Cargando…

In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil

BACKGROUND: Arsenite oxidase (EC 1.20.2.1) is a metalloenzyme that catalyzes the oxidation of arsenite into lesser toxic arsenate. In this study, 78 amino acid sequences of arsenite oxidase from unculturable bacteria available in metagenomic data of arsenic-contaminated soil have been characterized...

Descripción completa

Detalles Bibliográficos
Autores principales: Pal, Siddhartha, Sengupta, Kriti
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006529/
https://www.ncbi.nlm.nih.gov/pubmed/33779860
http://dx.doi.org/10.1186/s43141-021-00146-x
_version_ 1783672330299375616
author Pal, Siddhartha
Sengupta, Kriti
author_facet Pal, Siddhartha
Sengupta, Kriti
author_sort Pal, Siddhartha
collection PubMed
description BACKGROUND: Arsenite oxidase (EC 1.20.2.1) is a metalloenzyme that catalyzes the oxidation of arsenite into lesser toxic arsenate. In this study, 78 amino acid sequences of arsenite oxidase from unculturable bacteria available in metagenomic data of arsenic-contaminated soil have been characterized by using standard bioinformatics tools to investigate its phylogenetic relationships, three-dimensional structure and functional parameters. RESULTS: The phylogenetic relationship of all arsenite oxidase from unculturable microorganisms was revealed their closeness to bacterial order Rhizobiales. The higher aliphatic content showed that these enzymes are thermostable and could be used for in situ bioremediation. A representative protein from each phylogenetic cluster was analysed for secondary structure arrangements which indicated the presence of α-helices (~63%), β-sheets (57–60%) and turns (13–15%). The validated 3D models suggested that these proteins are hetero-dimeric with two chains whereas alpha chain is the main catalytic subunit which binds with arsenic oxides. Three representative protein models were deposited in Protein Model Database. The query enzymes were predicted with two conserved motifs, one is Rieske 3Fe-4S and the other is molybdopterin protein. CONCLUSIONS: Computational analysis of protein interactome revealed the protein partners might be involved in the whole process of arsenic detoxification by Rhizobiales. The overall report is unique to the best of our knowledge, and the importance of this study is to understand the theoretical aspects of the structure and functions of arsenite oxidase in unculturable bacteria residing in arsenic-contaminated sites. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s43141-021-00146-x.
format Online
Article
Text
id pubmed-8006529
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Springer Berlin Heidelberg
record_format MEDLINE/PubMed
spelling pubmed-80065292021-04-12 In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil Pal, Siddhartha Sengupta, Kriti J Genet Eng Biotechnol Research BACKGROUND: Arsenite oxidase (EC 1.20.2.1) is a metalloenzyme that catalyzes the oxidation of arsenite into lesser toxic arsenate. In this study, 78 amino acid sequences of arsenite oxidase from unculturable bacteria available in metagenomic data of arsenic-contaminated soil have been characterized by using standard bioinformatics tools to investigate its phylogenetic relationships, three-dimensional structure and functional parameters. RESULTS: The phylogenetic relationship of all arsenite oxidase from unculturable microorganisms was revealed their closeness to bacterial order Rhizobiales. The higher aliphatic content showed that these enzymes are thermostable and could be used for in situ bioremediation. A representative protein from each phylogenetic cluster was analysed for secondary structure arrangements which indicated the presence of α-helices (~63%), β-sheets (57–60%) and turns (13–15%). The validated 3D models suggested that these proteins are hetero-dimeric with two chains whereas alpha chain is the main catalytic subunit which binds with arsenic oxides. Three representative protein models were deposited in Protein Model Database. The query enzymes were predicted with two conserved motifs, one is Rieske 3Fe-4S and the other is molybdopterin protein. CONCLUSIONS: Computational analysis of protein interactome revealed the protein partners might be involved in the whole process of arsenic detoxification by Rhizobiales. The overall report is unique to the best of our knowledge, and the importance of this study is to understand the theoretical aspects of the structure and functions of arsenite oxidase in unculturable bacteria residing in arsenic-contaminated sites. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s43141-021-00146-x. Springer Berlin Heidelberg 2021-03-29 /pmc/articles/PMC8006529/ /pubmed/33779860 http://dx.doi.org/10.1186/s43141-021-00146-x Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Research
Pal, Siddhartha
Sengupta, Kriti
In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil
title In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil
title_full In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil
title_fullStr In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil
title_full_unstemmed In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil
title_short In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil
title_sort in silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006529/
https://www.ncbi.nlm.nih.gov/pubmed/33779860
http://dx.doi.org/10.1186/s43141-021-00146-x
work_keys_str_mv AT palsiddhartha insilicoanalysisofphylogenystructureandfunctionofarseniteoxidasefromunculturablemicrobiomeofarseniccontaminatedsoil
AT senguptakriti insilicoanalysisofphylogenystructureandfunctionofarseniteoxidasefromunculturablemicrobiomeofarseniccontaminatedsoil