Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes.
Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes.
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DOI：
10.1186/1471-2164-14-611
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发表时间：
2013-09-11
期刊：
影响因子：
4.4
通讯作者：
Metcalf WW
中科院分区：
文献类型：
--
作者：
Doroghazi JR;Metcalf WW
放线菌是一组不同的医学，工业和生态重要的细菌，研究了它们引起的疾病以及它们的治疗方法。放线菌的基因组显示，这些细菌有大量的天然产物基因簇，尽管其中许多很难在实验室中与产品联系起来。由于在最常见的生物合成机制中存在高度相似的重复结构域：聚酮酶（PKS）和非核糖体肽合成酶（NRPS），因此难以对这些簇进行大规模比较。我们已经使用比较基因组学提供了一组102个封闭的基因组的基因组特征的概述，从这个重要的细菌组，重点是天然产物的生物合成基因。我们专注于代表性很强的属，并确定其中基因簇家族的发生。分枝杆菌、链霉菌和弗兰克氏菌中天然产物基因簇的保护表明天然产物在每个属的生物学中发挥着至关重要的作用。天然产品种类的丰富程度也被发现在不同属之间差异很大，揭示了尚未被理解的潜在模式。天然产物基因簇的大规模分析为目前在该领域未得到充分利用的假设制定提供了有用的基础。随着可获得的基因组序列数量的不断增加，这类研究对于研究天然产物的多样性和生态学将越来越有必要。
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). 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. 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.
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DOI：
10.1126/science.1176667
发表时间：
2009-08-28
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Fischbach MA;Walsh CT
通讯作者：
Walsh CT
影响因子：
2.8
作者：
Challis, Gregory L.
通讯作者：
Challis, Gregory L.
影响因子：
11
作者：
Doroghazi, James R.;Buckley, Daniel H.
通讯作者：
Buckley, Daniel H.
影响因子：
14.8
作者：
Dunbar, Kyle L.;Melby, Joel O.;Mitchell, Douglas A.
通讯作者：
Mitchell, Douglas A.
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.