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Integron Gene Cassettes: A Repository of Novel Protein Folds with Distinct Interaction Sites
Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those s...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548836/ https://www.ncbi.nlm.nih.gov/pubmed/23349695 http://dx.doi.org/10.1371/journal.pone.0052934 |
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author | Sureshan, Visaahini Deshpande, Chandrika N. Boucher, Yan Koenig, Jeremy E. Stokes, H. W. Harrop, Stephen J. Curmi, Paul M. G. Mabbutt, Bridget C. |
author_facet | Sureshan, Visaahini Deshpande, Chandrika N. Boucher, Yan Koenig, Jeremy E. Stokes, H. W. Harrop, Stephen J. Curmi, Paul M. G. Mabbutt, Bridget C. |
author_sort | Sureshan, Visaahini |
collection | PubMed |
description | Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-α, α+β and α/β fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein–protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions. |
format | Online Article Text |
id | pubmed-3548836 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-35488362013-01-24 Integron Gene Cassettes: A Repository of Novel Protein Folds with Distinct Interaction Sites Sureshan, Visaahini Deshpande, Chandrika N. Boucher, Yan Koenig, Jeremy E. Stokes, H. W. Harrop, Stephen J. Curmi, Paul M. G. Mabbutt, Bridget C. PLoS One Research Article Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-α, α+β and α/β fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein–protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions. Public Library of Science 2013-01-18 /pmc/articles/PMC3548836/ /pubmed/23349695 http://dx.doi.org/10.1371/journal.pone.0052934 Text en © 2013 Sureshan et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Sureshan, Visaahini Deshpande, Chandrika N. Boucher, Yan Koenig, Jeremy E. Stokes, H. W. Harrop, Stephen J. Curmi, Paul M. G. Mabbutt, Bridget C. Integron Gene Cassettes: A Repository of Novel Protein Folds with Distinct Interaction Sites |
title | Integron Gene Cassettes: A Repository of Novel Protein Folds with Distinct Interaction Sites |
title_full | Integron Gene Cassettes: A Repository of Novel Protein Folds with Distinct Interaction Sites |
title_fullStr | Integron Gene Cassettes: A Repository of Novel Protein Folds with Distinct Interaction Sites |
title_full_unstemmed | Integron Gene Cassettes: A Repository of Novel Protein Folds with Distinct Interaction Sites |
title_short | Integron Gene Cassettes: A Repository of Novel Protein Folds with Distinct Interaction Sites |
title_sort | integron gene cassettes: a repository of novel protein folds with distinct interaction sites |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548836/ https://www.ncbi.nlm.nih.gov/pubmed/23349695 http://dx.doi.org/10.1371/journal.pone.0052934 |
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