Smoking gun for a rare mutation mechanism

Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS

The linear chromosome of Streptomyces exhibits a highly compartmentalized structure with a conserved central region flanked by variable arms. As double strand break (DSB) repair mechanisms play a crucial role in shaping the genome plasticity of Streptomyces, we investigated the role of EndoMS/NucS, a recently characterized endonuclease involved in a non-canonical mismatch repair (MMR) mechanism in archaea and actinobacteria, that singularly corrects mismatches by creating a DSB. We showed that Streptomyces mutants lacking NucS display a marked colonial phenotype and a drastic increase in spontaneous mutation rate. In vitro biochemical assays revealed that NucS cooperates with the replication clamp to efficiently cleave G/T, G/G and T/T mismatched DNA by producing DSBs. These findings are consistent with the transition-shifted mutational spectrum observed in the mutant strains and reveal that NucS-dependent MMR specific task is to eliminate G/T mismatches generated by the DNA polymerase during replication. Interestingly, our data unveil a crescent-shaped distribution of the transition frequency from the replication origin towards the chromosomal ends, shedding light on a possible link between NucS-mediated DSBs and Streptomyces genome evolution.

Tunneling Effect in Proton Transfer: Transfer Matrix Approach

The transfer matrix (TM) method was applied to calculate the transmission probability (TP) for proton transfer reactions. The tunneling factors in the reaction rate constants were also evaluated using the TPs. To test this method, TPs for the Eckart potentials modeled as a guanine-cytosine base pair were calculated by the TM method and compared to TPs by the analytical solution. As a result, the errors in the TPs by the TM method were quite small. The tunneling factors for the guanine-thymine (G-T) and adenine-cytosine (A-C) mispair reactions were then evaluated by the TM method. A shoulder appears on each potential for these reactions [Odai, K.; Umesaki,K. J. Phys. Chem. A. 2021, 125, 8196-8204]. As a result, the shoulder for the G-T mispair reaction contributes significantly to the tunneling, while the shoulder for the A-C mispair reaction contributes little to the tunneling. These results are difficult to obtain with methods such as Wigner's tunneling factor.

Mismatch Recognition by Saccharomyces cerevisiae Msh2-Msh6: Role of Structure and Dynamics

The mismatch repair (MMR) pathway maintains genome integrity by correcting errors such as mismatched base pairs formed during DNA replication. In MMR, Msh2–Msh6, a heterodimeric protein, targets single base mismatches and small insertion/deletion loops for repair. By incorporating the fluorescent nucleoside base analog 6-methylisoxanthopterin (6-MI) at or adjacent to a mismatch site to probe the structural and dynamic elements of the mismatch, we address how Msh2–Msh6 recognizes these mismatches for repair within the context of matched DNA. Fluorescence quantum yield and rotational correlation time measurements indicate that local base dynamics linearly correlate with Saccharomyces cerevisiae Msh2–Msh6 binding affinity where the protein exhibits a higher affinity (K_D ≤ 25 nM) for mismatches that have a significant amount of dynamic motion. Energy transfer measurements measuring global DNA bending find that mismatches that are both well and poorly recognized by Msh2–Msh6 experience the same amount of protein-induced bending. Finally, base-specific dynamics coupled with protein-induced blue shifts in peak emission strongly support the crystallographic model of directional binding, in which Phe 432 of Msh6 intercalates 3′ of the mismatch. These results imply an important role for local base dynamics in the initial recognition step of MMR.

Cigarette smoking as a risk factor for diabetic nephropathy: A systematic review and meta-analysis of prospective cohort studies

Background

Observational studies suggested that tobacco smoking was associated with diabetic nephropathy (DN). However, the results were conflicting and inconsistent. In the study, we performed a meta-analysis to assess the relationship between tobacco smoking and the development of DN.

Materials and methods

We searched in PubMed, Embase, Web of Science and the Cochrane Library (CENTRAL) from database inception until Mar 8, 2018, and updated our search on May 1, 2018. We screened the reference lists of the retrieved articles. Only original prospective cohort studies which have investigated the association between smoking and DN incidence or its progression were included. Pooled HRs and 95% confidence intervals (CIs) were calculated using a random effects model.

Results

A total of 9 prospective cohort studies were identified, including more than 203337 participants. Compared with those of no smoking, smoking participants increased the risk of developing DN (HR = 1.07, 95% CI: 1.01–1.13, P = 0.01). The subgroup analysis showed that the current and total smoking may increase the risk of DN, but these results did not reach statistical significance (current: HR = 1.69, 95% CI = 0.79–3.64, p = 0.17; total: HR = 1.17, 95% CI = 0.97–1.41, p = 0.10), whereas former smoking significantly increased the risk of DN (HR = 1.04, 95% CI = 1.03–1.05, p<0.001). Compared with no-smokers, smokers showed an elevated risk of developing DN (HR = 1.05; 95% CI, 1.00–1.11, P = 0.05). In patients with T2DM, those who smoked were at an increased risk of developing DN, as compared to those who had never smoked (HR = 1.05; 95% CI, 1.00–1.11, P = 0.05). However, compared to no smoking, smoking did not increase the risk of DN development in patients with T2DM (HR = 1.15; 95% CI, 0.9–1.47, P = 0.25). Univariate and multivariate meta-regression did not find any confounding factors. No publication bias was found in the meta-analysis.

Conclusions

The present study highlighted that smoking was an independent risk factor for DN, especially in patients with T1DM. This is the first meta-analysis of prospective cohort studies to discuss the relationship between smoking and DN.