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Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes
BACKGROUND: Actinomycetes are a diverse group of medically, industrially and ecologically important bacteria, studied as much for the diseases they cause as for the cures they hold. The genomes of actinomycetes revealed that these bacteria have a large number of natural product gene clusters, althou...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848822/ https://www.ncbi.nlm.nih.gov/pubmed/24020438 http://dx.doi.org/10.1186/1471-2164-14-611 |
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author | Doroghazi, James R Metcalf, William W |
author_facet | Doroghazi, James R Metcalf, William W |
author_sort | Doroghazi, James R |
collection | PubMed |
description | BACKGROUND: Actinomycetes are a diverse group of medically, industrially and ecologically important bacteria, studied as much for the diseases they cause as for the cures they hold. The genomes of actinomycetes revealed that these bacteria have a large number of natural product gene clusters, although many of these are difficult to tie to products in the laboratory. Large scale comparisons of these clusters are difficult to perform due to the presence of highly similar repeated domains in the most common biosynthetic machinery: polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). RESULTS: We have used comparative genomics to provide an overview of the genomic features of a set of 102 closed genomes from this important group of bacteria with a focus on natural product biosynthetic genes. We have focused on well-represented genera and determine the occurrence of gene cluster families therein. Conservation of natural product gene clusters within Mycobacterium, Streptomyces and Frankia suggest crucial roles for natural products in the biology of each genus. The abundance of natural product classes is also found to vary greatly between genera, revealing underlying patterns that are not yet understood. CONCLUSIONS: A large-scale analysis of natural product gene clusters presents a useful foundation for hypothesis formulation that is currently underutilized in the field. Such studies will be increasingly necessary to study the diversity and ecology of natural products as the number of genome sequences available continues to grow. |
format | Online Article Text |
id | pubmed-3848822 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-38488222013-12-04 Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes Doroghazi, James R Metcalf, William W BMC Genomics Research Article BACKGROUND: Actinomycetes are a diverse group of medically, industrially and ecologically important bacteria, studied as much for the diseases they cause as for the cures they hold. The genomes of actinomycetes revealed that these bacteria have a large number of natural product gene clusters, although many of these are difficult to tie to products in the laboratory. Large scale comparisons of these clusters are difficult to perform due to the presence of highly similar repeated domains in the most common biosynthetic machinery: polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). RESULTS: We have used comparative genomics to provide an overview of the genomic features of a set of 102 closed genomes from this important group of bacteria with a focus on natural product biosynthetic genes. We have focused on well-represented genera and determine the occurrence of gene cluster families therein. Conservation of natural product gene clusters within Mycobacterium, Streptomyces and Frankia suggest crucial roles for natural products in the biology of each genus. The abundance of natural product classes is also found to vary greatly between genera, revealing underlying patterns that are not yet understood. CONCLUSIONS: A large-scale analysis of natural product gene clusters presents a useful foundation for hypothesis formulation that is currently underutilized in the field. Such studies will be increasingly necessary to study the diversity and ecology of natural products as the number of genome sequences available continues to grow. BioMed Central 2013-09-11 /pmc/articles/PMC3848822/ /pubmed/24020438 http://dx.doi.org/10.1186/1471-2164-14-611 Text en Copyright © 2013 Doroghazi and Metcalf; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Doroghazi, James R Metcalf, William W Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes |
title | Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes |
title_full | Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes |
title_fullStr | Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes |
title_full_unstemmed | Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes |
title_short | Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes |
title_sort | comparative genomics of actinomycetes with a focus on natural product biosynthetic genes |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848822/ https://www.ncbi.nlm.nih.gov/pubmed/24020438 http://dx.doi.org/10.1186/1471-2164-14-611 |
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