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Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi
Secondary metabolites (SM) produced by fungi and bacteria have long been of exceptional interest owing to their unique biomedical ramifications. The traditional discovery of new natural products that was mainly driven by bioactivity screening has now experienced a fresh new approach in the form of g...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449301/ https://www.ncbi.nlm.nih.gov/pubmed/30859257 http://dx.doi.org/10.1007/s00253-019-09708-z |
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author | Tran, Phuong Nguyen Yen, Ming-Ren Chiang, Chen-Yu Lin, Hsiao-Ching Chen, Pao-Yang |
author_facet | Tran, Phuong Nguyen Yen, Ming-Ren Chiang, Chen-Yu Lin, Hsiao-Ching Chen, Pao-Yang |
author_sort | Tran, Phuong Nguyen |
collection | PubMed |
description | Secondary metabolites (SM) produced by fungi and bacteria have long been of exceptional interest owing to their unique biomedical ramifications. The traditional discovery of new natural products that was mainly driven by bioactivity screening has now experienced a fresh new approach in the form of genome mining. Several bioinformatics tools have been continuously developed to detect potential biosynthetic gene clusters (BGCs) that are responsible for the production of SM. Although the principles underlying the computation of these tools have been discussed, the biological background is left underrated and ambiguous. In this review, we emphasize the biological hypotheses in BGC formation driven from the observations across genomes in bacteria and fungi, and provide a comprehensive list of updated algorithms/tools exclusively for BGC detection. Our review points to a direction that the biological hypotheses should be systematically incorporated into the BGC prediction and assist the prioritization of candidate BGC. |
format | Online Article Text |
id | pubmed-6449301 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-64493012019-04-17 Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi Tran, Phuong Nguyen Yen, Ming-Ren Chiang, Chen-Yu Lin, Hsiao-Ching Chen, Pao-Yang Appl Microbiol Biotechnol Mini-Review Secondary metabolites (SM) produced by fungi and bacteria have long been of exceptional interest owing to their unique biomedical ramifications. The traditional discovery of new natural products that was mainly driven by bioactivity screening has now experienced a fresh new approach in the form of genome mining. Several bioinformatics tools have been continuously developed to detect potential biosynthetic gene clusters (BGCs) that are responsible for the production of SM. Although the principles underlying the computation of these tools have been discussed, the biological background is left underrated and ambiguous. In this review, we emphasize the biological hypotheses in BGC formation driven from the observations across genomes in bacteria and fungi, and provide a comprehensive list of updated algorithms/tools exclusively for BGC detection. Our review points to a direction that the biological hypotheses should be systematically incorporated into the BGC prediction and assist the prioritization of candidate BGC. Springer Berlin Heidelberg 2019-03-12 2019 /pmc/articles/PMC6449301/ /pubmed/30859257 http://dx.doi.org/10.1007/s00253-019-09708-z Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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. |
spellingShingle | Mini-Review Tran, Phuong Nguyen Yen, Ming-Ren Chiang, Chen-Yu Lin, Hsiao-Ching Chen, Pao-Yang Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi |
title | Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi |
title_full | Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi |
title_fullStr | Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi |
title_full_unstemmed | Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi |
title_short | Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi |
title_sort | detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi |
topic | Mini-Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449301/ https://www.ncbi.nlm.nih.gov/pubmed/30859257 http://dx.doi.org/10.1007/s00253-019-09708-z |
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