Genome-wide analysis to detect multi-drug resistance genes in Mycobacterium tuberculosis strains SWLPK and MNPK resourced from Pakistan
Development of multidrug-resistant tuberculosis is the after effect of various mutational occasions, which leads to the development of protection from hostile to multiple tuberculosis drugs. In this study, we identified drug resistance genes, their evolutionary analysis, mutational variation, and do...
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Society of Eminent Biological Scientists
2022-03-01
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| Series: | International Journal of Applied and Experimental Biology |
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| Online Access: | https://submissions.eminentscientists.com/index.php/IJAEB/article/view/5 |
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| author | Maria Rafique Muhammad Ibrahim Sumaira Kanwal Habib Bokhari Farrukh Jamil Annam Hussain Muhammad Asif Rasheed |
| author_facet | Maria Rafique Muhammad Ibrahim Sumaira Kanwal Habib Bokhari Farrukh Jamil Annam Hussain Muhammad Asif Rasheed |
| author_sort | Maria Rafique |
| collection | DOAJ |
| description | Development of multidrug-resistant tuberculosis is the after effect of various mutational occasions, which leads to the development of protection from hostile to multiple tuberculosis drugs. In this study, we identified drug resistance genes, their evolutionary analysis, mutational variation, and docking to characterize the drug target potentials of two Mycobacterium tuberculosis strains SWLPK and MNPK resourced from Pakistan. For this purpose, we used different bioinformatics tools including the RAST server for annotation, and UniProt, NCBI, BLAST and MUSCLE for data retrieval and analysis. Evolutionary relationships were drawn using MEGA 7. A 3D structure was modelled by I-TASSER, while refinement and minimizations were performed using the UCSF Chimera 1.14.1. Moreover, the Ramachandran plot was used to check the quality of the proteins, while PatchDock was used for the docking analysis. Based on the comparison with the reference genome (M. tuberculosis H37RV), the SWLPK and MNPK strains encoded 24 multi-drug resistance genes. The drug resistance genes of nearby strains had developmental relatedness and comparable useful attributes imperative to their ecological specialties. The docking analysis revealed that the proteins accurately bound at their binding region just like the reference protein H37Rv (NuoG). We identified 24 multi-drug resistance genes in the SWLPK and MNPK strains. Moreover, there were a few missing drug resistance genes found in H37Rv, which were not present in the MNPK and SWLPK strains. The 24 genes reported in the MNPK and SWLPK strains might have a major contribution in drug resistance. |
| format | Article |
| id | doaj-art-56ae2f903a5b4c3db715ca64c843698c |
| institution | OA Journals |
| issn | 2790-6523 2790-6531 |
| language | English |
| publishDate | 2022-03-01 |
| publisher | Society of Eminent Biological Scientists |
| record_format | Article |
| series | International Journal of Applied and Experimental Biology |
| spelling | doaj-art-56ae2f903a5b4c3db715ca64c843698c2025-08-20T02:28:46ZengSociety of Eminent Biological ScientistsInternational Journal of Applied and Experimental Biology2790-65232790-65312022-03-0112495710.56612/ijaeb.v1i2.55Genome-wide analysis to detect multi-drug resistance genes in Mycobacterium tuberculosis strains SWLPK and MNPK resourced from PakistanMaria Rafique0Muhammad Ibrahim1Sumaira Kanwal2Habib Bokhari3Farrukh Jamil4Annam Hussain5Muhammad Asif Rasheed6Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, PakistanGenomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, PakistanGenomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, PakistanKohsar University Murree, KUM Admin/Academic Block, Kashmir Point Campus Murree, Punjab - PakistanGenomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, PakistanGenomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, PakistanGenomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, PakistanDevelopment of multidrug-resistant tuberculosis is the after effect of various mutational occasions, which leads to the development of protection from hostile to multiple tuberculosis drugs. In this study, we identified drug resistance genes, their evolutionary analysis, mutational variation, and docking to characterize the drug target potentials of two Mycobacterium tuberculosis strains SWLPK and MNPK resourced from Pakistan. For this purpose, we used different bioinformatics tools including the RAST server for annotation, and UniProt, NCBI, BLAST and MUSCLE for data retrieval and analysis. Evolutionary relationships were drawn using MEGA 7. A 3D structure was modelled by I-TASSER, while refinement and minimizations were performed using the UCSF Chimera 1.14.1. Moreover, the Ramachandran plot was used to check the quality of the proteins, while PatchDock was used for the docking analysis. Based on the comparison with the reference genome (M. tuberculosis H37RV), the SWLPK and MNPK strains encoded 24 multi-drug resistance genes. The drug resistance genes of nearby strains had developmental relatedness and comparable useful attributes imperative to their ecological specialties. The docking analysis revealed that the proteins accurately bound at their binding region just like the reference protein H37Rv (NuoG). We identified 24 multi-drug resistance genes in the SWLPK and MNPK strains. Moreover, there were a few missing drug resistance genes found in H37Rv, which were not present in the MNPK and SWLPK strains. The 24 genes reported in the MNPK and SWLPK strains might have a major contribution in drug resistance.https://submissions.eminentscientists.com/index.php/IJAEB/article/view/5antibioticsmulti-drug resistancegenomicsin silico analysisstrains |
| spellingShingle | Maria Rafique Muhammad Ibrahim Sumaira Kanwal Habib Bokhari Farrukh Jamil Annam Hussain Muhammad Asif Rasheed Genome-wide analysis to detect multi-drug resistance genes in Mycobacterium tuberculosis strains SWLPK and MNPK resourced from Pakistan International Journal of Applied and Experimental Biology antibiotics multi-drug resistance genomics in silico analysis strains |
| title | Genome-wide analysis to detect multi-drug resistance genes in Mycobacterium tuberculosis strains SWLPK and MNPK resourced from Pakistan |
| title_full | Genome-wide analysis to detect multi-drug resistance genes in Mycobacterium tuberculosis strains SWLPK and MNPK resourced from Pakistan |
| title_fullStr | Genome-wide analysis to detect multi-drug resistance genes in Mycobacterium tuberculosis strains SWLPK and MNPK resourced from Pakistan |
| title_full_unstemmed | Genome-wide analysis to detect multi-drug resistance genes in Mycobacterium tuberculosis strains SWLPK and MNPK resourced from Pakistan |
| title_short | Genome-wide analysis to detect multi-drug resistance genes in Mycobacterium tuberculosis strains SWLPK and MNPK resourced from Pakistan |
| title_sort | genome wide analysis to detect multi drug resistance genes in mycobacterium tuberculosis strains swlpk and mnpk resourced from pakistan |
| topic | antibiotics multi-drug resistance genomics in silico analysis strains |
| url | https://submissions.eminentscientists.com/index.php/IJAEB/article/view/5 |
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