molecules Article Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in Arabidopsis thaliana Mohamed Ragab AbdelGawwad 1, *, Aida Marić 2 , Abdullah Ahmed Al-Ghamdi 3 and Ashraf A. Hatamleh 3 1 Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, 71210 Sarajevo, Bosnia and Herzegovina 2 Centre for Research in Agricultural Genomics, UAB-Edifici CRAG, Cerdanyola, 08193 Barcelona, Spain 3 Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia * Correspondence: mragab@ius.edu.ba; Tel.: +387-3-3957-203 Academic Editor: Rino Ragno   Received: 10 May 2019; Accepted: 26 June 2019; Published: 8 July 2019 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. Keywords: DNA mismatch repair; MSH; docking site; interactome 1. Introduction Living organisms are exposed to different damaging factors at all times. Therefore, maintenance of genome stability and integrity is one of the key roles of a cell. DNA damaging factors jeopardize the integrity of the DNA and can come from endogenous and exogenous sources [1]. Just as there are many damaging factors, organisms developed diverse pathways to fight against deleterious DNA damage and to retain genomic stability [2–8]. Plants are in special need of effective DNA repair machinery. They do not have a continuous germ line, but meristematic cells give rise to the gametes. These meristematic cells divide and potentially accumulate mutations during the lifetime of plants. Without repair, these mutations will be passed on to the next generation. While DNA repair pathways are well Molecules 2019, 24, 2493; doi:10.3390/molecules24132493 www.mdpi.com/journal/molecules Molecules 2019, 24, 2493 2 of 19 understood in yeast and mammalians, our knowledge in plants falls farbehind. Therefore, there is a need for more research that will shed additional light on this interesting and powerful part of plant genomes. This work focuses on the mismatch repair (MMR) pathway in Arabidopsis thaliana. Mismatch repair MMR is post-replicative DNA repair machinery. It is able to recognize non-Watson–Crick pairing as well as insertion/deletion loops (IDLs) [9]. Additionally, MMR has several other functions; it controls homologous recombination (HR) and most probably prevents synapse formation between divergent sequences [9]. Together with DNA polymerases and exonucleolytic proofreading, MMR keeps high fidelity of DNA with only one mispair every 1010 bases [10]. The mismatch creates a nick in the DNA helix and is recognized by MutS or its eukaryotic counterparts—MutS homolog (MSH) proteins. The MSH recruits downstream proteins that make a nick in the new strand. Exonuclease is then recruited to cut out part of the DNA strand surrounding the mismatch. The gap is finally filled in by DNA polymerase and sealed with DNA ligase. On the other hand, since proofreading exonucleases have limited capabilities, IDLs will mostly be repaired by MMR machinery. Besides its role in post-replicative point mutation repair, MMR plays an important dual role in homologous recombination. First, MMR recognizes mismatches in recombination intermediates, but on the other hand, MMR is able to prevent recombination between diverged sequences and excessive exchange of their genetic material [11,12]. Extensive duplication events enabled MSH proteins of MMR to specialize and recognize a variety of mismatches [13,14]. The MSH proteins are present throughout all kingdoms of life, suggesting conservation of MMR through the evolution [15]. The versatility of MSH proteins in eukaryotes enables MMR to recognize a surprising amount of different mutations. This work will focus on MutS homologue (MSH) proteins in plants. Arabidopsis thaliana encodes seven MSH homologs. AtMSH1 is thought to be the only non-nucleus-based MSH protein. It is dually targeted to mitochondria and chloroplast and plays a very important role in maintaining the stability of their genomes [16]. AtMSH1 mutants show anincreasein the reorganization of the mitochondrial genome and result in decreased abiotic stress response, fluctuation in growth dynamics, extended flowering and maturity, and reduced heat tolerance and sterility [17,18]. AtMSH2 protein is involved in the initiation of MMR and recognition of mismatch. Besides, it is involved in the control of DNA HR and prevents recombination of divergent strands [19]. Additionally, AtMSH2 is part of the repair pathway of UV-induced DNA damage [20]. AtMSH3 is an MMR protein that works in conjunction with AtMSH2. Together, they form a MutS beta heterodimer that recognizes damage and initiates repair of DNA loops of different sizes [14]. AtMSH4 is a somewhat different member of the plant MSH family which is not directly involved in MMR. Instead, MSH4 regulates meiotic recombination and keeps it at a normal level. AtMSH4 is only present in floral tissues, which is in line with its role in reproduction [21]. AtMSH5 works in association with AtMSH4. It is expressed in flower tissue and promotes proper segregation during chiasma formation in prophase I. AtMSH5 mutation leads to serious fertility reduction [22,23]. AtMSH6 forms a MutS alpha heterodimer with MSH2 that recognizes base–base mismatches and short (trinucleotide) IDLs. AtMSH7 is a plant-specific MSH protein. With AtMSH2, it forms a MutS gamma heterodimer that recognizes only T/G mismatch and initiates mismatch repair. Due to the complexity of the topic and limited amount of information available on AtMSH proteins, the aim of this work is to shed additional light on the function of AtMSHs, leaning on the predicted structure, detailed interactome analysis of the proteins, and docking prediction. 2. Results 2.1. Multiple Sequence Alignment ClustalOmega aligned sequences of seven AtMSH proteins and retrieved results are shown in Supplementary Materials Figure S1. Residues were colored based on their physicochemical properties (small and hydrophobic residues are in red; acidic in blue; basic in magenta; and hydroxyl, sulfhydryl, and amine in green). These results are quantified and available in the form of a percent identity matrix in Table 1. Multiple sequence alignment MSA showed highest identity between MSH6–MSH7. This is Molecules 2019, 24, 2493 3 of 19 in line with previous research that suggested MSH7 diverged from MSH6 [14]. The second highest scoring pair was the MSH2–MSH3 dimer. The highest divergence was noticed for the MSH1 protein. This is in line with the expected results since MSH1 is a mitochondrial protein. Table 1. The identity matrix percent of similarities among AtMSH proteins. Percent Identity Protein MSH1 MSH4 MSH5 MSH6 MSH7 MSH2 MSH3 MSH1 100.00 19.08 18.03 22.86 21.49 19.09 20.36 MSH4 19.08 100.00 22.51 24.53 25.29 24.56 22.88 MSH5 18.03 22.51 100.00 23.60 22.33 22.93 24.16 MSH6 22.86 24.53 23.60 100.00 33.30 23.95 26.30 Molecules MSH72019, 24, 21.49 x FOR PEER REVIEW 25.29 22.33 33.30 100.00 25.37 25.56 3 of 18 MSH2 19.09 24.56 22.93 23.95 25.37 100.00 27.93 TheMSH3 second highest 20.36 scoring22.88 pair was the24.16 MSH2–MSH3 26.30dimer. The highest 25.56 divergence 27.93 was noticed 100.00 for the MSH1 protein. This is in line with the expected results since MSH1 is a mitochondrial protein. 2.2. Phylogenetic Profile Rendering 2.2. Phylogenetic Profile Rendering Results retrieved from Phylogeny.fr for A. thaliana MSH proteins are visible in cladogram (Figure 1). During Results retrieved the long course offrom Phylogeny.fr evolution, for A.of thaliana MutS genes MSH proteins endosymbiotic bacteria are gavevisible rise to in cladogram a specialized (Figure group of1). MSHDuring theThis genes. longwas course of evolution, achieved throughMutS genes multiple of endosymbiotic duplication bacteria events [24]. gave rise to a The phylogenetic specialized group of MSH genes. This was achieved through multiple duplication events [24].The tree supports the theory that MSH1 was originally a mitochondrial gene. This will be further elaborated phylogenetic in tree supports the theory that MSH1 was originally a mitochondrial gene. This will be the discussion. further elaborated in the discussion. Figure 1. Cladogramphylogenetic tree representing the evolutionary relationships of AtMSH proteins. Figure 1. Cladogramphylogenetic tree representing the evolutionary relationships of AtMSH proteins. 2.3. Protein 3D Structure Prediction and Refinement 2.3. Protein 3D Structure Prediction and Refinement Three-dimensional modeling is a cornerstone of modern structural biology. Determination of the proteinThree-dimensional structure is the mostmodeling important is a step cornerstone towardsofthe modern structural determination of biology. Determination its function, determining of the protein possible structure ligands is the and docking most sites, andimportant step towards finding conserved the domains. motifs and determination of its function, The structures here are determining possible ligands and docking sites, and finding conserved the result of a bioinformatics approach and are based on homology modeling. The results motifs and domains. of the The 3D structures here are the result of a structure prediction are given in Figure 2.bioinformatics approach and are based on homology modeling. The results of the 3D structure prediction are given in Figure 2. 2.4. Protein 3D Structure Validation 2.4. Protein 3D Structure Validation Both experimental and in silico models of the 3D structure have to be validated before being named Both experimental acceptable. Bioinformaticand toolsinuse silico models different of the 3D references structurea have to validate model;tomeasuring be validatedbondbefore being distances, named acceptable. Bioinformatic tools use different references to validate a model; bond energy, torsion angles, B-factor, free energy of the molecule, etc. The results of the Ramachandran measuring bond distances, plot bondfor assessment energy, torsion protein each AtMSH angles, model B-factor, arefree energy visible of the2.molecule, in Figure etc. The results Further validation was doneof the in Ramachandran plot assessment for each AtMSH protein model are Model Quality Assessment Programs (MQAPs) such as PROCHECK, which certify the stereochemicalvisible in Figure 2. Further validationofwas properties thedone modelinand ModeluseQuality the free Assessment energy scoring Programs (MQAPs) tool dDFIRE such energy to assess as PROCHECK, functions which by ab certify initio the stereochemical refolding properties of fully unfolded terminalof the model with segments and use the freestructures secondary energy scoring tool dDFIRE while keeping the restto assess energy functions by ab initio refolding of fully unfolded terminal segments of the proteins fixed in their native conformations [25]. Summary of results from all the validation with secondary structures tools while is shown keeping in Table the tools 2. The rest ofrender the proteins the MSH fixed in their models native conformations. [25]. Summary as reliable. of results from all the validation tools is shown in Table 2. The tools render the MSH models as reliable. 2.5. Protein Domain Identification Domains are conserved regions of protein that can be a strong indicator of its function. Conserved regions of MSH proteins, as detected by SMART (Simple Modular Architecture Research Tool), are listed in Table 3. All proteins share a MUTSac domain [26]. This is the ATPase domain of the MSH proteins located at the C-terminal [27]. Although detailed information is not available from Molecules 2019, 24, 2493 4 of 19 2.5. Protein Domain Identification Domains are conserved regions of protein that can be a strong indicator of its function. Conserved regions of2019, Molecules MSH 24, proteins, x FOR PEERas detected by SMART (Simple Modular Architecture Research Tool), REVIEW 4 of 18are listed in Table 3. All proteins share a MUTSac domain [26]. This is the ATPase domain of the MSH proteins MSH1 located at the 100.00 19.08 C-terminal 18.03 [27]. Although 22.86 detailed 21.49 information 19.09 is not 20.36 available from the MSH4 19.08 100.00 22.51 24.53 25.29 24.56 22.88 eukaryotic MUTSac MSH5 domain; 18.03 the prokaryotic 22.51 model 100.00 suggests 23.60 that only one 22.33 monomer 22.93 of the MSH 24.16 dimer binds ADP MSH6through the MUTSac24.53 22.86 domain. Mismatch 23.60 recognition 100.00 initiates 33.30 ATP23.95 binding which 26.30 results in conformational MSH7 change 21.49 of the 25.29 dimer and its movement 22.33 along the 33.30 DNA. Another 100.00 25.37 domain 25.56that was present inMSH2 all MSH protein19.09 except 24.56 22.93 MSH123.95 mitochondrial is MUTSd.25.37 100.00 27.93 MSH3 20.36 22.88 24.16 26.30 25.56 27.93 100.00 MSH1 MSH2 MSH3 Figure 2. Cont. Molecules 2019, 24, 2493 5 of 19 Molecules 2019, 24, x FOR PEER REVIEW 5 of 18 MSH4 MSH5 MSH6 MSH7 Figure 2. MSH1-MSH7 proteins’ 3D structure prediction visualized by PyMOL (left) and validated by Ramachandran plot (right). N-terminus and C-terminus are indicated. Molecules 2019, 24, 2493 6 of 19 Table 2. 3D structure prediction verification tools of MSH proteins. RAMPAGE Protein PROCHECK (G-Factor) dDFIRE (Residues in Allowed Region) MSH1 98.1% −0.28 −1755.42 MSH2 98.9% −0.05 −2105.67 MSH3 98.0% −0.18 −2052.20 MSH4 98.1% −0.16 −1753.06 MSH5 98.7% −0.23 −1797.04 MSH6 98.1% −0.18 −2093.36 MSH7 98.3% −0.19 −1841.97 Table 3. Domains of MSH proteins. Protein Domain and Accession AtMSH1 AtMSH2 AtMSH3 AtMSH4 AtMSH5 AtMSH6 AtMSH7 MUTSac Start 761 659 810 546 562 1076 846 (SM000534) End 947 855 1006 733 757 1268 1043 MUTSd Start - 314 440 190 211 716 573 (SM000533) End - 642 793 531 547 1056 822 Pfam:MutS_I Start 125 22 105 - - 380 268 (PF01624) End 228 129 218 - - 496 382 Pfam:MutS_II Start - 142 235 - - 505 388 (PF05188) End - 284 361 - - 676 542 Pfam:GIY-YIG Start 1024 - - - - - - (PF01541) End 1091 - - - - - - TUDOR Start - - - - - 121 - (PF00567) End - - - - - 179 - This is a DNA-binding domain of MutSfamily, anda core domain made up of two subdomains that bind the DNA as levers. This domain is homologous to domain III of MutS in Thermusaquaticus [28]. Both MutS_I and MutS_II domains were identified by Pfam. They are homologous to domain II of Thermusaquaticus [29]. These domains functionally resemblethe RNase H domain that is responsible for RNA digestion and related to reverse transcriptase action. Similarly, MutS_II corresponds to domain II of MutS of Thermusaquaticus and is involved in DNA binding by MutS. Of all MSH homologues in A. thaliana, GIY-YIG domain is present only in MSH1. This is a catalytic domain present at the N-terminal of endonuclease [30] and its connection to DNA repair has already been inferred [31]. Finally, the TUDOR domain is present only in MSH6.The proteins that contain the Tudor domain are known as histone modification and categorized as chromatin remodeling proteins. Gene expression and DNA replication are greatly affected by histone modifications and chromatin remodeling, but how these processes are incorporated has not been fully investigated. It obvious that TUDOR domain proteins are development regulators carrying out functions that are not disclosed in plants [32]. 2.6. Interactome Analysis Before interactome analysis, proteins were assessed for solvent accessibility using the Protein Predict server. The results showed high solvent accessibility of all homologs which was an indication that we can expect extensive interactions and interactome profiles. The interactome analysis was a keystone of this work. It provided valuable information about proteins and protein families that interact with MSH homologues of A. thaliana (Table 4; Supplementary Materials Figure S9). All AtMSH homologues interact with thethree core proteins MLH1, MLH3, and PMS1 (Postmeiotic Segregation 1). Molecules 2019, 24, 2493 7 of 19 This wasexpected since these are the plant eukaryotic counterparts of bacterial MutL and play important roles in MMR. All the AtMSH proteins, with the exception of AtMSH4, interacted with PCNA1 and PCNA2 (proliferating cell nuclear antigen), which play important roles in DNA replication as sliding clamps that enable elongation of leading strands [33]. Four out of seven homologues (MSH1, MSH2, MSH6, and MSH7) interact with TIL1 and/or TIL2—proteins with important physiological roles in plant growth and development. Extensive interactions were noticed between MSH homologues, RECQSIM and ERCC1. These proteins are an important part of other DNA damage repair pathways. Seven out of ten MSH4 interactors were not seen in any other homologue, which is an indication of a specific role of this protein. MSH5 extensively interacted with DNA helicases (RECQ4A, RECQSIM, RecQI3, RECQI1, RECQ4B). 2.7. Protein Subcellular Localization Organelles are in charge of different cellular processes and hold different sets of proteins. Therefore, protein localization represents an important step in deciphering protein function, but is also suggested to be key to functional diversity [34]. Localization of AtMSH proteins is given in Table 5. Table 4. Interactors of AtMSH proteins as retrieved by interactome analysis in STRING. Interactor MSH CV Name Accession Function MUTL-homologue 1; correcting IDLs in MMR coming MLH1 AT4G09140.1 from DNA replication, DNA damage or heterologous 0.999 recombination in meiosis MUTL protein homolog 3; correcting IDLs in MMR MLH3 AT4G35520.1 coming from DNA replication, DNA damage or 0.996 heterologous recombination in meiosis Postmeiotic segregation 1; correcting non-Watson–Crick base pairing and IDLs in MMR; PMS1 AT4G02460.1 0.999 coming from DNA replication, DNA damage or heterologous recombination in meiosis Proliferating cellular nuclear antigen 1; auxiliary PCNA1 AT1G07370.1 protein of DNA polδ; controls eukaryotic 0.992 DNA replication AtMSH1 proliferating cell nuclear antigen 2; auxiliary protein of PCNA2 AT2G29570.1 0.991 DNA polδ; controls eukaryotic DNA replication MUTS homolog 2; (see Introduction for MSH2 AT3G18524.1 0.981 detailed description) MUTS-homolog 5; (see Introduction for MSH5 AT3G20475.1 0.981 detailed description) RECA homolog 3; plays role in recombination ability RECA3 AT3G10140.1 0.980 DNA strand transfer TILTED 1; DNA polymerase II; involved in DNA replication. Important physiological role (timing and determination of cell fate during plant embryogenesis TIL1 AT1G08260.1 0.974 and root pole development; required for proper shoot (SAM) and root apical meristem (RAM) function; required for flowering repression TILTED 2; DNA polymerase II; involved in DNA TIL2 AT2G27120.1 replication, promotes cell cycle and cell type 0.974 patterning. Contributes to flowering time repression Molecules 2019, 24, 2493 8 of 19 Table 4. Cont. Interactor MSH CV Name Accession Function MUTL-homologue 1; correcting IDLs in MMR coming MLH1 AT4G09140.1 from DNA replication, DNA damage or heterologous 0.999 recombination in meiosis MUTL protein homolog 3; correcting IDLs in MMR MLH3 AT4G35520.1 coming from DNA replication, DNA damage or 0.997 heterologous recombination in meiosis Postmeiotic segregation 1; correcting non-Watson–Crick base pairing and IDLs in MMR; coming from DNA PMS1 AT4G02460.1 0.999 replication, DNA damage or heterologous recombination in meiosis. proliferating cellular nuclear antigen 1; auxiliary protein PCNA1 AT1G07370.1 0.997 of DNA polδ; controls eukaryotic DNA replication proliferating cell nuclear antigen 2; auxiliary protein of PCNA2 AT2G29570.1 0.998 DNA polδ; controls eukaryotic DNA replication AtMSH2 MUTS homolog 7; (see Introduction for MSH7 AT3G24495.1 0.997 detailed description) MUTS homolog 6; (see Introduction for MSH6 AT4G02070.1 0.983 detailed description) DNA repair endonuclease UVH1; probably involved in NER and repair of UV light damage, and oxidative UVH1 AT5G41150.1 0.991 damage. In vitro, repairs DSBs and is required for homologous recombination TILTED 1; DNA polymerase II; involved in DNA replication. Important physiological role (timing and determination of cell fate during plant embryogenesis and TIL1 AT1G08260.1 0.974 root pole development; required for proper shoot (SAM) and root apical meristem (RAM) function; required for flowering repression RECQ helicase SIM; Involved in DNA repair; 30 -50 helicase RECQSIM AT5G27680.1 0.991 specific for plants DNA excision repair protein ERCC-1; involved in NER. In vitro, repairs DSBs and is required for homologous ERCC1 AT3G05210.1 0.990 recombination. UVH1/RAD1-ERCC1/RAD10 complex acts as endonuclease MUTL-homologue 1; correcting IDLs in MMR coming MLH1 AT4G09140.1 from DNA replication, DNA damage or heterologous 0.999 recombination in meiosis MUTL protein homolog 3; correcting IDLs in MMR MLH3 AT4G35520.1 coming from DNA replication, DNA damage or 0.997 heterologous recombination in meiosis Postmeiotic segregation 1; correcting non-Watson-Crick base pairing and IDLs in MMR; coming from DNA PMS1 AT4G02460.1 0.999 replication, DNA damage or heterologous recombination in meiosis proliferating cellular nuclear antigen 1; auxiliary protein PCNA1 AT1G07370.1 0.955 of DNA polδ; controls eukaryotic DNA replication AtMSH3 proliferating cell nuclear antigen 2; auxiliary protein of PCNA2 AT2G29570.1 0.968 DNA polδ; controls eukaryotic DNA replication AT2G02550 AT2G02550.2 PIN domain-containing protein; nuclease 0.965 exonuclease 1; dsDNAexonuclease. May be involved in AT1G29630 AT1G29630.2 0.965 DNA mismatch repair (MMR) AT1G18090 AT1G18090.1 50 -30 exonuclease family protein 0.965 DNA excision repair protein ERCC-1; involved in NER. In vitro, repairs DSBs and is required for homologous ERCC1 AT3G05210.1 0.953 recombination. UVH1/RAD1-ERCC1/RAD10 complex acts as endonuclease RECQ helicase SIM; Involved in DNA repair; 30 -50 helicase RECQSIM AT5G27680.1 0.863 specific for plants Molecules 2019, 24, 2493 9 of 19 Table 4. Cont. Interactor MSH CV Name Accession Function MUTL-homologue 1; correcting IDLs in MMR coming MLH1 AT4G09140.1 from DNA replication, DNA damage or heterologous 0.999 recombination in meiosis MUTL protein homolog 3; correcting IDLs in MMR MLH3 AT4G35520.1 coming from DNA replication, DNA damage or 0.999 heterologous recombination in meiosis Postmeiotic segregation 1; correcting non-Watson–Crick base pairing and IDLs in MMR; coming from DNA PMS1 AT4G02460.1 0.998 replication, DNA damage or heterologous recombination in meiosis MUTS-homologue 5; (see Introduction for MSH5 AT3G20475.1 0.987 detailed description) AtMSH4 DNA repair protein RAD51-like 1; binds ss- and dsDNA; DNA-dependent ATPase; repair of meiotic DBSs generated RAD51 AT5G20850.1 0.984 by AtSPO11-1 and in homologous recombination. Important for vegetative growth and root mitosis MMS andUV sensitive 81; part of endonuclease complex. MUS81 AT4G30870.1 Involved in DNA repair and homologous recombination 0.980 (HR) in somatic cells. Meiotic recombination protein SPO11-1; part of meiotic ATSPO11-1 AT3G13170.1 recombination. Cleaves DNA to make DSB and start 0.970 meiotic recombination RCK AT3G27730.1 ROCK-N-ROLLERS; DNA helicase important for meiosis 0.964 Disruption of meiotic control 1; May participate in meiotic DMC1 AT3G22880.1 0.958 recombination sporulation 11-2; involved in meiotic recombination. SPO11-2 AT1G63990.1 Cleaves DNA to make DSB and start meiotic 0.931 recombination MUTL-homologue 1; correcting IDLs in MMR coming MLH1 AT4G09140.1 from DNA replication, DNA damage or heterologous 0.999 recombination in meiosis MUTL protein homolog 3; correcting IDLs in MMR MLH3 AT4G35520.1 coming from DNA replication, DNA damage or 0.999 heterologous recombination in meiosis Postmeiotic segregation 1; correcting non-Watson-Crick base pairing and IDLs in MMR; coming from DNA PMS1 AT4G02460.1 0.999 replication, DNA damage or heterologous recombination in meiosis proliferating cellular nuclear antigen 1; auxiliary protein PCNA1 AT1G07370.1 0.993 of DNA polδ; controls eukaryotic DNA replication AtMSH5 proliferating cell nuclear antigen 2; auxiliary protein of PCNA2 AT2G29570.1 0.993 DNA polδ; controls eukaryotic DNA replication ATP-dependent DNA helicase Q-like 4A; DNA helicase RECQ4A AT1G10930.1 0.994 possibly involved in repair of DNA RECQ helicase SIM; Involved in DNA repair; 30 -50 helicase RECQSIM AT5G27680.1 0.991 specific for plants ATP-dependent DNA helicase Q-like 3; DNA helicase; RecQI3 AT4G35740.1 possible role in DNA repair. Mediates DNA strand 0.991 annealing RECQ helicase l1; DNA helicase; possible role in DNA RECQI1 AT3G05740.1 0.991 repair RECQ helicase L4B; DNA helicase; possible role in DNA RECQ4B AT1G60930.1 0.991 repair; promotes crossovers Molecules 2019, 24, 2493 10 of 19 Table 4. Cont. Interactor MSH CV Name Accession Function MUTL-homologue 1; correcting IDLs in MMR coming MLH1 AT4G09140.1 from DNA replication, DNA damage or heterologous 0.999 recombination in meiosis MUTL protein homolog 3; correcting IDLs in MMR MLH3 AT4G35520.1 coming from DNA replication, DNA damage or 0.998 heterologous recombination in meiosis Postmeiotic segregation 1; correcting non-Watson–Crick base pairing and IDLs in MMR; coming from DNA PMS1 AT4G02460.1 0.999 replication, DNA damage or heterologous recombination in meiosis proliferating cellular nuclear antigen 1; auxiliary protein PCNA1 AT1G07370.1 0.995 of DNA polδ; controls eukaryotic DNA replication AtMSH6 proliferating cell nuclear antigen 2; auxiliary protein of PCNA2 AT2G29570.1 0.996 DNA polδ; controls eukaryotic DNA replication MUTS-homologue 5; (see Introduction for MSH5 AT3G20475.1 0.984 detailed description) MUTS homolog 2; (see Introduction for MSH2 AT3G18524.1 0.983 detailed description) TILTED 1; DNA polymerase II; involved in DNA replication. Important physiological role (timing and determination of cell fate during plant embryogenesis and TIL1 AT1G08260.1 0.974 root pole development; required for proper shoot (SAM) and root apical meristem (RAM) function; required for flowering repression TILTED 2; DNA polymerase II; involved in DNA TIL2 AT2G27120.1 replication, promotes cell cycle and cell type patterning. 0.974 Contributes to flowering time repression RECQ helicase SIM; Involved in DNA repair; 30 -50 helicase RECQSIM AT5G27680.1 0.970 specific for plants MUTL-homologue 1; correcting IDLs in MMR coming MLH1 AT4G09140.1 from DNA replication, DNA damage or heterologous 0.999 recombination in meiosis. MUTL protein homolog 3; correcting IDLs in MMR MLH3 AT4G35520.1 coming from DNA replication, DNA damage or 0.997 heterologous recombination in meiosis Postmeiotic segregation 1; correcting non-Watson–Crick base pairing and IDLs in MMR; coming from DNA PMS1 AT4G02460.1 0.999 replication, DNA damage or heterologous recombination in meiosis proliferating cellular nuclear antigen 1; auxiliary protein PCNA1 AT1G07370.1 0.996 of DNA polδ; controls eukaryotic DNA replication AtMSH7 proliferating cell nuclear antigen 2; auxiliary protein of PCNA2 AT2G29570.1 0.995 DNA polδ; controls eukaryotic DNA replication MUTS-homologue 5; (see Introduction for MSH5 AT3G20475.1 0.984 detailed description) MUTS homolog 2; (see Introduction for MSH2 AT3G18524.1 0.997 detailed description) TILTED 1; DNA polymerase II; involved in DNA replication Important physiological role (timing and determination of cell fate during plant embryogenesis and TIL1 AT1G08260.1 0.976 root pole development; required for proper shoot (SAM) and root apical meristem (RAM) function; required for flowering repression TILTED 2; DNA polymerase II; involved in DNA TIL2 AT2G27120.1 replication, promotes cell cycle and cell type patterning. 0.976 Contributes to flowering time repression RECQ helicase SIM; Involved in DNA repair; 30 -50 helicase RECQSIM AT5G27680.1 0.968 specific for plants Molecules 2019, 24, 2493 11 of 19 Table 5. Subcellular localization of AtMSH proteins. Protein Subcellular Localization Subnuclear Localization Mitochondrion - MSH1 Chloroplast - MSH2 Nucleus Nucleolus MSH3 Nucleus Nucleolus MSH4 Nucleus Nucleolus MSH5 Nucleus Nucleolus MSH6 Nucleus Nucleolus MSH7 Nucleus Nucleolus 2.8. Docking Site Prediction Proteins develop their functionality through interactions with other macromolecules (DNA, RNA, other proteins, etc.). Therefore, understanding protein–protein interaction is crucial for elucidation of its function and the analysis of the whole proteome. Results obtained from ClusPro and SPIDDER were in line with each other. Each AtMSH protein was docked against its most interesting interactors. The results from ClusProareare are shown in Supplementary Materials Figures S2–S8. In order to confirm the results, the docking was done in SPPIDER http://sppider.cchmc.org/ and the results coincided with the ClusPro analysis and were accompanied by tables indicating active sites of AtMSH protein and its interactor (Supplementary Materials Table S1). 3. Discussion DNA, just like all organic molecules, can undergo chemical changes. However, structural changes on DNA have much larger and far-reaching consequences. DNA mutations can arise as result of DNA replication slips or spontaneous chemical changes stemming from exposure to different damaging factors. Therefore, cells had to evolve mechanisms to cope with these damages. One of them is the mismatch repair pathway. Most important proteins of this MMR are MutS homologs (MSHs). Evolutionary conservation of the MMR pathway and MSH orthologs in the plant and animal kingdoms, being higher in comparison to bacterial counterparts, allows us to transfer knowledge from A. thaliana to animals. Plants carry seven homologs of MSH, compared to five homologs in humans and six in yeast.Therefore, it was very interesting to check for functions of plant MSH homologs in MMR, estimate potential redundancy in their role, and look for new avenues in which they function. Although the majority of MutS homologs belong to the same protein family, a certain degree of functional diversity among MSH proteins was observed. Phylogenetic analysis of plant MutS homologs confirmed this functional specification. This is especially striking in the example of MSH6 and MSH7 which diverged recently but have different functions. It would be of great importance to find out which amino acids are responsible for this functional specification. It is of great significance to look at genes and their occurrence from an evolutionary perspective. This is why the first step was to look at MSA and a phylogenetic tree of MSH proteins. MSA revealed a ~200 amino acid long conserved region at the C-terminal that suggested the core domain of the AtMSH protein family and a common ancestor of these proteins. This is in line with previous studies [35]. As indicated by Culligan et al.,the first duplication event enabled one copy to encode the mitochondrial MSH1 protein and the other copy gave rise to a diversified MSH family. The secondnuclear duplication gave rise to ancestors of (i) MSH6 and MSH7 and (ii) MSH2, MSH3, MSH4, and MSH5. Further duplication and specialization enabled MSH6, the MSH7 ancestor, to form subfamilies of MSH6 and MSH7. On the other hand, duplication gave rise to the meiosis-specific MSH4 subfamily and ancestor of MSH2, MSH3, and MSH5. By further duplication, the later three diverged into separate genes. This diversification was followed by specialization in function. Further analysis showed that the conserved region identified as a core domain by MSA is a MUTSac domain. Some regions are conserved only in subfamilies of MSHs, so they can confer specific functions to these proteins. Pfam:MutS_I (PF01624) is a domain with unknown Molecules 2019, 24, 2493 12 of 19 function, but judging by its presence in all MSH proteins except MSH4 and MSH5, which does not have DNA mismatch binding ability, it is reasonable to hypothesize that MutS_I is a DNA binding domain, as suggested by studies in corresponding domains of Thermusaquaticus. The interactome of MSH proteins shown here shows that these proteins have crucial roles in plants: (i) they maintain the stability of nuclear and organellar DNA and (ii) control numerous physiological processes. This is not the first time that proteins of DNA repair mechanisms were found to influence physiological characteristics of plants [36]. Subcellular localization indicates that MSH homologs are predominantly placed in the nucleus. The only exception is MSH1, which is localized in mitochondria and chloroplast. This was proved to be essential for substoichiometric shifting in plant mitochondria, stability of plastid genome, and consequently for plant growth, through interactions described below [37]. MLH1–MLH3 with MSH homologs suggests similar roles for plant homologues. It is important to note that MLH1 mutants in A. thaliana exhibit reduced fertility [38,39]. This is another important physiological trait directly influenced by MSH homologs. Proposed mechanisms of MLH1 function and its interaction with MSH homologs are certainly worth investigating further in plants.MSH homologs, with the exception of MSH4, extensively interact with replication factors PCNA1 and PCNA2. This is another proof of their importance for maintenance of DNA integrity, as these proteins have already been extensively studied in relation to DNA repair [35]. Additionally, these proteins have been correlated with the control of shoot differentiation and meristem organization, indicating another venue influenced by MSH proteins [40]. MSH1 interacts extensively with proteins involved in replication and recombination. The results shown here support the hypothesis that replication initiation is mediated by recombination, which would explain interaction with both groups of proteins. One of the physiological roles influenced by MSH homologs includes plant growth, controlled by the mitochondrial genome rearrangements through the interaction of MSH1–RECA3 proteins. RECA3 is a protein involved in recombination and strand transfer activity, whose mutants were found to influence plant growth, leaf variegation, and altered leaf morphology [41–43]. MSH1–RECA3 interaction is supported by the same subcellular localization and involvement in the same substoichiometric shifting process. RECA3 interacts with MSH1 through the AAA domain, but it is possible to see a hole in the docking site (Supplementary Materials Figure S2). Using the results obtained in the BindN program, which identified DNA-binding residues in the interacting site (Arg212, Ser213, Arg214, Gly216, Ser94, Thr95), we can hypothesize that it is the area where DNA binds. Extensive interaction of MSH (MSH1, MSH2, MSH6 and MSH7) proteins was observed in relation to DNA polymerase epsilon catalytic subunit A (TIL1/POL2a/TILTED1) and/or DNA polymerase epsilon catalytic subunit B (TIL2/POL2b/TILTED2) [44]. Partial interaction through domains (MUTSac, Pfam:MutS_II, Pfam:MutS_I) was supported by interactions through electrostatic charges. TIL1 and TIL2 proteins alter root and shoot development, repress flowering, homologous recombination, abscisic acid signaling, and cell cycling [41,43]. This way, MSH homologs could be involved in the control of physiological characteristics of plants. Thus far, it was discovered that TIL1 mutants (abo4-1) have higher rates of homologous recombination and display pleiotropic defects in both vegetative and reproductive development, but the mechanism behind this was not investigated [45]. Another interesting protein found in the interactome was RECQSIM. Important information about it come from the work of Bagherieh-Najjar et al. who indicated that RECQSIM has a role in DNA repair and recombination, but they did not propose the mechanism behind this repair [46]. MSH2, MSH3, MSH5, MSH6, and MSH7 interactions with RECQSIM (through MUTSac, Pfam:MutS_II, Pfam:MutS_I domains, mostly supported by electrostatic charges),which is indicated here, proposes a possible model by which RECQSIM can contribute to DNA repair and genome stability, and consequently, influence plant growth and development. MSH5 interacts with six members of the RECQ family. This extensive MSH5–RECQ interaction indicates the important role of the RECQ family for plant DNA stability and fertility. ERCC1 and UVH1 are proteins involved in nucleotide excision repair and in mitotic homologous recombination [47,48]. AtMSH homologs were found to interact with AtRAD1 Molecules 2019, 24, 2493 13 of 19 and AtRAD10 at the highest confidence value. AtMSH2 interacts with AtERCC1 and AtUVH1 through theC-terminal domain MUTSac between the 659th and 855th residue; while AtMSH3 interacts with UVH1 through MUTSd, a DNA-binding domain. Therefore, we can assume that MutSβ (MSH2–MSH3 heterodimer) is responsible for HR. This is in line with research done in yeast [49]. MSH4 is a special member of the MSH protein family. It has a role exclusively in meiotic recombination and not in MMR. It has a special interactome and different domain profile, where MSH4 shares only MUTSac (ATPase domain) and MUTSd (DNA-binding domain) with other MSH proteins and does not contain any MMR-related domains. As meiosis-specific protein, MSH4 interacts with AtSPO11-1 and AtSPO11-2 proteins through the MUTSac domain. AtSPO11-1 and AtSPO11-2 are components of topoisomerase 6, responsible for formation of DSBs [50]. Localization of MSH5 is dependent on the occurrence of MSH4; therefore, they do not have a redundant role [22]. Instead, MSH5 plays an important role in stabilizing chiasma during meiosis, and directly influences the fertility of the plant. MSH5 extensively interacts with RECQ homologs. It was found in E. coli and S. cerevisiae, and the mutation in RECQ leads to increased levels of recombination. This functional link to recombination and their interaction with AtMSH5 is a sign that they could have the same function in plants. What the exact mechanism of interaction between MSH5 and RECQ is a line of research worth exploring further. AtRECQ2 disrupts D-loops and prevents non-productive recombination events or channel repair pathways into non-productive recombination. Knowing that AtMSH5 is involved in meiosis regulation, AtMSH5–AtRECQ2 interaction is potentially very important for the fertility of plants, but to our knowledge, this has not been explored yet. 4. Materials and Methods 4.1. Sequences Retrieving and Multiple Sequence Alignment MSA The amino acid sequences of seven AtMSH homologs were first retrievedfrom the National Center for Biotechnology Information (NCBI) [51] and the Arabidopsis Information Resource (TAIR) [52] (Table 6). Obtained sequences were aligned using the Clustal Omega tool [53–56]. Table 6. AtMSH proteins accession numbersfrom the National Center for Biotechnology Information (NCBI) and the Arabidopsis Information Resource (TAIR). Accession Number Protein Name Sequence Length NCBI TAIR AtMSH1 Q84LK0.1 AT3G24320.1 1118 aa AtMSH2 O24617.1 AT3G18524.1 937 aa AtMSH3 O65607.2 AT4G25540.1 1081 aa AtMSH4 F4JP48.1 AT4G17380.1 792 aa AtMSH5 F4JEP5.1 AT3G20475.1 807 aa AtMSH6 O04716.2 AT4G02070.1 1324 aa AtMSH7 Q9SMV7.1 AT3G24495.1 1109 aa 4.2. Phylogenetic Profile Rendering Sequences of AtMSH proteins were submitted for phylogenetic analysis in Phylogeny.fr. One Click mode was used here to construct a phylogenetic tree of AtMSH homologues using the neighbor joining method [57,58]. 4.3. Protein 3D Structure Prediction and Refinement The 3D structure of MSH homologues in A. thaliana has not been determined yet. Therefore, the homology modeling method was used to predict their 3D structure. Amino acid sequences of MSH proteins were submitted to Phyre2 (Protein Homology/analogY Recognition Engine V 2.0) portal [59]. In order to obtain structures closer to native state, the .pdb files retrieved from Phyre2 Molecules 2019, 24, 2493 14 of 19 were refined using the protein structure refinement server 3Drefine [60,61]. 3Drefine is a free web server that brings the structure closer to a native state. It uses a two-step approach. First, hydrogen bonds are optimized, and second, energy at the atomic level is minimized. The critical assessment of techniques for protein structure prediction (CASP), which is used as the gold standard for the assessment of bioinformatics tools, recognized 3Drefine as a tool that brings structural improvement at the global and local levels of protein structure. Three-dimensional visualization of the protein surface was done using PyMOL software [62]. Additional visualization of 3D structure was done in DeepView-Swiss-PdbViewer available at ExPASy Bioinformatics Resource Portal [63]. DeepView is a powerful tool for macromolecular modeling that enables visualization of electrostatic potentials of proteins [64]. 4.4. Protein 3D Structure Validation After 3D structures were predicted as described above, these models were validated using several tools. First, the RAMPAGE tool was used for assessment of the Ramachandran plot [65]. A Ramachandran plot aligns backbone angles ψ (C–Cα bond) and ϕ (C–N bond) [66]. This is arguably the best assessment of the 3D structure prediction. 4.5. Protein Domain Identification In order to identify functional domains of AtMSH proteins, SMART (Simple Modular Architecture Research Tool); Normal mode was used [67,68]. Besides SMART default HMMER search that uses hidden Markov models, Pfam domains were included. 4.6. Interactome Analysis Following domain identification, proteins underwent interactome analysis. This was done in order to identify which proteins interact with AtMSH proteins. For interactome analysis, a STRING (functional protein association network) database was used [69]. STRING integrates information scattered over multiple databases in order to report on physical and functional protein–protein interactions. Protein sequences were submitted to STRING and parameters were set to show 10 interactors of highest confidence (>0.900). 4.7. Protein Localization Localization is an important indication of protein function and biological interaction. Subcellular localization was done using online tools and literature. The PSI-predictor (Plant Subcellular Localization integrative predictor) was exploited [70]. It combines group voting and a neural network to integrate data from 11 independent predictors and outperforms all of them individually. For AtMSHproteins that were localized to the nucleus, further characterization was done in order to check in which part of the nucleus they are localized. This was done using Nuc-Ploc: predicting protein subnuclear localization [71]. 4.8. Docking Site Prediction The AtMSH homologs and their corresponding interactorswere submitted to docking site prediction tools, in order to visualize regions responsible for interaction. Two docking tools were used in this study: ClusPro and SPPIDER [72–75]. In 2004, when it was published, ClusPro was first a completely automated program for computational protein docking. ClusPro creates over 70,000 possible conformations, evaluates complexes, and selects ones with the highest surface complementarities and optimal electrostatic characteristics. ClusPro showed very good results in the Critical Assessment of Prediction of Interactions (CAPRI) and confirmed that cluster size-based ranking is reliable for identification of near-native conformations [76]. Solvent accessibility-based Protein–Protein Interface identification and Recognition (SPPIDER) offers a user-friendly website and is able to detect protein Molecules 2019, 24, 2493 15 of 19 interfaces in two ways [77]; it has a different approach compared to other interface prediction tools. It uses relative solvent accessibility (RSA) as a reference point and calculates the RSA of an amino acid in (a) predicted and (b) unbound state. Here, RSA loss was set to at least 4% after the formation of the complex. Supplementary Materials: The following are available online. Figure S1: Multiple Sequence Alignment of MSH Proteins. Figure S2: MSH1 interactions. Single MSH1 is shown on the left in yellow and interaction is on the right. MLH1: magenta; MLH3: red; MSH2: green; PCNA1: cyan; PCNA2: light-red; PMS1: blue; RECA3: red; TIL1: gray; TIL2: bright red. Figure S3: MSH2 interactions. Single MSH2 is shown on the left in purple and interaction is on the right. ERCC1: red; MLH1: green; MLH3: slate blue; MSH6: yellow; MSH7: lemon; PCNA1: beige; PCNA2: orange; PMS1: light blue; RECQSIM: white; TIL1: red; UVH1: blue. Figure S4: MSH3 interactions. Single MSH3 is shown on the left in purple and interaction is on the right. Interactions from top to bottom: At1G18090: blue; At1G29630: red; At2G02550: yellow; ERCC1: green; MLH1: cyan; MLH3: orange; PCNA1: light green; PCNA2: beige; PMS1: yellow; RECQSIM: blue. Figure S5: MSH4 interactions. Single MSH4 is shown on the left in purple and interaction is on the right. Interactions from top to bottom: MLH1: white; MLH3: light blue; MUS81: red; PMS1: blue; RAD51: green; SPO11-1: orange; SPO11-2: cyan; MSH5: yellow; DMC1: wheat. Figure S6: MSH5 interactions. Single MSH5 is shown on the left in purple and interaction is on the right. Interactions from top to bottom: MLH1: yellow; MLH3: red; PCNA1: red; PCNA2: orange; PMS: cyan; RECQ4A: red; RECQ4B: blue; RECQl1: green; RECQl3: orange; RECQSIM: yellow. Figure S7: MSH6 interactions. Single MSH6 is shown on the left in purple and interaction is on the right. Interactions from top to bottom: MLH1: red; MLH3: green; MSH2: yellow; MSH5: orange; PCNA1: blue; PCNA2: turquoise; PMS1: cyan; RECQSIM: beige; TIL1: orange; TIL2: orange. Figure S8: MSH7 interactions. Single MSH7 is shown on the left in purple and interaction is on the right. Interactions from top to bottom: MLH1: red; MLH3: green; MSH2: orange; MSH5: blue; PCNA1: green; PCNA2: orange; PMS1: cyan; RECQSIM: blue; TIL1: green; TIL2: gray. Figure S9: STRING Interactome of AtMSHs. (A) MSH1; (B) MSH2; (C) MSH3; (D) MSH4; (E) MSH5; (F) MSH6; (G) MSH7. Table S1: Docking sites of protein–protein interactions; MSH homologs and their interactome. Author Contributions: M.R.A. and A.M. designed and supervised the study. M.R.A. and A.M. performed data analyses, wrote the manuscript, and reviewed and approved the final manuscript. M.R.A. conceived of the study, and designed it and coordination and helped to draft the manuscript. While A.M. Carried out the expirmental work; 3-d Structure prediction and validation, domain analysis, subcellular localization, interactome and docking sites. A.A.A.-G. participated in the manuscript design and He provided us the related articles and He helped to draft the manuscript. A.A.H. particpated in the discussion part and He helped to figures and tables editing during the review process. Funding: This research received no external funding. Acknowledgments: The authors would like to extend their thanks to International University of Sarajevo, Research Center, Sarajevo, Bosnia and Herzegovina for facilitating the work and its support in implementing the project. The authors are grateful to the deanship of scientific research at King Saud University for funding the work through the research group project No. RG-1440-054. 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