Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in <i>Arabidopsis thaliana</i>
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...
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MDPI AG
2019-07-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/24/13/2493 |
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| author | Mohamed Ragab AbdelGawwad Aida Marić Abdullah Ahmed Al-Ghamdi Ashraf A. Hatamleh |
| author_facet | Mohamed Ragab AbdelGawwad Aida Marić Abdullah Ahmed Al-Ghamdi Ashraf A. Hatamleh |
| author_sort | Mohamed Ragab AbdelGawwad |
| collection | DOAJ |
| description | 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 <i>Arabidopsis thaliana</i> 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 <i>Arabidopsis thaliana</i> 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 <i>A. thaliana</i>. 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. |
| first_indexed | 2024-12-11T09:46:03Z |
| format | Article |
| id | doaj.art-bc11dd3b856148ccaf2e60f4f35e8c66 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-11T09:46:03Z |
| publishDate | 2019-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-bc11dd3b856148ccaf2e60f4f35e8c662022-12-22T01:12:34ZengMDPI AGMolecules1420-30492019-07-012413249310.3390/molecules24132493molecules24132493Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in <i>Arabidopsis thaliana</i>Mohamed Ragab AbdelGawwad0Aida Marić1Abdullah Ahmed Al-Ghamdi2Ashraf A. Hatamleh3Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, 71210 Sarajevo, Bosnia and HerzegovinaCentre for Research in Agricultural Genomics, UAB-Edifici CRAG, Cerdanyola, 08193 Barcelona, SpainDepartment of Botany and Microbiology, College of Sciences, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Botany and Microbiology, College of Sciences, King Saud University, Riyadh 11451, Saudi ArabiaDue 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 <i>Arabidopsis thaliana</i> 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 <i>Arabidopsis thaliana</i> 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 <i>A. thaliana</i>. 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.https://www.mdpi.com/1420-3049/24/13/2493DNA mismatch repairMSHdocking siteinteractome |
| spellingShingle | Mohamed Ragab AbdelGawwad Aida Marić Abdullah Ahmed Al-Ghamdi Ashraf A. Hatamleh Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in <i>Arabidopsis thaliana</i> Molecules DNA mismatch repair MSH docking site interactome |
| title | Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in <i>Arabidopsis thaliana</i> |
| title_full | Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in <i>Arabidopsis thaliana</i> |
| title_fullStr | Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in <i>Arabidopsis thaliana</i> |
| title_full_unstemmed | Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in <i>Arabidopsis thaliana</i> |
| title_short | Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in <i>Arabidopsis thaliana</i> |
| title_sort | interactome analysis and docking sites of muts homologs reveal new physiological roles in i arabidopsis thaliana i |
| topic | DNA mismatch repair MSH docking site interactome |
| url | https://www.mdpi.com/1420-3049/24/13/2493 |
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