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Research Paper

Analysis of ATG4C function in vivo

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Pages 2912-2933 | Received 22 Sep 2022, Accepted 05 Jul 2023, Published online: 17 Jul 2023

References

  • Deretic V, Saitoh T, Akira S. Autophagy in infection, inflammation and immunity. Nat Rev Immunol. 2013 Oct;13(10):722–737. doi: 10.1038/nri3532
  • Rubinsztein DC, Marino G, Kroemer G. Autophagy and aging. Cell. 2011 Sep 2;146(5):682–695.
  • Levine B, Kroemer G. Biological functions of autophagy genes: a disease perspective. Cell. 2019 Jan 10;176(1–2):11–42.
  • Klionsky DJ, Abdelmohsen K, Abe A, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy. 2016;12(1):1–222. doi: 10.1080/15548627.2015.1100356
  • Ichimura Y, Kirisako T, Takao T, et al. A ubiquitin-like system mediates protein lipidation. Nature. 2000 Nov 23;408(6811):488–492.
  • Wu X, Won H, Rubinsztein DC. Autophagy and mammalian development. Biochem Soc Trans. 2013 Dec;41(6):1489–1494. doi: 10.1042/BST20130185
  • Fernandez AF, Lopez-Otin C. The functional and pathologic relevance of autophagy proteases. J Clin Invest. 2015 Jan;125(1):33–41. doi: 10.1172/JCI73940
  • Lopez-Otin C, Marino G. Tagged ATG8-coding constructs for the in vitro and in vivo assessment of ATG4 activity. Methods Enzymol. 2017;587:189–205.
  • Tanida I, Tanida-Miyake E, Ueno T, et al. The human homolog of Saccharomyces cerevisiae Apg7p is a protein-activating enzyme for multiple substrates including human Apg12p, GATE-16, GABARAP, and MAP-LC3. J Biol Chem. 2001 Jan 19;276(3):1701–1706.
  • He H, Dang Y, Dai F, et al. Post-translational modifications of three members of the human MAP1LC3 family and detection of a novel type of modification for MAP1LC3B. J Biol Chem. 2003 Aug 1;278(31):29278–29287.
  • Hemelaar J, Lelyveld VS, Kessler BM, et al. A single protease, Apg4B, is specific for the autophagy-related ubiquitin-like proteins GATE-16, MAP1-LC3, GABARAP, and Apg8L. J Biol Chem. 2003 Dec 19;278(51):51841–51850.
  • Scherz-Shouval R, Sagiv Y, Shorer H, et al. The COOH terminus of GATE-16, an intra-golgi transport modulator, is cleaved by the human cysteine protease HsApg4A. J Biol Chem. 2003 Apr 18;278(16):14053–14058.
  • Tanida I, Sou YS, Ezaki J, et al. HsAtg4B/HsApg4B/autophagin-1 cleaves the carboxyl termini of three human Atg8 homologues and delipidates microtubule-associated protein light chain 3- and GABAA receptor-associated protein-phospholipid conjugates. J Biol Chem. 2004 Aug 27;279(35):36268–36276.
  • Puente XS, Sanchez LM, Overall CM, et al. Human and mouse proteases: a comparative genomic approach. Nat Rev Genet. 2003 Jul;4(7):544–558.
  • López-Otín C, Overall CM. Protease degradomics: a new challenge for proteomics. Nat Rev Mol Cell Biol. 2002 Jul;3(7):509–519. doi: 10.1038/nrm858
  • Marino G, Fernandez AF, Cabrera S, et al. Autophagy is essential for mouse sense of balance. J Clin Investig. 2010 Jul;120(7):2331–2344.
  • Fernandez AF, Barcena C, Martinez-Garcia GG, et al. Autophagy couteracts weight gain, lipotoxicity and pancreatic beta-cell death upon hypercaloric pro-diabetic regimens. Cell Death Dis. 2017 Aug 3;8(8):e2970.
  • Cabrera S, Fernandez AF, Marino G, et al. Atg4b/autophagin-1 regulates intestinal homeostasis and protects mice from experimental colitis. Autophagy. 2013 Aug;9(8):1188–1200.
  • Cabrera S, Marino G, Fernandez AF, et al. Autophagy, proteases and the sense of balance. Autophagy. 2010 Oct;6(7):961–963.
  • Tamargo-Gomez I, Martinez-Garcia GG, Suarez MF, et al. ATG4D role in mAtg8s delipidation and neuroprotection. Autophagy. 2021 Jun;17(6):1558–1560.
  • Kuma A, Komatsu M, Mizushima N. Autophagy-monitoring and autophagy-deficient mice. Autophagy. 2017 Oct 3;13(10):1619–1628.
  • Kabeya Y, Mizushima N, Ueno T, et al. LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. The EMBO J. 2000 Nov 1;19(21):5720–5728.
  • Tanida I, Minematsu-Ikeguchi N, Ueno T, et al. Lysosomal turnover, but not a cellular level, of endogenous LC3 is a marker for autophagy. Autophagy. 2005 Jul;1(2):84–91.
  • Rubinsztein DC, Cuervo AM, Ravikumar B, et al. In search of an “autophagomometer”. Autophagy. 2009 Jul;5(5):585–589.
  • Haspel J, Shaik RS, Ifedigbo E, et al. Characterization of macroautophagic flux in vivo using a leupeptin-based assay. Autophagy. 2011 Jun;7(6):629–642.
  • Sahani MH, Itakura E, Mizushima N. Expression of the autophagy substrate SQSTM1/p62 is restored during prolonged starvation depending on transcriptional upregulation and autophagy-derived amino acids. Autophagy. 2014 Mar;10(3):431–441. doi: 10.4161/auto.27344
  • Lum JJ, DeBerardinis RJ, Thompson CB. Autophagy in metazoans: cell survival in the land of plenty. Nat Rev Mol Cell Biol. 2005 Jun;6(6):439–448. doi: 10.1038/nrm1660
  • Smith-Blair N. Mechanisms of diaphragm fatigue. AACN Clin Issues: Advanc Pract Acute Critical Care. 2002 May;13(2):307–319. doi: 10.1097/00044067-200205000-00014
  • Tamargo-Gomez I, Marino G. AMPK: regulation of metabolic dynamics in the context of autophagy. Int J Mol Sci. 2018 Nov 29;19(12):3812.
  • Crow MT, Kushmerick MJ. Chemical energetics of slow- and fast-twitch muscles of the mouse. J Gen Physiol. 1982 Jan;79(1):147–166. doi: 10.1085/jgp.79.1.147
  • Levine S, Kaiser L, Leferovich J, et al. Cellular adaptations in the diaphragm in chronic obstructive pulmonary disease. N Engl J Med. 1997 Dec 18;337(25):1799–1806.
  • Petrof BJ, Stedman HH, Shrager JB, et al. Adaptations in myosin heavy chain expression and contractile function in dystrophic mouse diaphragm. Am J Physiol. 1993 Sep;265(3 Pt 1):C834–41.
  • Burns DP, Roy A, Lucking EF, et al. Sensorimotor control of breathing in the mdx mouse model of duchenne muscular dystrophy. J Physiol. 2017 Nov 1;595(21):6653–6672.
  • Shen S, Kepp O, Kroemer G. The end of autophagic cell death? Autophagy. 2012 Jan;8(1):1–3. doi: 10.4161/auto.8.1.16618
  • Marino G, Niso-Santano M, Baehrecke EH, et al. Self-consumption: the interplay of autophagy and apoptosis. Nat Rev Mol Cell Biol. 2014 Feb;15(2):81–94.
  • Pendas AM, Folgueras AR, Llano E, et al. Diet-induced obesity and reduced skin cancer susceptibility in matrix metalloproteinase 19-deficient mice. Mol Cell Biol. 2004 Jun;24(12):5304–5313.
  • Balbin M, Fueyo A, Tester AM, et al. Loss of collagenase-2 confers increased skin tumor susceptibility to male mice. Nat Genet. 2003 Nov;35(3):252–257.
  • Matsushita H, Vesely MD, Koboldt DC, et al. Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature. 2012 Feb 8;482(7385):400–404.
  • DuPage M, Mazumdar C, Schmidt LM, et al. Expression of tumour-specific antigens underlies cancer immunoediting. Nature. 2012 Feb 8;482(7385):405–409.
  • Durgan J, Lystad AH, Sloan K, et al. Non-canonical autophagy drives alternative ATG8 conjugation to phosphatidylserine. Mol Cell. 2021 May 6;81(9):2031–2040 e8.
  • Katayama H, Kogure T, Mizushima N, et al. A sensitive and quantitative technique for detecting autophagic events based on lysosomal delivery. Chem Biol. 2011 Aug 26;18(8):1042–1052.
  • Tamargo-Gomez I, Martinez-Garcia GG, Suarez MF, et al. ATG4D is the main ATG8 delipidating enzyme in mammalian cells and protects against cerebellar neurodegeneration. Cell Death Differ. 2021 Sep;28(9):2651–2672.
  • Alirezaei M, Kemball CC, Flynn CT, et al. Short-term fasting induces profound neuronal autophagy. Autophagy. 2010 Aug;6(6):702–710.
  • Mizushima N, Yamamoto A, Matsui M, et al. In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker. Mol Biol Cell. 2004 Mar;15(3):1101–1111.
  • Guo JY, Teng X, Laddha SV, et al. Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in ras-driven lung cancer cells. Genes Dev. 2016 Aug 1;30(15):1704–1717.
  • Barnard AM, Lott DJ, Batra A, et al. Imaging respiratory muscle quality and function in duchenne muscular dystrophy. J Neurol. 2019 Nov;266(11):2752–2763.
  • Hawkins EC, Bettis AK, Kornegay JN. Expiratory dysfunction in young dogs with golden retriever muscular dystrophy. Neuromuscul Disorders. 2020 Nov;30(11):930–937. doi: 10.1016/j.nmd.2020.09.027
  • Fajardo VA, Chambers PJ, Juracic ES, et al. Sarcolipin deletion in mdx mice impairs calcineurin signalling and worsens dystrophic pathology. Hum Mol Genet. 2018 Dec 1;27(23):4094–4102.
  • Girardot T, Rimmele T, Venet F, et al. Apoptosis-induced lymphopenia in sepsis and other severe injuries. Apoptos. 2017 Feb;22(2):295–305.
  • Zhang S, Hama Y, Mizushima N. The evolution of autophagy proteins – diversification in eukaryotes and potential ancestors in prokaryotes. J Cell Sci. 2021 Jul 1;134(13). doi: 10.1242/jcs.233742
  • Agrotis A, Pengo N, Burden JJ, et al. Redundancy of human ATG4 protease isoforms in autophagy and LC3/GABARAP processing revealed in cells. Autophagy. 2019 Jun;15(6):976–997.
  • Wu F, Li Y, Wang F, et al. Differential function of the two Atg4 homologues in the aggrephagy pathway in caenorhabditis elegans. J Biol Chem. 2012 Aug 24;287(35):29457–29467.
  • Hill SE, Kauffman KJ, Krout M, et al. Maturation and clearance of autophagosomes in neurons depends on a specific cysteine protease isoform, ATG-4.2. Dev Cell. 2019 Apr 22;49(2):251–266 e8.
  • Luhr M, Saetre F, Engedal N. The long-lived protein degradation assay: an efficient method for quantitative determination of the autophagic flux of endogenous proteins in adherent cell lines. Bio Protoc. 2018 May 5;8(9):e2836.
  • Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method. Methods. 2001 Dec;25(4):402–408. doi: 10.1006/meth.2001.1262
  • Gonzalez-Obeso E, Docio I, Olea E, et al. Guinea pig oxygen-sensing and carotid body functional properties. Front Physiol. 2017;8:285. doi: 10.3389/fphys.2017.00285