Inactivation of the mitochondrial protease Afg3l2 results in severely diminished respiratory chain activity and widespread defects in mitochondrial gene expression

English version

Autoři: Gautam Pareek ^aff001; Leo J. Pallanck ^aff001
Působiště autorů: Department of Genome Sciences, University of Washington, Seattle, United States of America ^aff001
Vyšlo v časopise: Inactivation of the mitochondrial protease Afg3l2 results in severely diminished respiratory chain activity and widespread defects in mitochondrial gene expression. PLoS Genet 16(10): e32767. doi:10.1371/journal.pgen.1009118
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1009118

Souhrn

The m-AAA proteases play a critical role in the proteostasis of inner mitochondrial membrane proteins, and mutations in the genes encoding these proteases cause severe incurable neurological diseases. To further explore the biological role of the m-AAA proteases and the pathological consequences of their deficiency, we used a genetic approach in the fruit fly Drosophila melanogaster to inactivate the ATPase family gene 3-like 2 (AFG3L2) gene, which encodes a critical component of the m-AAA proteases. We found that null alleles of Drosophila AFG3L2 die early in development, but partial inactivation of AFG3L2 using RNAi allowed survival to the late pupal and adult stages of development. Flies with partial inactivation of AFG3L2 exhibited behavioral defects, neurodegeneration, accumulation of unfolded mitochondrial proteins, and diminished respiratory chain (RC) activity. Further work revealed that the reduced RC activity was primarily a consequence of severely diminished mitochondrial transcription and translation. These defects were accompanied by activation of the mitochondrial unfolded protein response (mito-UPR) and autophagy. Overexpression of mito-UPR components partially rescued the AFG3L2-deficient phenotypes, indicating that protein aggregation partly accounts for the defects of AFG3L2-deficient animals. Our work suggests that strategies designed to activate mitochondrial stress pathways and mitochondrial gene expression could be therapeutic in the diseases caused by mutations in AFG3L2.

Klíčová slova:

Drosophila melanogaster – Gene expression – Immune serum – Mitochondria – Proteases – Pupae – Ribosomes – RNA interference

Zdroje

1. Gustafsson CM, Falkenberg M, Larsson NG. Maintenance and Expression of Mammalian Mitochondrial DNA. Annual review of biochemistry. 2016;85:133–60. doi: 10.1146/annurev-biochem-060815-014402 27023847

2. Sun N, Youle RJ, Finkel T. The Mitochondrial Basis of Aging. Molecular cell. 2016;61(5):654–66. doi: 10.1016/j.molcel.2016.01.028 26942670

3. Moehle EA, Shen K, Dillin A. Mitochondrial proteostasis in the context of cellular and organismal health and aging. The Journal of biological chemistry. 2019;294(14):5396–407. doi: 10.1074/jbc.TM117.000893 29622680

4. Whitworth AJ, Pallanck LJ. PINK1/Parkin mitophagy and neurodegeneration-what do we really know in vivo? Current opinion in genetics & development. 2017;44:47–53.

5. Pickles S, Vigie P, Youle RJ. Mitophagy and Quality Control Mechanisms in Mitochondrial Maintenance. Curr Biol. 2018;28(4):R170–R85. doi: 10.1016/j.cub.2018.01.004 29462587

6. Vincow ES, Thomas RE, Merrihew GE, Shulman NJ, Bammler TK, MacDonald JW, et al. Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective. Autophagy. 2019;15(9):1592–605. doi: 10.1080/15548627.2019.1586258 30865561

7. Gerdes F, Tatsuta T, Langer T. Mitochondrial AAA proteases—towards a molecular understanding of membrane-bound proteolytic machines. Biochimica et biophysica acta. 2012;1823(1):49–55. doi: 10.1016/j.bbamcr.2011.09.015 22001671

8. Quiros PM, Langer T, Lopez-Otin C. New roles for mitochondrial proteases in health, ageing and disease. Nat Rev Mol Cell Biol. 2015;16(6):345–59. doi: 10.1038/nrm3984 25970558

9. Patron M, Sprenger HG, Langer T. m-AAA proteases, mitochondrial calcium homeostasis and neurodegeneration. Cell research. 2018;28(3):296–306. doi: 10.1038/cr.2018.17 29451229

10. Qi Y, Liu H, Daniels MP, Zhang G, Xu H. Loss of Drosophila i-AAA protease, dYME1L, causes abnormal mitochondria and apoptotic degeneration. Cell Death Differ. 2016;23(2):291–302. doi: 10.1038/cdd.2015.94 26160069

11. Pareek G, Thomas RE, Pallanck LJ. Loss of the Drosophila m-AAA mitochondrial protease paraplegin results in mitochondrial dysfunction, shortened lifespan, and neuronal and muscular degeneration. Cell Death Dis. 2018;9(3):304. doi: 10.1038/s41419-018-0365-8 29467464

12. Pareek G, Thomas RE, Vincow ES, Morris DR, Pallanck LJ. Lon protease inactivation in Drosophila causes unfolded protein stress and inhibition of mitochondrial translation. Cell Death Discov. 2018;4:51.

13. Thomas RE, Andrews LA, Burman JL, Lin WY, Pallanck LJ. PINK1-Parkin pathway activity is regulated by degradation of PINK1 in the mitochondrial matrix. PLoS genetics. 2014;10(5):e1004279. doi: 10.1371/journal.pgen.1004279 24874806

14. Gratz SJ, Ukken FP, Rubinstein CD, Thiede G, Donohue LK, Cummings AM, et al. Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila. Genetics. 2014;196(4):961–71. doi: 10.1534/genetics.113.160713 24478335

15. Maltecca F, Magnoni R, Cerri F, Cox GA, Quattrini A, Casari G. Haploinsufficiency of AFG3L2, the gene responsible for spinocerebellar ataxia type 28, causes mitochondria-mediated Purkinje cell dark degeneration. J Neurosci. 2009;29(29):9244–54. doi: 10.1523/JNEUROSCI.1532-09.2009 19625515

16. Di Bella D, Lazzaro F, Brusco A, Plumari M, Battaglia G, Pastore A, et al. Mutations in the mitochondrial protease gene AFG3L2 cause dominant hereditary ataxia SCA28. Nat Genet. 2010;42(4):313–21. doi: 10.1038/ng.544 20208537

17. Koppen M, Metodiev MD, Casari G, Rugarli EI, Langer T. Variable and tissue-specific subunit composition of mitochondrial m-AAA protease complexes linked to hereditary spastic paraplegia. Mol Cell Biol. 2007;27(2):758–67. doi: 10.1128/MCB.01470-06 17101804

18. Martinelli P, La Mattina V, Bernacchia A, Magnoni R, Cerri F, Cox G, et al. Genetic interaction between the m-AAA protease isoenzymes reveals novel roles in cerebellar degeneration. Human molecular genetics. 2009;18(11):2001–13. doi: 10.1093/hmg/ddp124 19289403

19. Greene JC, Whitworth AJ, Kuo I, Andrews LA, Feany MB, Pallanck LJ. Mitochondrial pathology and apoptotic muscle degeneration in Drosophila parkin mutants. Proceedings of the National Academy of Sciences of the United States of America. 2003;100(7):4078–83. doi: 10.1073/pnas.0737556100 12642658

20. Zhu M, Li X, Tian X, Wu C. Mask loss-of-function rescues mitochondrial impairment and muscle degeneration of Drosophila pink1 and parkin mutants. Hum Mol Genet. 2015;24(11):3272–85. doi: 10.1093/hmg/ddv081 25743185

21. Zurita Rendon O, Shoubridge EA. LONP1 Is Required for Maturation of a Subset of Mitochondrial Proteins, and Its Loss Elicits an Integrated Stress Response. Molecular and cellular biology. 2018;38(20).

22. Almajan ER, Richter R, Paeger L, Martinelli P, Barth E, Decker T, et al. AFG3L2 supports mitochondrial protein synthesis and Purkinje cell survival. J Clin Invest. 2012;122(11):4048–58. doi: 10.1172/JCI64604 23041622

23. Suzuki YJ, Carini M, Butterfield DA. Protein carbonylation. Antioxidants & redox signaling. 2010;12(3):323–5.

24. Konig T, Troder SE, Bakka K, Korwitz A, Richter-Dennerlein R, Lampe PA, et al. The m-AAA Protease Associated with Neurodegeneration Limits MCU Activity in Mitochondria. Molecular cell. 2016;64(1):148–62. doi: 10.1016/j.molcel.2016.08.020 27642048

25. Tsai CW, Wu Y, Pao PC, Phillips CB, Williams C, Miller C, et al. Proteolytic control of the mitochondrial calcium uniporter complex. Proceedings of the National Academy of Sciences of the United States of America. 2017;114(17):4388–93. doi: 10.1073/pnas.1702938114 28396416

26. Kwong JQ, Molkentin JD. Physiological and pathological roles of the mitochondrial permeability transition pore in the heart. Cell metabolism. 2015;21(2):206–14. doi: 10.1016/j.cmet.2014.12.001 25651175

27. Tufi R, Gleeson TP, von Stockum S, Hewitt VL, Lee JJ, Terriente-Felix A, et al. Comprehensive Genetic Characterization of Mitochondrial Ca(2+) Uniporter Components Reveals Their Different Physiological Requirements In Vivo. Cell reports. 2019;27(5):1541–50 e5. doi: 10.1016/j.celrep.2019.04.033 31042479

28. Baughman JM, Perocchi F, Girgis HS, Plovanich M, Belcher-Timme CA, Sancak Y, et al. Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter. Nature. 2011;476(7360):341–5. doi: 10.1038/nature10234 21685886

29. De Stefani D, Raffaello A, Teardo E, Szabo I, Rizzuto R. A forty-kilodalton protein of the inner membrane is the mitochondrial calcium uniporter. Nature. 2011;476(7360):336–40. doi: 10.1038/nature10230 21685888

30. Kamer KJ, Mootha VK. MICU1 and MICU2 play nonredundant roles in the regulation of the mitochondrial calcium uniporter. EMBO reports. 2014;15(3):299–307. doi: 10.1002/embr.201337946 24503055

31. Nolden M, Ehses S, Koppen M, Bernacchia A, Rugarli EI, Langer T. The m-AAA protease defective in hereditary spastic paraplegia controls ribosome assembly in mitochondria. Cell. 2005;123(2):277–89. doi: 10.1016/j.cell.2005.08.003 16239145

32. Bratic A, Wredenberg A, Gronke S, Stewart JB, Mourier A, Ruzzenente B, et al. The bicoid stability factor controls polyadenylation and expression of specific mitochondrial mRNAs in Drosophila melanogaster. PLoS genetics. 2011;7(10):e1002324. doi: 10.1371/journal.pgen.1002324 22022283

33. Durigon R, Mitchell AL, Jones AW, Manole A, Mennuni M, Hirst EM, et al. LETM1 couples mitochondrial DNA metabolism and nutrient preference. EMBO Mol Med. 2018;10(9).

34. Pearce SF, Rebelo-Guiomar P, D'Souza AR, Powell CA, Van Haute L, Minczuk M. Regulation of Mammalian Mitochondrial Gene Expression: Recent Advances. Trends Biochem Sci. 2017;42(8):625–39. doi: 10.1016/j.tibs.2017.02.003 28285835

35. Antonicka H, Shoubridge EA. Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis. Cell Rep. 2015;10(6):920–32. doi: 10.1016/j.celrep.2015.01.030 25683715

36. Pimenta de Castro I, Costa AC, Lam D, Tufi R, Fedele V, Moisoi N, et al. Genetic analysis of mitochondrial protein misfolding in Drosophila melanogaster. Cell death and differentiation. 2012;19(8):1308–16. doi: 10.1038/cdd.2012.5 22301916

37. Davis MY, Trinh K, Thomas RE, Yu S, Germanos AA, Whitley BN, et al. Glucocerebrosidase Deficiency in Drosophila Results in alpha-Synuclein-Independent Protein Aggregation and Neurodegeneration. PLoS genetics. 2016;12(3):e1005944. doi: 10.1371/journal.pgen.1005944 27019408

38. Qureshi MA, Haynes CM, Pellegrino MW. The mitochondrial unfolded protein response: Signaling from the powerhouse. J Biol Chem. 2017;292(33):13500–6. doi: 10.1074/jbc.R117.791061 28687630

39. Aparicio R, Rana A, Walker DW. Upregulation of the Autophagy Adaptor p62/SQSTM1 Prolongs Health and Lifespan in Middle-Aged Drosophila. Cell Rep. 2019;28(4):1029–40.e5. doi: 10.1016/j.celrep.2019.06.070 31340141

40. Nezis IP, Simonsen A, Sagona AP, Finley K, Gaumer S, Contamine D, et al. Ref(2)P, the Drosophila melanogaster homologue of mammalian p62, is required for the formation of protein aggregates in adult brain. J Cell Biol. 2008;180(6):1065–71. doi: 10.1083/jcb.200711108 18347073

41. Simonsen A, Cumming RC, Brech A, Isakson P, Schubert DR, Finley KD. Promoting basal levels of autophagy in the nervous system enhances longevity and oxidant resistance in adult Drosophila. Autophagy. 2008;4(2):176–84. doi: 10.4161/auto.5269 18059160

42. Pareek G, Pallanck LJ. Inactivation of Lon protease reveals a link between mitochondrial unfolded protein stress and mitochondrial translation inhibition. Cell Death Dis. 2018;9(12):1168. doi: 10.1038/s41419-018-1213-6 30518747

43. Pierson TM, Adams D, Bonn F, Martinelli P, Cherukuri PF, Teer JK, et al. Whole-exome sequencing identifies homozygous AFG3L2 mutations in a spastic ataxia-neuropathy syndrome linked to mitochondrial m-AAA proteases. PLoS Genet. 2011;7(10):e1002325. doi: 10.1371/journal.pgen.1002325 22022284

44. Jourdain AA, Boehm E, Maundrell K, Martinou JC. Mitochondrial RNA granules: Compartmentalizing mitochondrial gene expression. J Cell Biol. 2016;212(6):611–4. doi: 10.1083/jcb.201507125 26953349

45. Atorino L, Silvestri L, Koppen M, Cassina L, Ballabio A, Marconi R, et al. Loss of m-AAA protease in mitochondria causes complex I deficiency and increased sensitivity to oxidative stress in hereditary spastic paraplegia. J Cell Biol. 2003;163(4):777–87. doi: 10.1083/jcb.200304112 14623864

46. Jia Y, Xu RG, Ren X, Ewen-Campen B, Rajakumar R, Zirin J, et al. Next-generation CRISPR/Cas9 transcriptional activation in Drosophila using flySAM. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(18):4719–24. doi: 10.1073/pnas.1800677115 29666231

47. Samstag CL, Hoekstra JG, Huang CH, Chaisson MJ, Youle RJ, Kennedy SR, et al. Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase gamma. PLoS Genet. 2018;14(11):e1007805. doi: 10.1371/journal.pgen.1007805 30452458

48. Scaduto RC Jr., Grotyohann LW. Measurement of mitochondrial membrane potential using fluorescent rhodamine derivatives. Biophysical journal. 1999;76(1 Pt 1):469–77.

49. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nature protocols. 2008;3(6):1101–8. doi: 10.1038/nprot.2008.73 18546601

50. Baggio F, Bratic A, Mourier A, Kauppila TE, Tain LS, Kukat C, et al. Drosophila melanogaster LRPPRC2 is involved in coordination of mitochondrial translation. Nucleic acids research. 2014;42(22):13920–38. doi: 10.1093/nar/gku1132 25428350

51. Koontz L. TCA precipitation. Methods in enzymology. 2014;541:3–10. doi: 10.1016/B978-0-12-420119-4.00001-X 24674058

52. Finnegan PM, Brown GG. In organello transcription in maize mitochondria and its sensitivity to inhibitors of RNA synthesis. Plant Physiol. 1987;85(1):304–9. doi: 10.1104/pp.85.1.304 16665676

53. Lee W, Choi HI, Kim MJ, Park SY. Depletion of mitochondrial DNA up-regulates the expression of MDR1 gene via an increase in mRNA stability. Exp Mol Med. 2008;40(1):109–17. doi: 10.3858/emm.2008.40.1.109 18305404

54. Zylber E, Vesco C, Penman S. Selective inhibition of the synthesis of mitochondria-associated RNA by ethidium bromide. J Mol Biol. 1969;44(1):195–204. doi: 10.1016/0022-2836(69)90414-8 5811827

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