Crosstalk between autophagy and DNA repair systems

2021 Turkish Journal of Biology  
Autophagy and DNA repair are two essential biological mechanisms that maintain 2 cellular homeostasis. Impairment of these mechanisms was associated with several 3 pathologies such as premature aging, neurodegenerative diseases, and cancer. Intrinsic or 4 extrinsic stress stimuli (e.g., reactive oxygen species or ionizing radiation) cause DNA 5 damage. As a biological stress response, autophagy is activated following insults that threaten 6 DNA integrity. Hence, in collaboration with DNA damage
more » ... repair and response mechanisms, 7 autophagy contributes to the maintenance of genomic stability and integrity. Yet, connections 8 and interactions between these two systems are not fully understood. In this review article, 9 current status of the associations and crosstalk between autophagy and DNA repair systems 10 is documented and discussed. 11 12 13 14 15 16 Maintenance of cellular homeostasis in living organisms requires a balance between anabolic 2 and catabolic reactions. Various endogenous and exogenous insults lead to the activation of 3 cellular and organismal stress response mechanisms. Macroautophagy (autophagy herein) is 4 one of the major and evolutionarily conserved stress response pathways. 5 As a catabolic system, autophagy controls degradation of several cellular 6 components, including long-lived proteins, aggregated proteins and even whole organelles 7 (Kocaturk et al., 2019). Hence, autophagy generally contributes to stress resistance and 8 survival of cells. Under certain conditions, excessive autophagic activity was shown to 9 trigger cell death (Oral et al., 2016). Abnormalities in the autophagic activity were associated 10 with various diseases, including neurodegenerative diseases and cancer (Peker and Gozuacik, 11 2020; Gozuacik et al., 2017) underlining the importance of autophagy for cellular and 12 organismal health, opening the way for autophagy-based treatment approaches (Bayraktar et 13 al., 2016; Unal et al., 2020; Gozuacik et al., 2014). As the key molecule of inheritance, DNA 14 is the essence of life. Exposed to damaging agents and insults, DNA gradually accumulates 15 lesions. All sorts of damages to DNA might potentially result in detrimental outcomes for 16 cells. These lesions also cause loss of genetic information and even trigger genomic 17 instability and rearrangements. Fortunately, in healthy individuals, most of these lesions are 18 repaired by the activation of DNA damage response (DDR) and following DNA damage 19 repair mechanisms. Although autophagic machinery works in the cytoplasm, recent studies 20 pointed out the presence of direct and indirect connections and crosstalk between these stress 21 response systems that are spatially separated. In this review article, we briefly describe autophagy and DNA repair pathways and 1 dissect molecular and cellular outcomes of interactions and crosstalk between these 2 pathways. 3 2 Mechanisms of mammalian autophagy 4 Autophagy is a major catabolic process that is observed in all eukaryotic cells. 5 Autophagosomes (or autophagic vesicles) are cytoplasmic double-membrane vesicles that 6 engulf and sequester various cargo molecules, including organelles, proteins and other 7 cellular constituents. Following fusion of autophagosomes with lysosomes, cargo molecules 8 are degraded, and cellular building blocks, such as amino acids, fatty acids and sugars are 9 recycled. As such, autophagy serves as a primary response mechanism that facilitates 10 adaptation to metabolic and other types of stress. Autophagy can be activated by lack of 11 nutrients, growth factor deprivation or endoplasmic reticulum (ER) stress etc., but genotoxic 12 insults such as irradiation, drugs and toxins also trigger autophagy (Eberhart et al., 2016) . 13 Various signaling pathways have been implicated in the regulation of autophagy. 14 Kinase complexes, receptor-mediated events, GTPases, and ubiquitylation-like protein 15 conjugation systems operate in different stages of autophagy. mTORC1 (mammalian target 16 of rapamycin 1) and mTORC2 (mammalian target of rapamycin 2) are the major kinase 17 complexes playing a role in the activation of autophagy. mTORC1 complex is composed of 18 mTOR kinase, mLST8, DEPTOR, Tti/Tel2, RAPTOR, and PRAS40 proteins, whereas 19 mTORC2 contains RICTOR and mSIN1 instead of RAPTOR and PRAS40 proteins (Tian et 20 al., 2019). Under basal conditions, mTORC1 orchestrates protein synthesis and growth of cells. In this 1 context, mTORC1 remains active leading to the phosphorylation of autophagy initiation 2 complex proteins ATG13 and ULK1 and blocks autophagy. However, upon nutrient 3 shortage, mTOR complexes are inhibited and autophagy is activated. Autophosphorylation 4 of ULK1 further promotes its activity and induces phosphorylation of several autophagy 5 proteins, including ATG13 and FIP200 (Hosokawa et al., 2009); mTOR complexes are also 6 found to be associated with lysosomes where autophagic cargos are degraded. 7 Amino acid availability leads to the recruitment of mTORC1 to lysosomes through a 8 mechanism involving amino acid sensing by the RAG family of GTPases. Lysosomal 9 mTORC1 leads to the phosphorylation of the TFE/MITF family of transcription factors and 10 results in their cytosolic sequestration. The abundance of amino acids results in the release 11 of mTORC1 from the lysosomes, thereby its inactivation. Phosphorylation free TFE/MITF 12 transcription factors translocate to the nucleus where they control both the transcription of 13 autophagy and lysosome biogenesis genes (Ozturk et al., 2019; Settembre et al., 2013). 14 In addition to mTOR, another serine/threonine kinase, AMPK, senses intracellular 15 AMP/ATP ratio and accordingly initiates autophagy. When the level of AMP increases in 16 cells, it binds and allosterically activates AMPK. Binding of AMP to AMPK leads to the 17 activation of the kinase by autophosphorylation as well as by upstream kinases CaMKK and 18 LKB1 (Hawley et al., 1996; Woods et al., 2005) AMPK regulates autophagy in several 19 different ways. AMPK may directly activate autophagy through phosphorylation and 20 activation of ULK1 (Kim et al., 2011). On the other hand, phosphorylation-dependent activation of tuberous sclerosis 2 (TSC2) 1 complex by AMPK also regulates mTORC1 activity which further modulates autophagy 2 (Tripathi et al., 2013). 3 The autophagy process requires the formation of autophagosomes which are double 4 membrane vesicles. Autophagic isolation membranes can either be de novo synthesized or 5 they are derived from existing membrane sources, including ER, mitochondria and their 6 contact sites (MAMs), Golgi membranes or plasma membrane (Ravikumar et al., 2010). 7 Autophagosome nucleation requires activation of another protein complex having a type-III 8 PI3-kinase, VPS34. The PI3 lipid kinase complex contains VPS34, Beclin-1, Atg14, Vps15 9 and AMBRA1 autophagy proteins. The complex leads to the phosphorylation of membrane-10 associated phosphoinositol lipids (PI) and converts them into phosphoinositol-3-phosphates 11 (PI3Ps). PI3P lipids on biological membranes facilitate recruitment of lipid-binding proteins 12 (such as DFCP1 and WIPI proteins) onto membranes, marking autophagosome nucleation 13 sites (Carlsson and Simonsen, 2015). 14 Two ubiquitylation-like conjugation systems are involved in the elongation of 15 autophagic membranes: The ATG12-5-16 system and the ATG8/LC3-lipid conjugation 16 system. First, ATG7 acts as an E1-like enzyme and activates ATG12. Then ATG12 17 conjugates with ATG5 with the help of the E2-like enzyme ATG10. Following the 18 conjugation of ATG12 and ATG5, the complex interacts with another autophagy protein 19 ATG16L. Forming ATG12-5-16 complex performs an E3-like function in the second 20 conjugation system (Kuma et al., 2002; Fujita et al., 2008). The second system leads to the activation of ATG8/LC3 proteins (MAP1LC3 or simply LC3 1 protein, GATE-16 and GABARAP1/2 proteins) through the involvement of E1-like enzyme 2 ATG7 and E2-like enzyme ATG3. Of note, before lipid conjugation, ATG8/LC3 proteins 3 should be primed by ATG4 proteins through a C-terminal cleavage (Li et al., 2011). Once 4 ATG8 proteins are activated, the ATG12-5-16 complex from the first system serves as an 5 E3-like ligase and facilitates the conjugation of ATG8 proteins to lipid molecules, such as 6 phosphatidylethanolamine (PE). Lipidated ATG8 proteins promote isolation membrane 7 expansion and autophagic vesicle completion (Lystad and Simonsen, 2019). Moreover, 8 recent data indicate formation of mTOR-inhibition-sensitive higher molecular weight 9 regulatory complexes, including ATG12-5-16 and the adaptor protein GNB2L1 (RACK1) as 10 key components (Erbil et al., 2016). 11 In the case of selective autophagy, cargo-autophagosome interaction requires specific 12 receptor proteins containing LC3-interacting motifs (LIR motifs) and ubiquitin-binding 13 domains (UBA). SQSTM1/p62, NBR1, NDP52 (also known as a CALCOCO2), OPTN, NIX 14 (also known as BNIP3L) were documented as cargo selective autophagy receptor proteins 15 (Johansen and Lamark, 2020) 16 Autophagic cargos have to be degraded to finalize their journey. Autophagosomes 17 fuse with lysosomes, and the resulting compartments, autolysosomes are responsible for 18 degradation. The fusion process requires several proteins and complexes, such as SNARE 19 proteins (e.g., syntaxin 17 (STX17), SNAP29 and VAMP8, integral lysosomal proteins (e.g., 20 LAMP-2) and RAB proteins (e.g., RAB5 and RAB7) (Bento et al., 2013) .
doi:10.3906/biy-2103-51 fatcat:uh5nbkp3nvgxdmrvqxhpox44u4