Discovery of recombinases enables genome mining of cryptic biosynthetic gene clusters in Burkholderiales species.
Discovery of recombinases enables genome mining of cryptic biosynthetic gene clusters in Burkholderiales species.
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重组酶的发现使得对伯克霍尔德氏菌目中隐秘的生物合成基因簇的基因组挖掘成为可能。
DOI：
10.1073/pnas.1720941115
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发表时间：
2018-05-01
影响因子：
11.1
通讯作者：
Zhang Y
中科院分区：
文献类型：
--
作者：
Wang X;Zhou H;Chen H;Jing X;Zheng W;Li R;Sun T;Liu J;Fu J;Huo L;Li YZ;Shen Y;Ding X;Müller R;Bian X;Zhang Y
由隐基因簇生物合成的天然产物代表了一个很大程度上未开发的药物发现来源。然而，通过启动子工程挖掘这些产物受到缺乏流线型遗传工具的限制，特别是在非模式生物合成基因簇（BGC）丰富的细菌中。在这里，我们描述了一对噬菌体重组酶的发现，以及重组酶辅助启动子工程的应用，以快速识别和激活两种目前缺乏有效遗传工具的Burkholderiales菌株中的几个隐藏的生物合成基因簇。在天然产物生产者中构建高效的基因组工程平台，加快了对其原生背景下的隐性bgc的挖掘，以及对宿主进行产量或结构优化的改进。这一策略使得从许多其他细菌中发现具有有趣生物活性的新型代谢物成为可能。细菌基因组编码许多隐生生物合成基因簇（BGCs），这些基因簇代表了很大程度上未开发的药物或农药来源。由于当地生产者无法获得简化的遗传工具，对隐产品的开采受到限制。利用噬菌体重组酶进行精确的基因组工程对基因组挖掘特别有用。然而，重组酶通常是宿主特异性的。基因组引导下新重组酶的发现及其瞬时表达可以促进隐性BGC的挖掘。在此，我们报道了一个遗传系统，利用来自Burkholderiales菌株DSM 7029的红色重组酶，对目前缺乏有效遗传工具的几种Burkholderiales物种进行了高效的基因组工程。利用特殊的重组酶辅助原位插入功能启动子，我们成功地挖掘了5个隐型非核糖体肽合成酶/聚酮合成酶BGCs，其中2个是沉默的。通过广泛的光谱表征鉴定了两类脂肽，glidopeptin和rhizomides。这种重组酶表达策略在其他细菌物种中也很有用，允许生物勘探潜在的可扩展发现具有吸引人的生物活性的新型代谢物。
Natural products biosynthesized by cryptic gene clusters represent a largely untapped source for drug discovery. However, mining of these products by promoter engineering is restricted by the lack of streamlined genetic tools, especially in nonmodel biosynthetic gene cluster (BGC)-rich bacteria. Here, we describe the discovery of a pair of bacteriophage recombinases and application of recombinase-assisted promoter engineering to rapidly identify and activate several cryptic biosynthetic gene clusters in two Burkholderiales strains that currently lack effective genetic tools. Construction of an efficient genome engineering platform in a natural product producer expedites mining of cryptic BGCs in their native backgrounds, and host melioration for yield or structure optimization. This strategy enables potentially scalable discovery of novel metabolites with intriguing bioactivities from many other bacteria. Bacterial genomes encode numerous cryptic biosynthetic gene clusters (BGCs) that represent a largely untapped source of drugs or pesticides. Mining of the cryptic products is limited by the unavailability of streamlined genetic tools in native producers. Precise genome engineering using bacteriophage recombinases is particularly useful for genome mining. However, recombinases are usually host-specific. The genome-guided discovery of novel recombinases and their transient expression could boost cryptic BGC mining. Herein, we reported a genetic system employing Red recombinases from Burkholderiales strain DSM 7029 for efficient genome engineering in several Burkholderiales species that currently lack effective genetic tools. Using specialized recombinases-assisted in situ insertion of functional promoters, we successfully mined five cryptic nonribosomal peptide synthetase/polyketide synthase BGCs, two of which were silent. Two classes of lipopeptides, glidopeptins and rhizomides, were identified through extensive spectroscopic characterization. This recombinase expression strategy offers utility within other bacteria species, allowing bioprospecting for potentially scalable discovery of novel metabolites with attractive bioactivities.
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DOI：
10.3390/molecules15010001
发表时间：
2009-12-24
期刊：
Molecules (Basel, Switzerland)
影响因子：
--
作者：
Avci-Adali M;Paul A;Wilhelm N;Ziemer G;Wendel HP
通讯作者：
Wendel HP
DOI：
10.1073/pnas.121164898
发表时间：
2001-06-05
影响因子：
11.1
作者：
Ellis, HM;Yu, DG;Court, DL
通讯作者：
Court, DL
伯克霍尔德氏菌基因组对非核糖体肽合成酶的挖掘揭示了新型铁载体和脂肽合成的巨大潜力。
影响因子：
3.4
作者：
Esmaeel Q;Pupin M;Kieu NP;Chataigné G;Béchet M;Deravel J;Krier F;Höfte M;Jacques P;Leclère V
通讯作者：
Leclère V
影响因子：
3.4
作者：
Bachmann, Brian O.;Van Lanen, Steven G.;Baltz, Richard H.
通讯作者：
Baltz, Richard H.
影响因子：
5.6
作者：
EGAN, SM;SCHLEIF, RF
通讯作者：
SCHLEIF, RF