Role of endonuclease III enzymes in uracil repair

Novel mutations found in Mycobacterium leprae DNA repair gene nth from central India

INTRODUCTION

The importance of DNA repair enzymes in maintaining genomic integrity is highlighted by the hypothesis that DNA damage by reactive oxygen/nitrogen species produced inside the host cell is essential for the mutagenesis process. Endonuclease III (Nth), formamidopyrimide (Fpg) and endonuclease VIII (Nei) DNA glycosylases are essential components of the bacterial base excision repair process. Mycobacterium leprae lost both fpg/nei genes during the reductive evolution event and only has the nth (ML2301) gene. This study aims to characterize the mutations in the nth gene of M. leprae strains and explore its correlation with drug-resistance.

METHOD

A total of 91 M. leprae positive DNA samples extracted from skin biopsy samples of newly diagnosed leprosy patients from NSCB Hospital Jabalpur were assessed for the nth gene as well as drug resistance-associated loci of the rpoB, gyrA and folP1 genes through PCR followed by Sanger sequencing.

RESULTS

Of these 91 patients, a total of two insertion frameshift mutations, two synonymous and seven nonsynonymous mutations were found in nth in seven samples. Sixteen samples were found to be resistant to ofloxacin and one was found to be dapsone resistant as per the known DRDR mutations. No mutations were found in the rpoB region. Interestingly, none of the nth mutations were identified in the drug-resistant associated samples.

CONCLUSION

The in-silico structural analysis of the non-synonymous mutations in the Nth predicted five of them were to be deleterious. Our results suggest that the mutations in the nth gene may be potential markers for phylogenetic and epidemiological studies.

DR0022 from Deinococcus radiodurans is an acid uracil-DNA glycosylase

Uracil-DNA glycosylase (UDG) initiates base excision repair (BER) by removing damaged or modified nucleobases during DNA repair or mammalian demethylation. The UDG superfamily consists of at least six families with a variety of catalytic specificities and functions. Deinococcus radiodurans, an extreme radiation resistant bacterium, contains multiple members of UDG enzymes within its genome. The present study reveals that the putative protein, DR0022, is a uracil-DNA glycosylase that requires acidic conditions for its glycosylase activity, which is the first case of such an enzyme within the UDG superfamily. The key residues in the catalytic motifs are investigated by biochemical, enzyme kinetics, and de novo structural prediction, as well as molecular modeling analyses. The structural and catalytic roles of several distinct residues are discussed in light of predicted and modeled DR0022 glycosylase structures. The spontaneous mutation rate analysis performed in a dr0022 deficient D. radiodurans strain indicated that the dr0022 gene plays a role in mutation prevention. Furthermore, survival rate analysis in a dr0022 deficient D. radiodurans strain demonstrated its role in stress resistance, including γ-irradiation. Additionally, the novel acid UDG activity in relationship to its in vivo roles is discussed. This work underscores the functional diversity in the UDG superfamily.

Biochemical and functional characterization of an endonuclease III from Thermococcus barophilus Ch5

Endonuclease III (EndoIII) is a bifunctional DNA glycosylase that is essential to excise thymine glycol (Tg) from DNA. Although EndoIII is widespread in bacteria, eukarya and Archaea, our understanding on archaeal EndoIII function remains relatively incomplete due to the limited reports. Herein, we characterized an EndoIII from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tba-EndoIII) biochemically, demonstrating that the enzyme can excise Tg from dsDNA and display maximum activity at 50 ~ 70 °C and at pH 6.0 ~ 9.0 without the requirement of a divalent metal ion. Importantly, Tba-EndoIII differs from other reported archaeal EndoIII homologues in thermostability and salt requirement. As observed in other EndoIII homologues, the conserved residues D155 and H157 in Helix-hairpin-Helix motif of Tba-EndoIII are essential for Tg excision. Intriguingly, we first dissected that the conserved residues C215 and C221 in the Fe-S cluster loop in Tba-EndoIII are involved in intermediate formation and Tg excision. Additionally, we first revealed that the conserved residue L48 is flexible for intermediate formation and AP cleavage, but plays no detectable role in Tg excision. Overall, our work has revealed additional archaeal EndoIII function and catalytic mechanism.

Biochemical characterization and mutational studies of a thermostable endonuclease III from Sulfolobus islandicus REY15A

Endonuclease III (EndoIII), which is ubiquitous in bacteria, Archaea and eukaryotes, plays an important role in excising thymine glycol (Tg) from DNA. Herein, we present evidence that an EndoIII from the hyperthermophilic crenarchaeon Sulfolobus islandicus REY15A (Sis-EndoIII) is capable of removing Tg from DNA at high temperature. Biochemical data show that the optimal temperature and pH of Sis-EndoIII are ca.70 °C and ca.7.0-8.0, respectively. Furthermore, the recombinant Sis-EndoIII retains relative weak activity without a divalent metal ion, and displays maximum activity in the presence of Mg²⁺ or Ca²⁺. Additionally, we first revealed the activation energy (E_a) of 39.7 ± 4.2 kcal/mol for Sis-EndoIII to remove Tg from dsDNA. As a bifunctional glycosylase, Sis-EndoIII possesses AP lyase activity in addition to glycosylase activity. Additionally, a covalent intermediate is formed between Sis-EndoIII and Tg-containing dsDNA. Mutational studies demonstrate that residues D50, K133 and D151 in Sis-EndoIII are responsible for removal of Tg from dsDNA and K133 and D151 are essential for formation of the covalent intermediate. To our knowledge, it is the first report of Tg excision by crenarchaeal EndoIII, thus augmenting our understanding on archaeal EndoIII function.

Mutational analysis of Thermococcus kodakarensis Endonuclease III reveals the roles of evolutionarily conserved residues

Endonuclease III (EndoIII) is nearly ubiquitous in all three domains of life. EndoIII family proteins exhibit a bifunctional (glycosylase/lyase) activity on oxidative/saturated pyrimidine bases, such as thymine glycol. Previous studies on EndoIII homologs have reported the presence of important residues involved in substrate binding and catalytic activity. However, a biochemical clarification of the roles of these residues as well as details of their evolutionary conservation is still lacking. This is particularly true for archaeal orthologs. The current study demonstrated the roles of the evolutionarily conserved residues of euryarchaeon Thermococcus kodakarensis EndoIII (TkoEndoIII). We utilized amino acid sequence analysis and homology modeling to identify highly conserved regions with potential key residues in the EndoIII proteins. Using Ala-substituted TkoEndoIII mutant proteins, residues of interest were quantitatively examined via DNA binding, glycosylase/AP lyase/bifunctional activity, and DNA trapping assays. The obtained results allowed us to determine the roles, as well as the significance of these roles in Schiff base formation (Lys140 as a nucleophile and Asp158), Tg recognition (His160), substrate binding (Arg59, Leu101, Trp102, and Gly136), β-elimination activities (Ser57 and Asp62), and [4Fe-4S] cluster formation (Cys208 and Cys215). Interestingly, a critical role played by the highly conserved Lys105 (predicted as being away from the catalytic site) in substrate binding, accompanied by a significant indirect effect on catalytic activity, were detected. Our results suggest that these particular residues play conserved roles among EndoIII orthologs across the domains. In addition to identifying the critical role of the highly conserved Lys105, the study provides a comprehensive understanding of the functions attributable to the evolutionarily conserved residues found in the EndoIII family, from Escherichia coli to humans.