Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in Arabidopsis thaliana

Abstract

Due to their sedentary lifestyle, plants are constantly exposed to different stress stimuli. Stress comes in variety of forms where factors like radiation, free radicals, “replication errors, polymerase slippage”, and chemical mutagens result in genotoxic or cytotoxic damage. In order to face “the base oxidation or DNA replication stress”, plants have developed many sophisticated mechanisms. One of them is the DNA mismatch repair (MMR) pathway. The main part of the MMR is the MutS homologue (MSH) protein family. The genome of Arabidopsis thaliana encodes at least seven homologues of the MSH family: AtMSH1, AtMSH2, AtMSH3, AtMSH4, AtMSH5, AtMSH6, and AtMSH7. Despite their importance, the functions of AtMSH homologs have not been investigated. In this work, bioinformatics tools were used to obtain a better understanding of MSH-mediated DNA repair mechanisms in Arabidopsis thaliana and to understand the additional biological roles of AtMSH family members. In silico analysis, including phylogeny tracking, prediction of 3D structure, interactome analysis, and docking site prediction, suggested interactions with proteins were important for physiological development of A. thaliana. The MSH homologs extensively interacted with both TIL1 and TIL2 (DNA polymerase epsilon catalytic subunit), proteins involved in cell fate determination during plant embryogenesis and involved in flowering time repression. Additionally, interactions with the RECQ protein family (helicase enzymes) and proteins of nucleotide excision repair pathway were detected. Taken together, the results presented here confirm the important role of AtMSH proteins in mismatch repair and suggest important new physiological roles.

Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

“…The accessions in group 1 were mainly black and cream in color, those in group 2 had a yellow seed coat, those in group 3 were brown and mixed in color, and those in group 4 were cream and mixed in color (Table S1). Notably, this is consistent with the fact that African cowpea accessions mainly have brown and speckled seed coats [38]. Conversely, Korean cowpea accessions had mostly cream and yellow seed coats in this study.…”

“…Therefore, the clustering was not strongly correlated with the collection sites from Jeonra and Gyeongsang provinces. Similarly, in a previous study, 492 Korean cowpea landrace accessions were poorly correlated with their collection sites [ 38 ]. However, in this study, 94% of the accessions from Gangwon province were clustered into group 2.…”

“…Because cowpea is mainly mixed with rice or used for rice cake stuffing in Korea, the seed size and seed coat color preferences could cause some genetic diversity in the Korean cowpea accessions. The human preference for lighter seed coat color during domestication has also been reported in peas [ 40 ] and chickpeas [ 38 ].…”

MutS homologue 4 and MutS homologue 5 Maintain the Obligate Crossover in Wheat Despite Stepwise Gene Loss following Polyploidization

“…The residual ;15% of chiasmata observed in mutSg mutants are interference insensitive and form via the class II pathway, which is partially dependent on the MUS81 endonuclease (Berchowitz et al, 2007;Higgins et al, 2008a). Based on a bioinformatics interactome analysis, MutSg in Arabidopsis is likely to function similarly to that in C. elegans in protecting recombination intermediates from dissolution by RECQ helicases (AbdelGawwad et al, 2019). In rice (Oryza sativa), MutSg promotes formation of the obligate CO and is required for 78% to 90% of chiasmata (Luo et al, 2013;Zhang et al, 2014;Wang et al, 2016).…”

Plant DNA Polymerases

“…The mismatch repair pathway, MMR, involves a sophisticated machinery that recognizes the mismatch, discriminates between the parental and daughter strand, and excises the nucleotides on the daughter strand [132]. DNA resynthesis is thought to be performed by Pol δ, although bioinformatics analyses using the STRING database [135] predict that Pol ε interacts with the MMR machinery [136].…”