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Tan J, Sun X, Zhao H, Guan H, Gao S, Zhou P. Double-strand DNA break repair: molecular mechanisms and therapeutic targets. MedComm (Beijing) 2023; 4:e388. [PMID: 37808268 PMCID: PMC10556206 DOI: 10.1002/mco2.388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/29/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Double-strand break (DSB), a significant DNA damage brought on by ionizing radiation, acts as an initiating signal in tumor radiotherapy, causing cancer cells death. The two primary pathways for DNA DSB repair in mammalian cells are nonhomologous end joining (NHEJ) and homologous recombination (HR), which cooperate and compete with one another to achieve effective repair. The DSB repair mechanism depends on numerous regulatory variables. DSB recognition and the recruitment of DNA repair components, for instance, depend on the MRE11-RAD50-NBS1 (MRN) complex and the Ku70/80 heterodimer/DNA-PKcs (DNA-PK) complex, whose control is crucial in determining the DSB repair pathway choice and efficiency of HR and NHEJ. In-depth elucidation on the DSB repair pathway's molecular mechanisms has greatly facilitated for creation of repair proteins or pathways-specific inhibitors to advance precise cancer therapy and boost the effectiveness of cancer radiotherapy. The architectures, roles, molecular processes, and inhibitors of significant target proteins in the DSB repair pathways are reviewed in this article. The strategy and application in cancer therapy are also discussed based on the advancement of inhibitors targeted DSB damage response and repair proteins.
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Affiliation(s)
- Jinpeng Tan
- Hengyang Medical CollegeUniversity of South ChinaHengyangHunan ProvinceChina
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Xingyao Sun
- Hengyang Medical CollegeUniversity of South ChinaHengyangHunan ProvinceChina
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Hongling Zhao
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Hua Guan
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Shanshan Gao
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Ping‐Kun Zhou
- Hengyang Medical CollegeUniversity of South ChinaHengyangHunan ProvinceChina
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
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Otahalova B, Volkova Z, Soukupova J, Kleiblova P, Janatova M, Vocka M, Macurek L, Kleibl Z. Importance of Germline and Somatic Alterations in Human MRE11, RAD50, and NBN Genes Coding for MRN Complex. Int J Mol Sci 2023; 24:ijms24065612. [PMID: 36982687 PMCID: PMC10051278 DOI: 10.3390/ijms24065612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The MRE11, RAD50, and NBN genes encode for the nuclear MRN protein complex, which senses the DNA double strand breaks and initiates the DNA repair. The MRN complex also participates in the activation of ATM kinase, which coordinates DNA repair with the p53-dependent cell cycle checkpoint arrest. Carriers of homozygous germline pathogenic variants in the MRN complex genes or compound heterozygotes develop phenotypically distinct rare autosomal recessive syndromes characterized by chromosomal instability and neurological symptoms. Heterozygous germline alterations in the MRN complex genes have been associated with a poorly-specified predisposition to various cancer types. Somatic alterations in the MRN complex genes may represent valuable predictive and prognostic biomarkers in cancer patients. MRN complex genes have been targeted in several next-generation sequencing panels for cancer and neurological disorders, but interpretation of the identified alterations is challenging due to the complexity of MRN complex function in the DNA damage response. In this review, we outline the structural characteristics of the MRE11, RAD50 and NBN proteins, the assembly and functions of the MRN complex from the perspective of clinical interpretation of germline and somatic alterations in the MRE11, RAD50 and NBN genes.
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Affiliation(s)
- Barbora Otahalova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
- Department of Biochemistry, Faculty of Natural Science, Charles University in Prague, 12800 Prague, Czech Republic
| | - Zuzana Volkova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics, Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine and General University Hospital in Prague, 12853 Prague, Czech Republic
- Correspondence: ; Tel.: +420-22496-4287
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Benamri I, Azzouzi M, Moussa A, Radouani F. An in silico analysis of rpoB mutations to affect Chlamydia trachomatis sensitivity to rifamycin. J Genet Eng Biotechnol 2022; 20:146. [DOI: 10.1186/s43141-022-00428-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/08/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Chlamydia trachomatis is an obligate intracellular gram-negative pathogen, responsible for diverse affections, mainly trachoma and sexually transmitted diseases. Antibiotics are the commonly used drugs to tackle chlamydiae infections. However, when overused or wrongly used this may lead to strains’ resistance to antibiotics, this phenomenon represents a real health problem worldwide. Numerous studies showed the association of Chlamydia trachomatis resistance with mutations in different genes; these mutations could have a deleterious or neutral impacts on the encoded proteins. The aim of this study is to perform an in silico analysis of C. trachomatis rpoB-encoded proteins using numerous bioinformatics tools and to identify the functional and structural-related effects of the mutations and consequently their impact on the bacteria sensitivity to antibiotics.
Results
The analysis revealed that the prediction of the damaging impact related to the mutations in rpoB-encoded proteins showed eight mutations: V136F, Q458K, V466A, A467T, H471N, H471Y, H471L, and I517M with big deleterious effects. Among them, six mutations, V136F, Q458K, V466A, A467T, H471N, and I517M, are located in a highly conserved regions decreasing the protein’s stability. Furthermore, the structures analysis showed that the mutations A467T, H471N, I517M, and V136F models had a high deviation compared to the wild type. Moreover, the prediction of protein-protein network indicated that rpoB wild type interacts strongly with 10 proteins of C. trachomatis, which are playing different roles at different levels.
Conclusion
As conclusion, the present study revealed that the changes observed in the encoded proteins can affect their functions and structures, in addition to their interactions with other proteins which impact the bacteria sensitivity to antibiotics. Consequently, the information revealed through this in silico analysis would be useful for deeper exploration to understand the mechanisms of C. trachomatis resistance and enable managing the infection to avoid its complications. We recommend further investigations and perform deeper experimental analysis with collaboration between bioinformaticians, physicians, biologists, pharmacists, and chemistry and biochemistry scientists.
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Harini K, Srivastava A, Kulandaisamy A, Gromiha MM. ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants. Nucleic Acids Res 2021; 50:D1528-D1534. [PMID: 34606614 PMCID: PMC8728258 DOI: 10.1093/nar/gkab848] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
Protein–nucleic acid interactions are involved in various biological processes such as gene expression, replication, transcription, translation and packaging. The binding affinities of protein–DNA and protein–RNA complexes are important for elucidating the mechanism of protein–nucleic acid recognition. Although experimental data on binding affinity are reported abundantly in the literature, no well-curated database is currently available for protein–nucleic acid binding affinity. We have developed a database, ProNAB, which contains more than 20 000 experimental data for the binding affinities of protein–DNA and protein–RNA complexes. Each entry provides comprehensive information on sequence and structural features of a protein, nucleic acid and its complex, experimental conditions, thermodynamic parameters such as dissociation constant (Kd), binding free energy (ΔG) and change in binding free energy upon mutation (ΔΔG), and literature information. ProNAB is cross-linked with GenBank, UniProt, PDB, ProThermDB, PROSITE, DisProt and Pubmed. It provides a user-friendly web interface with options for search, display, sorting, visualization, download and upload the data. ProNAB is freely available at https://web.iitm.ac.in/bioinfo2/pronab/ and it has potential applications such as understanding the factors influencing the affinity, development of prediction tools, binding affinity change upon mutation and design complexes with the desired affinity.
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Affiliation(s)
- Kannan Harini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Ambuj Srivastava
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Arulsamy Kulandaisamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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Roisné-Hamelin F, Pobiega S, Jézéquel K, Miron S, Dépagne J, Veaute X, Busso D, Du MHL, Callebaut I, Charbonnier JB, Cuniasse P, Zinn-Justin S, Marcand S. Mechanism of MRX inhibition by Rif2 at telomeres. Nat Commun 2021; 12:2763. [PMID: 33980827 PMCID: PMC8115599 DOI: 10.1038/s41467-021-23035-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Specific proteins present at telomeres ensure chromosome end stability, in large part through unknown mechanisms. In this work, we address how the Saccharomyces cerevisiae ORC-related Rif2 protein protects telomere. We show that the small N-terminal Rif2 BAT motif (Blocks Addition of Telomeres) previously known to limit telomere elongation and Tel1 activity is also sufficient to block NHEJ and 5' end resection. The BAT motif inhibits the ability of the Mre11-Rad50-Xrs2 complex (MRX) to capture DNA ends. It acts through a direct contact with Rad50 ATP-binding Head domains. Through genetic approaches guided by structural predictions, we identify residues at the surface of Rad50 that are essential for the interaction with Rif2 and its inhibition. Finally, a docking model predicts how BAT binding could specifically destabilise the DNA-bound state of the MRX complex. From these results, we propose that when an MRX complex approaches a telomere, the Rif2 BAT motif binds MRX Head in its ATP-bound resting state. This antagonises MRX transition to its DNA-bound state, and favours a rapid return to the ATP-bound state. Unable to stably capture the telomere end, the MRX complex cannot proceed with the subsequent steps of NHEJ, Tel1-activation and 5' resection.
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Affiliation(s)
- Florian Roisné-Hamelin
- Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Sabrina Pobiega
- Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Kévin Jézéquel
- Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Simona Miron
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jordane Dépagne
- CIGEx, Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Xavier Veaute
- CIGEx, Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Didier Busso
- CIGEx, Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Marie-Hélène Le Du
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Jean-Baptiste Charbonnier
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Philippe Cuniasse
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sophie Zinn-Justin
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphane Marcand
- Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France.
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Nuryady MM, Nurcahyo RW, Hindun I, Fatmawati D. Multidrug resistance protein structure of Trypanosoma evansi isolated from buffaloes in Ngawi District, Indonesia: A bioinformatics analysis. Vet World 2021; 14:33-39. [PMID: 33642783 PMCID: PMC7896887 DOI: 10.14202/vetworld.2021.33-39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/03/2020] [Indexed: 12/05/2022] Open
Abstract
Background and Aim: Trypanosomiasis, also known as surra, is an infectious disease with a wide host spectrum. In Indonesia, this disease is caused by Trypanosoma evansi. Various trypanocidal drugs have been used to treat this pathogen and subsequent disease. Yet, the long-term trypanocidal administration generates drug-resistant T. evansi. Some have identified genetic alterations in T. evansi transporter protein-coding genes that may be responsible for drug resistance. The Multidrug Resistance Protein E (MRPE) gene is a likely candidate gene responsible for the individual resistance. To date, no research has focused on T. evansi MRPE (TevMRPE) in this context. Hence, this research aimed at analyzing and characterizing the TevMRPE gene and protein using a bioinformatics approach. Materials and Methods: T. evansi was isolated from buffalo suffering from surra in Ngawi Regency, Indonesia. Isolated T. evansi was inoculated and cultured in male mice. The T. evansi genome was isolated from mouse blood with a parasitemia degree as high as 105. A polymerase chain reaction procedure was conducted to amplify the putative MRPE coding gene. The amplicon was sequenced and analyzed using MEGA X, BLAST, and I-tasser softwares. Results: The putative TevMRPE coding gene showed sequence similarity as high as 99.79% against the MRPE gene from Trypanosoma brucei gambiense. The protein profile and characteristics depicted that the putative TevMRPE protein was related to a family of Adenosine Triphosphate-Binding Cassette (ABC) transporter proteins. This family of transporter proteins plays a crucial role in the resistance toward several medicines. Conclusion: The obtained gene sequence in this research was identified as the TevMRPE. This gene is homologous to the T. brucei gambiense MRPE gene and possesses ligand active sites for Adenylyl Imidodiphosphate. In addition, MRPE contains enzyme active sites similar to the cystic fibrosis transmembrane conductance regulator. These data suggest that ABC transport proteins, like MRPE, may be necessary to confer trypanocidal drug resistance in T. evansi.
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Affiliation(s)
- Moh Mirza Nuryady
- Department of Biology Education, Faculty of Teacher Training and Education, Universitas Muhammadiyah Malang, Malang, Indonesia.,Master Program of Veterinary Science, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Raden Wisnu Nurcahyo
- Master Program of Veterinary Science, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Department of Parasitology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Iin Hindun
- Department of Biology Education, Faculty of Teacher Training and Education, Universitas Muhammadiyah Malang, Malang, Indonesia
| | - Diani Fatmawati
- Department of Biology Education, Faculty of Teacher Training and Education, Universitas Muhammadiyah Malang, Malang, Indonesia
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Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter. Int J Mol Sci 2020; 21:ijms21207606. [PMID: 33066695 PMCID: PMC7589834 DOI: 10.3390/ijms21207606] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
The ATP-binding cassette transporter A1 (ABCA1) is a membrane-bound exporter protein involved in regulating serum HDL level by exporting cholesterol and phospholipids to load up in lipid-poor ApoA-I and ApoE, which allows the formation of nascent HDL. Mutations in the ABCA1 gene, when presents in both alleles, disrupt the canonical function of ABCA1, which associates with many disorders related to lipid transport. Although many studies have reported the phenotypic effects of a large number of ABCA1 variants, the pathological effect of non-synonymous polymorphisms (nsSNPs) in ABCA1 remains elusive. Therefore, aiming at exploring the structural and functional consequences of nsSNPs in ABCA1, in this study, we employed an integrated computational approach consisting of nine well-known in silico tools to identify damaging SNPs and molecular dynamics (MD) simulation to get insights into the magnitudes of the damaging effects. In silico tools revealed four nsSNPs as being most deleterious, where the two SNPs (G1050V and S1067C) are identified as the highly conserved and functional disrupting mutations located in the NBD1 domain. MD simulation suggested that both SNPs, G1050V and S1067C, changed the overall structural flexibility and dynamics of NBD1, and induced substantial alteration in the structural organization of ATP binding site. Taken together, these findings direct future studies to get more insights into the role of these variants in the loss of the ABCA1 function.
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