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Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1
Deinococcus indicus DR1 is a novel Gram-negative bacterium, isolated from the Dadri wetlands in Uttar Pradesh, India. In addition to being radiation-resistant, the rod-shaped, red-pigmented organism shows extraordinary resistance to arsenic. The proteins of the corresponding ars gene cluster involve...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Research Network of Computational and Structural Biotechnology
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9807832/ https://www.ncbi.nlm.nih.gov/pubmed/36618989 http://dx.doi.org/10.1016/j.csbj.2022.12.015 |
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author | Ranganathan, Shrivaishnavi Sethi, Deepa Kasivisweswaran, Sandhya Ramya, L. Priyadarshini, Richa Yennamalli, Ragothaman M. |
author_facet | Ranganathan, Shrivaishnavi Sethi, Deepa Kasivisweswaran, Sandhya Ramya, L. Priyadarshini, Richa Yennamalli, Ragothaman M. |
author_sort | Ranganathan, Shrivaishnavi |
collection | PubMed |
description | Deinococcus indicus DR1 is a novel Gram-negative bacterium, isolated from the Dadri wetlands in Uttar Pradesh, India. In addition to being radiation-resistant, the rod-shaped, red-pigmented organism shows extraordinary resistance to arsenic. The proteins of the corresponding ars gene cluster involved in arsenic extrusion in D. indicus DR1 have not yet been characterized. Additionally, how these proteins regulate each other providing arsenic resistance is still unclear. Here, we present a computational model of the operonic structure and the corresponding characterization of the six proteins of the ars gene cluster in D. indicus DR1. Additionally, we show the expression of the genes in the presence of arsenic using qRT-PCR. The ars gene cluster consists of two transcriptional regulators (ArsR1, ArsR2), two arsenate reductases (ArsC2, ArsC3), one metallophosphatase family protein (MPase), and a transmembrane arsenite efflux pump (ArsB). The transcriptional regulators are trans-acting repressors, and the reductases reduce arsenate (As(5+)) ions to arsenite (As(3+)) ions for favourable extrusion. The proteins modelled using RoseTTAFold, and their conformationally stable coordinates obtained after MD simulation indicate their various functional roles with respect to arsenic. Excluding ArsB, all the proteins belong to the α + β class of proteins. ArsB, being a membrane protein, is fully α-helical, with 12 transmembrane helices. The results show the degree of similarity or divergence of the mechanism utilized by these proteins of ars gene cluster in D. indicus DR1 to confer high levels of arsenic tolerance. This structural characterization study of the ars genes will enable new and deeper insights of arsenic tolerance. |
format | Online Article Text |
id | pubmed-9807832 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Research Network of Computational and Structural Biotechnology |
record_format | MEDLINE/PubMed |
spelling | pubmed-98078322023-01-05 Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1 Ranganathan, Shrivaishnavi Sethi, Deepa Kasivisweswaran, Sandhya Ramya, L. Priyadarshini, Richa Yennamalli, Ragothaman M. Comput Struct Biotechnol J Research Article Deinococcus indicus DR1 is a novel Gram-negative bacterium, isolated from the Dadri wetlands in Uttar Pradesh, India. In addition to being radiation-resistant, the rod-shaped, red-pigmented organism shows extraordinary resistance to arsenic. The proteins of the corresponding ars gene cluster involved in arsenic extrusion in D. indicus DR1 have not yet been characterized. Additionally, how these proteins regulate each other providing arsenic resistance is still unclear. Here, we present a computational model of the operonic structure and the corresponding characterization of the six proteins of the ars gene cluster in D. indicus DR1. Additionally, we show the expression of the genes in the presence of arsenic using qRT-PCR. The ars gene cluster consists of two transcriptional regulators (ArsR1, ArsR2), two arsenate reductases (ArsC2, ArsC3), one metallophosphatase family protein (MPase), and a transmembrane arsenite efflux pump (ArsB). The transcriptional regulators are trans-acting repressors, and the reductases reduce arsenate (As(5+)) ions to arsenite (As(3+)) ions for favourable extrusion. The proteins modelled using RoseTTAFold, and their conformationally stable coordinates obtained after MD simulation indicate their various functional roles with respect to arsenic. Excluding ArsB, all the proteins belong to the α + β class of proteins. ArsB, being a membrane protein, is fully α-helical, with 12 transmembrane helices. The results show the degree of similarity or divergence of the mechanism utilized by these proteins of ars gene cluster in D. indicus DR1 to confer high levels of arsenic tolerance. This structural characterization study of the ars genes will enable new and deeper insights of arsenic tolerance. Research Network of Computational and Structural Biotechnology 2022-12-11 /pmc/articles/PMC9807832/ /pubmed/36618989 http://dx.doi.org/10.1016/j.csbj.2022.12.015 Text en © 2022 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Research Article Ranganathan, Shrivaishnavi Sethi, Deepa Kasivisweswaran, Sandhya Ramya, L. Priyadarshini, Richa Yennamalli, Ragothaman M. Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1 |
title | Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1 |
title_full | Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1 |
title_fullStr | Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1 |
title_full_unstemmed | Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1 |
title_short | Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1 |
title_sort | structural and functional mapping of ars gene cluster in deinococcus indicus dr1 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9807832/ https://www.ncbi.nlm.nih.gov/pubmed/36618989 http://dx.doi.org/10.1016/j.csbj.2022.12.015 |
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