondria. Annu Rev Biochem 76: 679–699. doi: 10.1146/annurev.biochem.76.060305.152028 17408359

4. Holt IJ, Reyes A (2012) Human Mitochondrial DNA Replication. Cold Spring Harbor Perspectives in Biology. doi: 10.1101/cshperspect.a012971 23209158

5. Holt IJ, Lorimer HE, Jacobs HT (2000) Coupled Leading- and Lagging-Strand Synthesis of Mammalian Mitochondrial DNA. Cell 100: 515–524. doi: 10.1016/S0092-8674(00)80688-1 10721989

6. Reyes A, Kazak L, Wood SR, Yasukawa T, Jacobs HT, et al. (2013) Mitochondrial DNA replication proceeds via a “bootlace” mechanism involving the incorporation of processed transcripts. Nucleic Acids Research 41: 5837–5850. doi: 10.1093/nar/gkt196 23595151

7. Lemire B (2005) Mitochondrial genetics. WormBook: 1–10. doi: 10.1895/wormbook.1.25.1.

8. Bratic I, Hench J, Henriksson J, Antebi A, Burglin TR, et al. (2009) Mitochondrial DNA level, but not active replicase, is essential for Caenorhabditis elegans development. Nucleic Acids Research 37: 1817–1828. doi: 10.1093/nar/gkp018 19181702

9. Addo MG, Cossard R, Pichard D, Obiri-Danso K, Rötig A, et al. (2010) Caenorhabditis elegans, a pluricellular model organism to screen new genes involved in mitochondrial genome maintenance. Biochim Biophys Acta 1802: 765–773. doi: 10.1016/j.bbadis.2010.05.007 20580819

10. Okimoto R, Macfarlane JL, Clary DO, Wolstenholme DR (1992) The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum.: 471–498.

11. Lorimer HE (2002) Analysis of Native Forms of Mitochondrial DNA by 2D Gel Electrophoresis. Methods in Molecular Biology: Mitochondrial DNA: Methods and Protocols. Totowa: The Humana Press. 15p. 12013816

12. Touchon M, Rocha EPC (2008) From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data. Biochimie 90: 648–659. doi: 10.1016/j.biochi.2007.09.015 17988781

13. Bowmaker M (2003) Mammalian Mitochondrial DNA Replicates Bidirectionally from an Initiation Zone. Journal of Biological Chemistry 278: 50961–50969. doi: 10.1074/jbc.M308028200 14506235

14. Yasukawa T, Reyes A, Cluett TJ, Yang MY, Bowmaker M, et al. (2006) Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand. The EMBO Journal 25: 5358–5371. doi: 10.1038/sj.emboj.7601392 17066082

15. Beanan MJ, Strome S (1992) Characterization of a germ-line proliferation mutation in C. elegans. Development, 116: 755–766. 1289064

16. Claytn DA (2003) Mitochondrial DNA replication: what we know. IUBMB Life 55(4–5):213–7. 14711006

17. Pohjoismäki JLO, Holmes JB, Wood SR, Yang MY, Yasukawa T, et al. (2010) Mammalian Mitochondrial DNA Replication Intermediates Are Essentially Duplex but Contain Extensive Tracts of RNA/DNA Hybrid. Journal of Molecular Biology 397: 1144–1155. doi: 10.1016/j.jmb.2010.02.029 20184890

18. Yasukawa T, Yang MY, Jacobs HT, Holt IJ (2005) A Bidirectional Origin of Replication Maps to the Major Noncoding Region of Human Mitochondrial DNA. Mol Cell 18: 651–662. doi: 10.1016/j.molcel.2005.05.002 15949440

19. Belanger KG, Mirzayan C, Kreuzer HE, Alberts BM, Kreuzer KN (1996) Two-dimensional gel analysis of rolling circle replication in the presence and absence of bacteriophage T4 primase. Nucleic Acids Research 24: 2166–2175. 8668550

20. Han Z, Stachow C (1994) Analysis of Schizosaccharomyces pombe mitochondrial DNA replication by two dimensional gel electrophoresis. Chromosoma 103: 162–170. 7924618

21. Kornberg A, Baker TA (1992) DNA Replication. South Orange: University Science Books. 931p. 25144096

22. Kreuzer KN (2000) Recombination-dependent DNA replication in phage T4. Trends in Biochemical Sciences 25: 165–173. doi: 10.1016/S0968-0004(00)01559–0 10754548

23. Gerhold JM, Aun A, Sedman T, Jõers P, Sedman J (2010) Strand invasion structures in the inverted repeat of Candida albicans mitochondrial DNA reveal a role for homologous recombination in replication. Mol Cell 39: 851–861. doi: 10.1016/j.molcel.2010.09.002 20864033

24. Griffith JD, Christiansen G (1978) Electron microscope visualization of chromatin and other DNA-protein complexes. Annual Review of Biophysics and Bioengineering: 19–35.

25. Jõers P, Jacobs HT (2013) Analysis of replication intermediates indicates that Drosophila melanogaster mitochondrial DNA replicates by a strand-coupled theta mechanism. PLoS ONE 8: e53249. doi: 10.1371/journal.pone.0053249 23308172

26. Backert S (2002) R-loop-dependent rolling-circle replication and a new model for DNA concatemer resolution by mitochondrial plasmid mp1. The EMBO Journal 21: 3128–3136. doi: 10.1093/emboj/cdf311 12065425

27. Chan SN, Harris L, Bolt EL, Whitby MC, Lloyd RG (1997) Sequence specificity and biochemical characterization of the RusA Holliday junction resolvase of Escherichia coli. J Biol Chem 272: 14873–14882. 9169457

28. Bolt EL, Lloyd RG (2002) Substrate specificity of RusA resolvase reveals the DNA structures targeted by RuvAB and RecG in vivo. Mol Cell 10: 187–198. 12150918

29. Lopes M, Cotta-Ramusino C, Liberi G, Foiani M (2003) Branch Migrating Sister Chromatid Junctions Form at Replication Origins through Rad51/Rad52-Independent Mechanisms. Mol Cell 12: 1499–1510. doi: 10.1016/S1097-2765(03)00473-8 14690603

30. Rokas A, Ladoukakis E, Zouros E (2003) Animal mitochondrial DNA recombination revisited. Trends in Ecology & Evolution 18:8 411–417. doi: 10.1126/science.1255641 25593191

31. Stewart JB, Larsson N-G (2014) Keeping mtDNA in shape between generations. PLoS Genet 10: e1004670. doi: 10.1371/journal.pgen.1004670 25299061

32. Hagström E, Freyer C, Battersby BJ, Stewart JB, Larsson N-G (2014) No recombination of mtDNA after heteroplasmy for 50 generations in the mouse maternal germline. Nucleic Acids Research 42: 1111–1116. doi: 10.1093/nar/gkt969 24163253

33. Sato A, Nakada K, Akimoto M, Ishikawa K, Ono T, et al. (2005) Rare creation of recombinant mtDNA haplotypes in mammalian tissues. Proc Natl Acad Sci USA 102: 6057–6062. doi: 10.1073/pnas.0408666102 15829586

34. Kolesar JE, Wang CY, Taguchi YV, Chou S-H, Kaufman BA (2012) Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome. Nucleic Acids Research. doi: 10.1093/nar/gks1324.

35. Pohjoismäki JLO, Goffart S, Taylor RW, Turnbull DM, Suomalainen A, et al. (2010) Developmental and pathological changes in the human cardiac muscle mitochondrial DNA organization, replication and copy number. PLoS ONE 5: e10426. doi: 10.1371/journal.pone.0010426 20454654

36. Pohjoismäki JLO, Goffart S, Tyynismaa H, Willcox S, Ide T, et al. (2009) Human heart mitochondrial DNA is organized in complex catenated networks containing abundant four-way junctions and replication forks. J Biol Chem 284: 21446–21457. doi: 10.1074/jbc.M109.016600 19525233

37. Ladoukakis ED, Theologidis I, Rodakis GC, Zouros E (2011) Homologous recombination between highly diverged mitochondrial sequences: examples from maternally and paternally transmitted genomes. Mol Biol Evol 28: 1847–1859. doi: 10.1093/molbev/msr007 21220759

38. Lunt DH, Hyman BC (1997) Animal mitochondrial DNA recombination. Nature 387: 247–247. doi: 10.1038/387247a0 9153388

39. White DJ, Wolff JN, Pierson M, Gemmell NJ (2008) Revealing the hidden complexities of mtDNA inheritance. Molecular Ecology 17: 4925–4942. doi: 10.1111/j.1365-294X.2008.03982.x 19120984

40. Sulston J, Du Z, Thomas K, Wilson R, Hillier L (1992) The C. elegans genome sequencing project: a beginning. Nature 356:37–41. 1538779

41. Sugimoto T, Mori C, Takanami T, Sasagawa Y, Saito R, et al. (2008) Caenorhabditis elegans par2.1/mtssb-1 is essential for mitochondrial DNA replication and its defect causes comprehensive transcriptional alterations including a hypoxia response. Experimental Cell Research 314: 103–114. doi: 10.1016/j.yexcr.2007.08.015 17900564

42. Oberto J, Breuil N, Hecker A, Farina F, Brochier-Armanet C, et al. (2009) Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance. Nucleic Acids Research 37: 5343–5352. doi: 10.1093/nar/gkp557 19578062

43. Suetomi K, Mereiter S, Mori C, Takanami T, Higashitani A (2013) Caenorhabditis elegans ATR checkpoint kinase ATL-1 influences life span through mitochondrial maintenance. Mitochondrion 13: 729–735. doi: 10.1016/j.mito.2013.02.004 23434802

44. Ichishita R, Tanaka K, Sugiura Y, Sayano T, Mihara K, et al. (2007) An RNAi Screen for Mitochondrial Proteins Required to Maintain the Morphology of the Organelle in Caenorhabditis elegans. Journal of Biochemistry 143: 449–454. doi: 10.1093/jb/mvm245.

45. Maleszka R, Skelly PJ, Clark-Walker GD (1991) Rolling circle replication of DNA in yeast mitochondria. EMBO J 10: 3923–3929. 1935911

46. Bendich AJ (1993) Reaching for the ring: the study of mitochondrial genome structure. Curr Genet 24: 279–290. doi: 10.1007/BF00336777 8252636

47. Ling F, Shibata T (2004) Mhr1p-dependent Concatemeric Mitochondrial DNA Formation for Generating Yeast Mitochondrial Homoplasmic Cells. Mol Biol Cell 15: 310–322. 14565971

48. Valach M, Farkas Z, Fricova D, Kovac J, Brejova B, et al. (2011) Evolution of linear chromosomes and multipartite genomes in yeast mitochondria. Nucleic Acids Research 39: 4202–4219. doi: 10.1093/nar/gkq1345 21266473

49. Chen XJ, Butow RA (2005) The organization and inheritance of the mitochondrial genome. Nat Rev Genet 6: 815–825. doi: 10.1038/nrg1708 16304597

50. Ling F, Shibata T (2002) Recombination-dependent mtDNA partitioning: in vivo role of Mhr1p to promote pairing of homologous DNA. EMBO J 21: 4730–4740. 12198175

51. Montooth KL, Rand DM (2008) The spectrum of mitochondrial mutation differs across species. PLoS Biol 6: e213. doi: 10.1371/journal.pbio.0060213 18752353

52. Park K, Debyser Z, Tabor S, Richardson CC, Griffith JD (1998) Formation of a DNA loop at the replication fork generated by bacteriophage T7 replication proteins. J Biol Chem 273: 5260–5270. 9478983

53. Miralles Fusté J, Shi Y, Wanrooij S, Zhu X, Jemt E, et al. (2014) In vivo occupancy of mitochondrial single-stranded DNA binding protein supports the strand displacement mode of DNA replication. PLoS Genet 10: e1004832. doi: 10.1371/journal.pgen.1004832 25474639

54. Lee S-H, Siaw GE-L, Willcox S, Griffith JD, Hsieh T-S (2013) Synthesis and dissolution of hemicatenanes by type IA DNA topoisomerases. Proceedings of the National Academy of Sciences 110: E3587–E3594. doi: 10.1073/pnas.1304103110 24003117

55. Lucas I, Hyrien O (2000) Hemicatenanes form upon inhibition of DNA replication. Nucleic Acids Research 28: 2187–2193. doi: 10.1093/nar/28.10.2187 10773090

56. Yang J, Bachrati CZ, Ou J, Hickson ID, Brown GW (2010) Human topoisomerase IIIalpha is a single-stranded DNA decatenase that is stimulated by BLM and RMI1. J Biol Chem 285: 21426–21436. doi: 10.1074/jbc.M110.123216 20445207

57. Chen XJ (2013) Mechanism of homologous recombination and implications for aging-related deletions in mitochondrial DNA. Microbiol Mol Biol Rev 77: 476–496. doi: 10.1128/MMBR.00007-13 24006472

58. Ling F, Yoshida M, Shibata T (2009) Heteroduplex joint formation free of net topological change by Mhr1, a mitochondrial recombinase. J Biol Chem 284: 9341–9353. doi: 10.1074/jbc.M900023200 19193646

59. Sage JM, Knight KL (2013) Human Rad51 promotes mitochondrial DNA synthesis under conditions of increased replication stress. Mitochondrion 13: 350–356. doi: 10.1016/j.mito.2013.04.004 23591384

60. Gissi C, Iannelli F, Pesole G (2008) Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 101: 301–320. doi: 10.1038/hdy.2008.62 18612321

61. Stiernagle T (1999) Maintenance of C. elegans. In: C. elegans: a practical approach. Oxford: Oxford University Press. pp. 51–68.

62. Stiernagle T (2005) Stain Maintenance. In: Wormbook, The C. elegans Research Community. doi: 10.1895/wormbook.1.7.1, http://www.wormbook.org. Accessed 29 October 2014.

63. Jõers P, Lewis SC, Fukuoh A, Parhiala M, Ellilä S, et al. (2013) Mitochondrial Transcription Terminator Family Members mTTF and mTerf5 Have Opposing Roles in Coordination of mtDNA Synthesis. PLoS Genet 9: e1003800. doi: 10.1371/journal.pgen.1003800 24068965

64. Pohjoismäki JLO, Goffart S, Spelbrink JN (2011) Replication stalling by catalytically impaired Twinkle induces mitochondrial DNA rearrangements in cultured cells. Mitochondrion 11: 630–634. doi: 10.1016/j.mito.2011.04.002 21540127

65. Lockshon D, Zweifel SG, Freeman-Cook LL, Lorimer HE, Brewer BJ, et al. (1995) A role for recombination junctions in the segregation of mitochondrial DNA in yeast. Cell 81: 947–955. 7781070

66. Thresher R, Griffith J (1992) Electron microscopic visualization of DNA and DNA-protein complexes as adjunct to biochemical studies. Meth Enzymol 211: 481–490. 1406322

Štítky
Genetika Reprodukčná medicína

Článok vyšiel v časopise

PLOS Genetics


2015 Číslo 2
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Aktuální možnosti diagnostiky a léčby litiáz
nový kurz
Autori: MUDr. Tomáš Ürge, PhD.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#