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Roles of Ubiquitination and Sumoylation in DNA Damage Response

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Roles of Ubiquitination and Sumoylation in DNA Damage Response Curr. Issues Mol. Biol. (2020) 35: 59-84. Roles of Ubiquitination and SUMOylation in DNA Damage Response Siyuan Su1,2, Yanqiong Zhang1,2 and Pengda Liu1,2* 1Lineberger Comprehensive Cancer Center, Te University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. 2Department of Biochemistry and Biophysics, Te University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.035.059 Abstract that genome instability leads to human disorders Ubiquitin and ubiquitin-like modifers, such as including cancer, understanding detailed molecu- SUMO, exert distinct physiological functions by lar mechanisms for ubiquitin and SUMO-related conjugating to protein substrates. Ubiquitination or regulations in DNA damage response may provide SUMOylation of protein substrates determine the novel insights into therapeutic modalities to treat fate of modifed proteins, including proteasomal human diseases associated with deregulated DNA degradation, cellular re-localization, alternations in damage response. binding partners and serving as a protein-binding platform, in a ubiquitin or SUMO linkage-depend- ent manner. DNA damage occurs constantly in Introduction living organisms but is also repaired by distinct DNA encodes for inheritable genetic information tightly controlled mechanisms including homolo- that is not only essential to exert normal cellular gous recombination, non-homologous end joining, function but also indispensable to maintain the inter-strand crosslink repair, nucleotide excision human society. Tus, DNA should be stable while repair and base excision repair. On sensing damaged versatile. Although certain genetic changes are DNA, a ubiquitination/SUMOylation landscape is permissible to drive evolution (usually at a low established to recruit DNA damage repair factors. mutation rate), improper damaged DNA need to Meanwhile, misloaded and mission-completed be repaired timely. With the development of tech- repair factors will be turned over by ubiquitin or nology, human beings are exposed to more DNA SUMO modifcations as well. Tese ubiquitination damaging cues nowadays such as wireless internet and SUMOylation events are tightly controlled (Wi-Fi) (Akdag et al., 2016), ultraviolet (UV) by both E3 ubiquitin/SUMO ligases and deubiq- radiation from sun exposure (Sinha and Häder, uitinases/deSUMOylases. In this review, we will 2002) and even microwave ovens (Sagripanti et al., summarize identifed ubiquitin and SUMO-related 1987) used on a daily basis. If the damaged DNA is modifcations and their function in distinct DNA detected and repaired to a level tolerated by cells, damage repair pathways, and provide evidence for cells will survive and may develop neoplastic trans- responsible E3 ligases, deubiquitinases, SUMOy- formation; otherwise cells will die and be cleared. lases and deSUMOylases in these processes. Given Damaged DNA is actively monitored by DNA caister.com/cimb 59 Curr. Issues Mol. Biol. Vol. 35 264 | Su et al. damage sensors and repaired by DNA damage damage leads to cell death (Nowsheen and Yang, repair factors. Notably, in most prokaryotes such 2012). Te fastest reaction in cell is through bio- as bacteria, a SOS response is commonly triggered chemical reactions-indeed protein translational by DNA damage to repair damaged DNA and also modifcations have been observed and proven to contributes to anti-antibiotic features (Kreuzer, play indispensable roles in this regard. For example, 2013). In this review, we will focus on DDR (DNA ATM, ATR or DNAPK controls phosphorylation damage response) in eukaryotes given its close of a large group of ‘SQ/TQ’ containing substrates relationship to human physiology and pathology including Chk1 and Chk2 (Chen and Poon, 2008), (Ciccia and Elledge, 2010). while as protein kinases themselves, Chk1 and Chk2 In response to genotoxic challenges, eukaryotes will further amplify the DNA damage signals by activate DNA damage checkpoints to suppress phosphorylating more substrates such as Cdc25A, DNA replication, arrest cell cycle, stop proliferation p53, PML, Plk3 and many others (Bartek and and meanwhile activate signal transduction path- Lukas, 2003). It is a kinase network or landscape ways to directly repair damaged DNA, or promote that transduces the DNA damage signals in an acute transcription of repair enzymes. Mechanisms sens- and spatial-tempo dependent manner (Chen and ing and repairing damaged DNA are conserved in Poon, 2008). In addition to extensively studied and eukaryotes. Factors inducing DNA damage can well-characterized protein kinase cascades in DDR, be divided into two categories: intrinsic factors ubiquitination and its close cousin, SUMOylation and exogenous factors. Te most frequent sources are other types of protein modifcations that exert of intrinsic DNA damage are from inaccurate indispensable roles in both sensing and repairing DNA replication, free radicals generated in vivo damaged DNA (Brinkmann et al., 2015; Wang, Z. et under oxidative stress or from normal biological al., 2017). In this review, we will summarize recent processes including meiotic recombination and progress on ubiquitin and SUMO-related regula- V(D)J recombination during antibody production tions on DDR, list all identifed ubiquitination (Hartlerode and Scully, 2009). Strong environmen- and SUMOylation events during DDR, further tal cues including UV radiation, X-ray, gamma-ray illustrate their physiological and pathological func- and other chemical mutagens also cause various tion and provide new insights into future research types of DNA damage, including DSBs (double- directions or therapeutic modalities targeting these strand breaks), SSBs (single-strand breaks), DNA identifed ubiquitination or SUMOylation events. base mutation, deletion, insertion, deamination, chemical modifcations and formation of pyrimi- dine dimmers. Accordingly, distinct DNA damage Overview of the ubiquitin responses are triggered. For example, UV-induced signalling DNA crosslinking is resolved by NER (nucleotide Ubiquitin is a 76 amino-acid protein highly con- excision repair) (Marteijn et al., 2014), unmatched, served among eukaryotic species. Usually ubiquitin modifed and damaged DNA bases are removed is considered as a modifer for proteins-atachment and reflled by the mismatch repair mechanism (Li, of ubiquitin moiety to a lysine residue on target 2008), SSBs and DSBs are repaired by either HR proteins regulates important cellular processes (homologous recombination) (Li and Heyer, 2008) including cellular trafcking, immune sensing, or NHEJ (non-homologous end joining) (Chang et protein translation, metabolism, cell cycle and al., 2017). Similar to prokaryotes, eukaryotes also autophagy (Finley, 2009). Protein ubiquitination utilize a SOS response in coordinating diferent is a three-step enzymatic reaction requiring three repair pathway choices in responding to severe types of enzymes, including E1 ubiquitin-activating DNA damages (Fu et al., 2008). Te eukaryotic enzyme, E2 ubiquitin-conjugating enzyme and E3 DNA damage repair systems include DSB repair, ubiquitin ligase. In mammals, there are one major inter-strand crosslink repair (ICLR), nucleotide E1, forty E2s and more than 600 E3s. E3 ubiquitin excision repair (NER) and base excision repair ligases are mainly divided into three families based (BER) (Hoeijmakers, 2001). on their structures and mechanisms of ubiquitin Cells would need acute responses to repair transfer, including RING (Really Interesting New damaged DNA-otherwise severe unrepaired DNA Gene), HECT (Homologous to E6-AP Carboxyl caister.com/cimb 60 Curr. Issues Mol. Biol. Vol. 35 Ubiquitin and SUMO Govern DNA Damage Response | 265 Terminus) and RBR (RING-Between-RING) linkages or branched chains (heterotypic) (Meyer domain containing E3 ubiquitin ligase families and Rape, 2014; Ohtake and Tsuchiya, 2017). (Zheng and Shabek, 2017). For RING and RBR Moreover, more than one poly-ubiquitin chain can families of E3 ligases, activated ubiquitin by E1 be covalently atached to the same ubiquitin mol- will be conjugated to E2, and it is the E2 enzyme ecule on diferent lysine residues (Suryadinata et al., directly transferring ubiquitin to substrates that are 2014). To make it more complicated, the ubiquitin determined by E3 ligases. While for HECT domain molecule itself also undergoes various post-trans- containing E3 ligases, ubiquitin will be transiently lational modifcation (PTM) events, including transferred from E2 to E3 then transferred to phosphorylation (Koyano et al., 2014) and acetyla- substrates. In this process, E3 ubiquitin ligases tion (Ohtake et al., 2015), adding another layer of determine the substrate specifcity. regulation on poly-ubiquitin chains. Tese distinct Notably, each ubiquitin contains seven lysine linkage composition and ubiquitin modifcations residues. Addition of a ubiquitin to a prior ubiqui- on substrates create unique languages coding for tin molecule can be linked through each of seven distinct biological meanings, which have been lysine residues in ubiquitin, or through a head-to- referred to as ‘ubiquitin codes’ (Komander and toe ligation, leading to formation of poly-ubiquitin Rape, 2012; Yau and Rape, 2016). chains in diferent linkages. According to the posi- Ubiquitination is a reversible protein modifca- tion of linked lysine residue, poly-ubiquitin chains tion and a result of a balance between adding and can be linked through M1 (head-to-toe), K6, K11, removing ubiquitin moieties. Various
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