Substrate DNA Promoting Binding of <i>Mycobacterium tuberculosis</i> MtrA by Facilitating Dimerization and Interpretation of Affinity by Minor Groove Width
In order to deepen the understanding of the role and regulation mechanisms of prokaryotic global transcription regulators in complex processes, including virulence, the associations between the affinity and binding sequences of <i>Mycobacterium tuberculosis</i> MtrA have been explored ex...
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MDPI AG
2023-10-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/10/2505 |
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| author | Aadil Ahmed Memon Xiang Fu Xiao-Yong Fan Lingyun Xu Jihua Xiao Mueed Ur Rahman Xiaoqi Yang Yu-Feng Yao Zixin Deng Wei Ma |
| author_facet | Aadil Ahmed Memon Xiang Fu Xiao-Yong Fan Lingyun Xu Jihua Xiao Mueed Ur Rahman Xiaoqi Yang Yu-Feng Yao Zixin Deng Wei Ma |
| author_sort | Aadil Ahmed Memon |
| collection | DOAJ |
| description | In order to deepen the understanding of the role and regulation mechanisms of prokaryotic global transcription regulators in complex processes, including virulence, the associations between the affinity and binding sequences of <i>Mycobacterium tuberculosis</i> MtrA have been explored extensively. Analysis of MtrA 294 diversified 26 bp binding sequences revealed that the sequence similarity of fragments was not simply associated with affinity. The unique variation patterns of GC content and periodical and sequential fluctuation of affinity contribution curves were observed along the sequence in this study. Furthermore, docking analysis demonstrated that the structure of the dimer MtrA-DNA (high affinity) was generally consistent with other OmpR family members, while Arg 219 and Gly 220 of the wing domain interacted with the minor groove. The results of the binding box replacement experiment proved that box 2 was essential for binding, which implied the differential roles of the two boxes in the binding process. Furthermore, the results of the substitution of the nucleotide at the 20th and/or 21st positions indicated that the affinity was negatively associated with the value of minor groove width precisely at the 21st position. The dimerization of the unphosphorylated MtrA facilitated by a low-affinity DNA fragment was observed for the first time. However, the proportion of the dimer was associated with the affinity of substrate DNA, which further suggested that the affinity was actually one characteristic of the stability of dimers. Based on the finding of 17 inter-molecule hydrogen bonds identified in the interface of the MtrA dimer, including 8 symmetric complementary ones in the conserved α4-β5-α5 face, we propose that hydrogen bonds should be considered just as important as salt bridges and the hydrophobic patch in the dimerization. Our comprehensive study on a large number of binding fragments with quantitative affinity values provided new insight into the molecular mechanism of dimerization, binding specificity and affinity determination of MtrA and clues for solving the puzzle of how global transcription factors regulate a large quantity of target genes. |
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| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T21:01:39Z |
| publishDate | 2023-10-01 |
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| series | Microorganisms |
| spelling | doaj.art-6b7fa4dc893f4cad993e2da9c1157b4d2023-11-19T17:27:47ZengMDPI AGMicroorganisms2076-26072023-10-011110250510.3390/microorganisms11102505Substrate DNA Promoting Binding of <i>Mycobacterium tuberculosis</i> MtrA by Facilitating Dimerization and Interpretation of Affinity by Minor Groove WidthAadil Ahmed Memon0Xiang Fu1Xiao-Yong Fan2Lingyun Xu3Jihua Xiao4Mueed Ur Rahman5Xiaoqi Yang6Yu-Feng Yao7Zixin Deng8Wei Ma9State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, ChinaState Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, ChinaShanghai Institute of Infectious Diseases and Biosecurity, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, ChinaShanghai Huaxin Biotechnology Co., Ltd., Room 604, Building 1, Tongji Chuangyuan, No. 99 South Changjiang Road, Baoshan District, Shanghai 200441, ChinaShanghai Huaxin Biotechnology Co., Ltd., Room 604, Building 1, Tongji Chuangyuan, No. 99 South Changjiang Road, Baoshan District, Shanghai 200441, ChinaState Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, ChinaShanghai Huaxin Biotechnology Co., Ltd., Room 604, Building 1, Tongji Chuangyuan, No. 99 South Changjiang Road, Baoshan District, Shanghai 200441, ChinaLaboratory of Bacterial Pathogenesis, Institutes of Medical Sciences, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, ChinaState Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, ChinaState Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, ChinaIn order to deepen the understanding of the role and regulation mechanisms of prokaryotic global transcription regulators in complex processes, including virulence, the associations between the affinity and binding sequences of <i>Mycobacterium tuberculosis</i> MtrA have been explored extensively. Analysis of MtrA 294 diversified 26 bp binding sequences revealed that the sequence similarity of fragments was not simply associated with affinity. The unique variation patterns of GC content and periodical and sequential fluctuation of affinity contribution curves were observed along the sequence in this study. Furthermore, docking analysis demonstrated that the structure of the dimer MtrA-DNA (high affinity) was generally consistent with other OmpR family members, while Arg 219 and Gly 220 of the wing domain interacted with the minor groove. The results of the binding box replacement experiment proved that box 2 was essential for binding, which implied the differential roles of the two boxes in the binding process. Furthermore, the results of the substitution of the nucleotide at the 20th and/or 21st positions indicated that the affinity was negatively associated with the value of minor groove width precisely at the 21st position. The dimerization of the unphosphorylated MtrA facilitated by a low-affinity DNA fragment was observed for the first time. However, the proportion of the dimer was associated with the affinity of substrate DNA, which further suggested that the affinity was actually one characteristic of the stability of dimers. Based on the finding of 17 inter-molecule hydrogen bonds identified in the interface of the MtrA dimer, including 8 symmetric complementary ones in the conserved α4-β5-α5 face, we propose that hydrogen bonds should be considered just as important as salt bridges and the hydrophobic patch in the dimerization. Our comprehensive study on a large number of binding fragments with quantitative affinity values provided new insight into the molecular mechanism of dimerization, binding specificity and affinity determination of MtrA and clues for solving the puzzle of how global transcription factors regulate a large quantity of target genes.https://www.mdpi.com/2076-2607/11/10/2505<i>Mycobacterium tuberculosis</i>MtrAquantitative affinityminor groove width (MGW)dimerization |
| spellingShingle | Aadil Ahmed Memon Xiang Fu Xiao-Yong Fan Lingyun Xu Jihua Xiao Mueed Ur Rahman Xiaoqi Yang Yu-Feng Yao Zixin Deng Wei Ma Substrate DNA Promoting Binding of <i>Mycobacterium tuberculosis</i> MtrA by Facilitating Dimerization and Interpretation of Affinity by Minor Groove Width Microorganisms <i>Mycobacterium tuberculosis</i> MtrA quantitative affinity minor groove width (MGW) dimerization |
| title | Substrate DNA Promoting Binding of <i>Mycobacterium tuberculosis</i> MtrA by Facilitating Dimerization and Interpretation of Affinity by Minor Groove Width |
| title_full | Substrate DNA Promoting Binding of <i>Mycobacterium tuberculosis</i> MtrA by Facilitating Dimerization and Interpretation of Affinity by Minor Groove Width |
| title_fullStr | Substrate DNA Promoting Binding of <i>Mycobacterium tuberculosis</i> MtrA by Facilitating Dimerization and Interpretation of Affinity by Minor Groove Width |
| title_full_unstemmed | Substrate DNA Promoting Binding of <i>Mycobacterium tuberculosis</i> MtrA by Facilitating Dimerization and Interpretation of Affinity by Minor Groove Width |
| title_short | Substrate DNA Promoting Binding of <i>Mycobacterium tuberculosis</i> MtrA by Facilitating Dimerization and Interpretation of Affinity by Minor Groove Width |
| title_sort | substrate dna promoting binding of i mycobacterium tuberculosis i mtra by facilitating dimerization and interpretation of affinity by minor groove width |
| topic | <i>Mycobacterium tuberculosis</i> MtrA quantitative affinity minor groove width (MGW) dimerization |
| url | https://www.mdpi.com/2076-2607/11/10/2505 |
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