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Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei
The Burkholderia genus includes many species that are known to survive in diverse environmental conditions including low nutrient environments. One species, Burkholderia pseudomallei is a versatile pathogen that can survive in a wide range of hosts and environmental conditions. In this study, we inv...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719362/ https://www.ncbi.nlm.nih.gov/pubmed/29215024 http://dx.doi.org/10.1038/s41598-017-17356-4 |
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author | Mohd-Padil, Hirzahida Damiri, Nadzirah Sulaiman, Suhaila Chai, Shiao-Fei Nathan, Sheila Firdaus-Raih, Mohd |
author_facet | Mohd-Padil, Hirzahida Damiri, Nadzirah Sulaiman, Suhaila Chai, Shiao-Fei Nathan, Sheila Firdaus-Raih, Mohd |
author_sort | Mohd-Padil, Hirzahida |
collection | PubMed |
description | The Burkholderia genus includes many species that are known to survive in diverse environmental conditions including low nutrient environments. One species, Burkholderia pseudomallei is a versatile pathogen that can survive in a wide range of hosts and environmental conditions. In this study, we investigated how a nutrient depleted growth environment evokes sRNA mediated responses by B. pseudomallei. Computationally predicted B. pseudomallei D286 sRNAs were mapped to RNA-sequencing data for cultures grown under two conditions: (1) BHIB as a nutrient rich media reference environment and (2) M9 media as a nutrient depleted stress environment. The sRNAs were further selected to identify potentially cis-encoded systems by investigating their possible interactions with their flanking genes. The mappings of predicted sRNA genes and interactions analysis to their flanking genes identified 12 sRNA candidates that may possibly have cis-acting regulatory roles that are associated to a nutrient depleted growth environment. Our approach can be used for identifying novel sRNA genes and their possible role as cis-mediated regulatory systems. |
format | Online Article Text |
id | pubmed-5719362 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-57193622017-12-08 Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei Mohd-Padil, Hirzahida Damiri, Nadzirah Sulaiman, Suhaila Chai, Shiao-Fei Nathan, Sheila Firdaus-Raih, Mohd Sci Rep Article The Burkholderia genus includes many species that are known to survive in diverse environmental conditions including low nutrient environments. One species, Burkholderia pseudomallei is a versatile pathogen that can survive in a wide range of hosts and environmental conditions. In this study, we investigated how a nutrient depleted growth environment evokes sRNA mediated responses by B. pseudomallei. Computationally predicted B. pseudomallei D286 sRNAs were mapped to RNA-sequencing data for cultures grown under two conditions: (1) BHIB as a nutrient rich media reference environment and (2) M9 media as a nutrient depleted stress environment. The sRNAs were further selected to identify potentially cis-encoded systems by investigating their possible interactions with their flanking genes. The mappings of predicted sRNA genes and interactions analysis to their flanking genes identified 12 sRNA candidates that may possibly have cis-acting regulatory roles that are associated to a nutrient depleted growth environment. Our approach can be used for identifying novel sRNA genes and their possible role as cis-mediated regulatory systems. Nature Publishing Group UK 2017-12-07 /pmc/articles/PMC5719362/ /pubmed/29215024 http://dx.doi.org/10.1038/s41598-017-17356-4 Text en © The Author(s) 2017 Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Mohd-Padil, Hirzahida Damiri, Nadzirah Sulaiman, Suhaila Chai, Shiao-Fei Nathan, Sheila Firdaus-Raih, Mohd Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei |
title | Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei |
title_full | Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei |
title_fullStr | Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei |
title_full_unstemmed | Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei |
title_short | Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei |
title_sort | identification of srna mediated responses to nutrient depletion in burkholderia pseudomallei |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719362/ https://www.ncbi.nlm.nih.gov/pubmed/29215024 http://dx.doi.org/10.1038/s41598-017-17356-4 |
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