Multiple zinc ions maintain the open conformation of the catalytic site in the DNA mismatch repair endonuclease MutL from Aquifex aeolicus

Biochemical charecterisation of UvrD helicase and RecJ exonuclease from Neisseria gonorrhoeae

UvrD helicase and RecJ exonuclease play a critical role in DNA repair and recombination process thereby involved in the maintenance of the genomic integrity. In addition to DNA repair pathways, UvrD helicase plays an important role in phase variation and maintenance of virulence in pathogenic bacteria while RecJ is a single-stranded DNA -specific 5'-3' exonuclease activity responsible for generating a long 3'ssDNA gap for DNA resynthesis by DNA ploymerases in mismatch repair (MMR). In spite of being vital for performing these functions, there have been few reports on the mismatch repair pathway in pathogenic bacteria and particularly the interplay of mismatch repair proteins in methylation independent mismatch repair. Purified UvrD helicase from Neisseria gonorrhoeae (FA1090) (NgoUvrD) exhibits 3'-5' polarity on ssDNA and unwinds blunt end duplex DNA as well as different DNA substrates with overhangs. While NgoUvrD binds to Ni2+, Mg2+. Mn2+, Zn2+ and Ca2+, only Mg2+ and Mn2+ support the helicase activity as well as ATPase activity. Interestingly, Zn2+ inhibits both the helicase as well as ATPase activity. ssDNA binding to NgoUvrD abrogates the inhibition by Zn2+. This study, for the first time reveals a unique role of zinc in regulating UvrD helicase activity in N. gonorrhoeae. RecJ exonuclease from Neisseria gonorrhoeae is a 566 amino acid protein that contains the characteristic motifs conserved among all RecJ homologs. Site-directed mutagenesis in the conserved DHH motif abrogated enzymatic activity in D160A and H161A mutants. Interestingly, substitution of histidine 161 with alanine or serine residues enhanced RecJ exonuclease activity while the corresponding mutation in other bacterial RecJs abrogated the activity. NgoRecJ degrades double-stranded DNA with 2, 4, 6 and 8 nucleotide 5' overhang substrates unlike E. coli RecJ which degrades ssDNA with 6-nts overhang. In the present investigation we have studied the interaction between UvrD helicase and RecJ proteins participating in methylation-independent MMR pathway. Our studies highlight novel properties of NgoUvrD and NgoRecJ proteins and specific interaction between these proteins which could play in genome maintenance, pathogenesis and virulence of Neisseria gonorrhoeae.

Epigenomic analysis of the myometrium during late implantation revealed regulatory elements in genes related to the cellular zinc homeostasis pathway in pigs

The myometrium, composed of the inner circular muscle (CM) and outer longitudinal muscle (LM), is crucial in establishing and maintaining early pregnancy. However, the molecular mechanisms involved are not well understood. In this study, we identified the transcriptomic features of the CM and LM collected from the mesometrial (M) and anti-mesometrial (AM) sides of the pig uterus on day 18 of pregnancy during the placentation initiation phase. Some genes in the cellular zinc ion level regulatory pathways (MT-1A, MT-1D, MT-2B, SLC30A2, and SLC39A2) were spatially and highly enriched in uterine CM at the mesometrial side. In addition, the histone modification profiles of H3K27ac and H3K4me3 in uterine CM and LM collected from the mesometrial side were characterized. Genomic regions associated with the expression of genes regulating the cellular zinc ion level were detected. Moreover, six highly linked variants in the H3K27ac-enriched region of the pig SLC30A2 gene were identified and found to be significantly associated with the total number born at the second parity (P < 0.05). In conclusion, the genes in the pathways of cellular zinc homeostasis and their regulatory elements identified have implications for pig reproduction trait improvement and warrant further investigations.

Preparation and Characterization of an Oyster Peptide-Zinc Complex and Its Antiproliferative Activity on HepG2 Cells

It is evident that zinc supplementation is essential for maintaining good health and preventing disease. In this study, a novel oyster peptide-zinc complex with an average molecular weight of 500 Da was prepared from oyster meat and purified using ultrafiltration, ultrasound, a programmed cooling procedure, chelating, and dialysis. The optimal chelating process parameters obtained through a response surface methodology optimization design are a peptide/zinc ratio of 15, pH of 6.53, reaction time of 80 min, and peptide concentration of 0.06 g/mL. Then, the structure of a peptide-zinc complex (named COP2-Zn) was investigated using the UV and infrared spectrums. The results showed that the maximum absorption peak was redshifted from 224.5 nm to 228.3 nm and the main difference of the absorption peaks was 1396.4 cm-1. The cytotoxicity and antiproliferative effects of COP2-Zn were evaluated. The results showed that COP2-Zn had a better antiproliferative effect than the unchelated peptide against HepG2 cells. A DNA flow cytometric analysis showed that COP2-Zn induced S-phase arrest in HepG2 cells in a dose-dependent manner. Additionally, the flow cytometer indicated that COP2-Zn significantly induced HepG2 cell apoptosis.

Catalytic mechanism of the zinc-dependent MutL endonuclease reaction

DNA mismatch repair endonuclease MutL binds two zinc ions. However, the endonuclease activity of MutL is drastically enhanced by other divalent metals such as manganese, implying that MutL binds another catalytic metal at some site other than the zinc-binding sites. Here, we solved the crystal structure of the endonuclease domain of Aquifex aeolicus MutL in the manganese- or cadmium-bound form, revealing that these metals compete with zinc at the same sites. Mass spectrometry revealed that the MutL yielded 5'-phosphate and 3'-OH products, which is characteristic of the two-metal-ion mechanism. Crystallographic analyses also showed that the position and flexibility of a highly conserved Arg of A. aeolicus MutL altered depending on the presence of zinc/manganese or the specific inhibitor cadmium. Site-directed mutagenesis revealed that the Arg was critical for the catalysis. We propose that zinc ion and its binding sites are physiologically of catalytic importance and that the two-metal-ion mechanism works in the reaction, where the Arg plays a catalytic role. Our results also provide a mechanistic insight into the inhibitory effect of a mutagen/carcinogen, cadmium, on MutL.

Probing the DNA-binding center of the MutL protein from the Escherichia coli mismatch repair system via crosslinking and Förster resonance energy transfer

As no crystal structure of full-size MutL bound to DNA has been obtained up to date, in the present work we used crosslinking and Förster resonance energy transfer (FRET) assays for probing the putative DNA-binding center of MutL from Escherichia coli. Several single-cysteine MutL variants (scMutL) were used for site-specific crosslinking or fluorophore modification. The crosslinking efficiency between scMutL proteins and mismatched DNA modified with thiol-reactive probes correlated with the distances from the Cys residues to the DNA calculated from a model of MutS-MutL-DNA complex. FRET-based investigation of DNA binding with different scMutL variants clearly showed that the highest signals were detected for the variants MutL(T218C) and MutL(A251C) indicating closeness of the positions 218 and 251 to DNA in the MutL-DNA complex. Indeed, the Cys218 and Cys251 of scMutL were crosslinked to the reactive DNA with the highest yield demonstrating their proximity to DNA in the MutL-DNA complex. The presence of MutS increased the yield of conjugate formation between the MutL variants and the modified DNA due to tighter MutL-DNA interactions caused by MutS binding to MutL.