Archives

  • 2018-07
  • 2018-10
  • 2018-11
  • 2019-04
  • 2019-05
  • 2019-06
  • 2019-07
  • 2019-08
  • 2019-09
  • 2019-10
  • 2019-11
  • 2019-12
  • 2020-01
  • 2020-02
  • 2020-03
  • 2020-04
  • 2020-05
  • 2020-06
  • 2020-07
  • 2020-08
  • 2020-09
  • 2020-10
  • 2020-11
  • 2020-12
  • 2021-01
  • 2021-02
  • 2021-03
  • 2021-04
  • 2021-05
  • 2021-06
  • 2021-07
  • 2021-08
  • 2021-09
  • 2021-10
  • 2021-11
  • 2021-12
  • 2022-01
  • 2022-02
  • 2022-03
  • 2022-04
  • 2022-05
  • It is essential to maintain genome

    2022-01-18

    It is essential to maintain genome integrity and stability which is assaulted by oxidative stress. To perform this function, all human cells have well developed repair systems. Base excision repair (BER) system is the most effective pathway responsible to revert back lesions caused by oxidative stress. BER repairs variety of lesions, except double strand DNA (dsDNA) break, e.g., oxidized bases, apurinic/apyrimidinic (AP) sites and single strand breaks of DNA (Hegde et al., 2008, Friedberg et al., 2004). Very first step of this pathway is the most crucial step which involves excision of oxidatively damaged bases by DNA glycosylase enzymes (Fig. 1). These enzymes remove damaged base by breaking glycosidic bond between base and deoxyribose sugar moiety (Krokan et al., 1997). Next step includes cleavage of DNA backbone by AP endonuclease (APE) or polynucleotide kinase (PNK), or by intrinsic AP lyase activity of DNA glycosylases. APE generates 3′-OH and 5′ deoxyribose phosphate (dRP) end. Then polymerase β (Pol β) clears 5′ termini and incorporate appropriate base at the abasic (damaged base) site. In final step, ligase enzyme joins the nick and DNA damage gets repaired (Mitra et al., 1997, Sobol et al., 2000, Matsumoto and Kim, 1995, Tomkinson et al., 2001). DNA glycosylases are key enzymes of this pathway which initiate the pathway. Many DNA glycosylases are reported to be present in human cells. These can be differentiated on the basis of their substrate affinity. The first BER enzyme Escherichia coli uracil glycosylase (UNG) was discovered by Tomas Lindahl. It removes deaminated cytosines and misincorporated uracils from DNA. In humans, two versions of UNG, UNG1 for nucleus and UNG2 for mitochondria are found. Primary role of UNG2 and one more enzyme SMUG1 is to remove 5-hydroxymethyluracil from DNA. UNG1 and SMUG1 belong to UDG super family. Thymines are removed from thymine:guanine mismatches that arise from deamination of methyl cytosine by two mismatch DNA glycosylases, TDG and MBD4 (MED1). TDG has a higher affinity for uracil than thymine and MBD4 removes uracil and thymine that are result of deamination of CpG and methylated CpG, respectively. TDG is also a member of UDG superfamily. All glycosylases belonging to UDG superfamily are monofunctional. Alkyladenine DNA glycosylase (AAG) also called 3-Methylpurine DNA glycosylase (MPG) has affinity for a larger number of alkylated bases including 3-methyladenine, guanines methylated at the N3 or N7 position, etheno adenine and guanine, hypoxanthine and 8-oxoguanine as well as other alkylated and oxidized DNA substrates. MPG/AAG is a monofunctional glycosylase. It consists of a single mixed α/β domain that makes it different from other glycosylases. 8-Oxoguanine paired to cytosine, FapyG and 8-oxoA are recognized and removed by 8-Oxoguanine DNA glycosylase (OGG1). OGG1 belongs to the HhH family of DNA glycosylases and is a bifunctional glycosylase. It consists of GlyPro-rich loop and a conserved aspartic GSK2879552 mg which initiates a nucleophilic attack on the ε-amino group of a conserved lysine. OGG1 is the only human glycosylase that efficiently removes 8-oxoG from DNA. If 8-oxoguanine (or FapyG) is stumble on by a replication fork before repair, adenine is often inserted opposite the base by the synthesizing polymerase. This adenine is recognized and removed by DNA glycosylase MUTYH. MUTYH also belongs to the helix-hairpin-helix (HhH) superfamily, along with HhH binding motif, it contains an iron sulfur cluster that is involved in DNA binding. It is a monofunctional glycosylase. MUTYH is the only glycosylase that removes adenine incorporated opposite 8-oxoG, although is also removed by the mismatch repair system (Fromme and Verdine, 2004, Grin and Zharkov, 2011, Nash et al., 1996, Wallace et al., 2012). Oxidized pyrimidines and formamidopyrimidines are recognized and removed by other four DNA glycosylases. Human NTH1 (belonging to nth family of E. coli) seems to be a housekeeping DNA glycosylase that scans the DNA for these damages. NTH1, like MUTYH contains an iron sulfur cluster and HhH motif. It recognizes a broad spectrum of oxidized pyrimidines (De Bont and van Larebeke, 2004, Hegde et al., 2008, Fromme and Verdine, 2004, Grin and Zharkov, 2011, Nash et al., 1996, Wallace et al., 2012). In contrast to NTH1, the NEIL proteins seems to have specialized functions.NEIL1, NEIL2 and NEIL3 are newly identified DNA glycosylases. These were identified, characterized and named NEIL (Nei like) in 2002 by Hazara and colleagues (Hazra et al., 2002a, Hazra et al., 2002b). These belong to nei family of glycosylase because of their structural homology and activity resemblance to E. coli glycosylase endonuclease VIII. NEIL1 is cell cycle regulated and it may be associated with the replication fork (Wallace et al., 2012). Common substrates for NEIL1 are Tg, Fapy-A, Fapy-G and 5-OHU, Gh, Sp, and DHU but it also takes DHT, 5fU, 5hmU, 5-OHC, urea, and even abasic sites as its substrates (Miller et al., 2004, Bandaru et al., 2002, Takao et al., 2002, Hu et al., 2005, Rosenquist et al., 2003, Katafuchi et al., 2004, Ocampo-Hafalla et al., 2006, Zhang et al., 2005, Zhao et al., 2010, Krishnamurthy et al., 2008). It shows unique substrate specificity for 8oxoG i.e., it removes 8oxoG present towards 3′ end of single-strand breaks but not from bubble structure (Parsons et al., 2005, Parsons et al., 2007). NEIL2 excises the similar lesions as NEIL1 but favour them in single-stranded DNA and recent evidences show that NEIL2 binds to RNA polymerase II and other transcription-associated proteins which suggests that NEIL2 may be associated with transcription. NEIL3 recognizes same substrates as NEIL2 and in humans is found in the thymus and testis. NEIL1 and 2 have a β/δ AP lyase activity that gives a phosphate attached to the 3′ side of the break while NEIL3 has poor AP lyase activity which mainly cleaves the DNA backbone by β-elimination (Wallace et al., 2012). NEIL1 has been found to remove lesions from a wide type of structures like dsDNA, ssDNA, interstrand crosslinks, bubbles and bulges (Fig. 2) (Miller et al., 2004, Bandaru et al., 2002, Takao et al., 2002, Hu et al., 2005, Rosenquist et al., 2003, Katafuchi et al., 2004, Ocampo-Hafalla et al., 2006, Zhang et al., 2005, Zhao et al., 2010, Krishnamurthy et al., 2008, Parsons et al., 2005, Couve et al., 2009). These activities are not found in NTH1 and OGG1. NTH1 and OGG1 cannot excise bases from ssDNA and bubble structures (Hu et al., 2005). NEIL1 also shows a distinctive function of maintaining telomere integrity. Zhou et al. analysed the repair of telomeric G4 DNA containing 8-oxoG and hydantoin lesions. Study was carried out using 8-oxoG-containing oligodeoxynucleotides as substrate in KCl solution. None of the DNA glycosylases were capable of removing 8-oxoG from telomeric G4 DNA. Similar results were obtained in their previous study with NaCl solution. Whereas, guanidinohydantoin, (S)- spiroiminodihydantoin and (R)- spiroiminodihydantoin in the quadruplex/triplex structure can be rapidly removed by human NEIL1 and NEIL3 but not by NEIL2 and NTH1. They also analysed lyase activity using telomeric quadruplex DNA with guanidinohydantoin as substrate, and formamide/EDTA buffer to stop the reaction to see the lyase activity after base removal. NEIL1 and NEIL3 were capable of hydrolyzing abasic sites, mainly at positions 10 and 11 Zhou et al., 2015.