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

Molecules ◽  
2019 ◽  
Vol 24 (13) ◽  
pp. 2493 ◽  
Author(s):  
Mohamed Ragab AbdelGawwad ◽  
Aida Marić ◽  
Abdullah Ahmed Al-Ghamdi ◽  
Ashraf A. Hatamleh
Keyword(s):  
Arabidopsis Thaliana ◽  
Mismatch Repair ◽  
Cell Fate ◽  
Excision Repair ◽  
3D Structure ◽  
In Silico Analysis ◽  
Protein Family ◽  
Dna Polymerase Epsilon ◽  
Dna Mismatch ◽  
Nucleotide Excision Repair Pathway

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.

Functional analysis of the Arabidopsis thaliana mismatch repair gene MSH2

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 651-657 ◽  
Author(s):  
Jules Adé ◽  
Yosr Haffani ◽  
François J Belzile
Keyword(s):  
Arabidopsis Thaliana ◽  
Mismatch Repair ◽  
Dna Mismatch Repair ◽  
Single Copy ◽  
Mismatch Repair Gene ◽  
Single Pair ◽  
Repair Gene ◽  
Dna Mutation ◽  
Over Expression ◽  
Dna Mismatch

The Arabidopsis thaliana MSH2 (AtMSH2) gene encodes a protein that belongs to a family of highly conserved proteins (MutS homologues (MSH)) involved in DNA mismatch repair. Sequence analysis strongly suggests that this single copy gene is indeed a homologue of MSH2, a gene known to play a central role in eukaryotic mismatch repair. In this report, we show that the AtMSH2 protein has functional attributes characteristic of previously described mismatch repair proteins. First, over-expression of this protein in Escherichia coli leads to a mutator phenotype similar to that reported previously for known functional homologues. Second, gel retardation assays revealed that the AtMSH2 protein has a 10-fold greater affinity for DNA containing a single pair of mismatched nucleotides versus perfectly matched DNA. These results provide experimental evidence that AtMSH2 is indeed a functional homologue of MutS.Key words: DNA mismatch repair, heteroduplex DNA, mutation rate.

scholarly journals Interactome analysis and docking sites prediction of (AtCHR8, AtCUL4 and AtERCC1/UVR7) proteins in Arabidopsis Thaliana

2020 ◽  
Vol 2 (1) ◽  
pp. 52-68
Author(s):  
Mohamed Ragab Abdel Gawwad ◽  
Ali Taha Ozdemir
Keyword(s):  
Dna Damage ◽  
Arabidopsis Thaliana ◽  
Protein Interactions ◽  
Excision Repair ◽  
Dna Lesions ◽  
Damage Recognition ◽  
Nucleotide Excision ◽  
Nucleotide Excision Repair Pathway ◽  
Docking Sites ◽  
Dna Damage Recognition

The UV irradiation is a major DNA damaging factor in plants. Arabidopsis thaliana uses various repair pathways for these kinds of DNA lesions. One of them is the nucleotide excision repair pathway. The AtCUL4, ERCC1/UVR7 and CHR8 are vital proteins for nucleotide excision pathway and mutations in these proteins cause flaws in the repair mechanism. Two of these proteins play crucial role during DNA damage recognition and the other is involved in the excision of damaged bases. During NER processes, Arabidopsis uses different sets of proteins during the DNA damage recognition for transcriptionally active and genomic DNA. In order to get better insight into these proteins, we used bioinformatics tools to predict, analyze, and validate 3D structures of ERCC1/UVR7, AtCUL4 and CHR8. We also predicted the subcellular and sub-nuclear localization of proteins. Subsequently, we predicted the docking sites for each individual proteins and searched for interacting residues which mediate the protein-protein interactions. 

scholarly journals DNA Mismatch Repair Catalyzed by Extracts of Mitotic, Postmitotic, and Senescent Drosophila Tissues and Involvement of mei-9 Gene Function for Full Activity

1998 ◽  
Vol 18 (3) ◽  
pp. 1436-1443 ◽  
Author(s):  
Arvinder Bhui-Kaur ◽  
Myron F. Goodman ◽  
John Tower
Keyword(s):  
Mismatch Repair ◽  
Dna Mismatch Repair ◽  
Specific Activity ◽  
Excision Repair ◽  
Crossing Over ◽  
Dna Mismatch ◽  
Nucleotide Excision ◽  
Repair Activity ◽  
Development And Aging

ABSTRACT Extracts of Drosophila embryos and adults have been found to catalyze highly efficient DNA mismatch repair, as well as repair of 1- and 5-bp loops. For mispairs T · G and G · G, repair is nick dependent and is specific for the nicked strand of heteroduplex DNA. In contrast, repair of A · A, C · A, G · A, C · T, T · T, and C · C is not nick dependent, suggesting the presence of glycosylase activities. For nick-dependent repair, the specific activity of embryo extracts was similar to that of extracts derived from the entirely postmitotic cells of young and senescent adults. Thus, DNA mismatch repair activity is expressed in Drosophila cells during both development and aging, suggesting that there may be a function or requirement for mismatch repair throughout the Drosophila life span. Nick-dependent repair was reduced in extracts of animals mutant for themei-9 gene. mei-9 has been shown to be required in vivo for certain types of DNA mismatch repair, nucleotide excision repair (NER), and meiotic crossing over and is theDrosophila homolog of the yeast NER gene rad1.

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