Enabling Access to Novel Bacterial Biosynthetic Potential From ONT Draft Genomic Data

IF 5.7 2区 生物学
Marco A. Campos-Magaña, Vitor A. P. Martins dos Santos, Luis Garcia-Morales
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引用次数: 0

Abstract

Natural products comprise a wide diversity of compounds with a range of biological activities, including antibiotics, anti-inflammatory and anti-tumoral molecules. However, we can only access a small portion of these compounds due to various technical difficulties. We have herein developed a novel and efficient approach for accessing biosynthetic gene clusters (BGCs) that encode natural products from soil bacteria. The pipeline uses a combination of long-read sequencing, antiSMASH for BGC identification and Transformation-associated recombination (TAR) for cloning the BGCs. We hypothesized that a genome assembly using Oxford Nanopore Technology (ONT) sequencing could facilitate the detection of large BGCs at a relatively fast and low-cost DNA sequencing. Despite the relative low accuracy and sequence mistakes due to high GC content and sequence repetitions frequently found in BGC containing bacteria, we demonstrate that ONT long-read sequencing and antiSMASH are effective for identifying novel BGCs and enabling TAR cloning to isolate the BGC in a desired vector. We applied this pipeline on a previously non-sequenced myxobacteria Aetherobacter fasciculatus SBSr002. Our approach enabled us to clone a previously unknown BGC into a genome engineering-ready vector, illustrating the capabilities of this powerful and cost-effective strategy.

Abstract Image

从ONT基因组数据草案中获得新的细菌生物合成潜力
天然产物包括多种具有多种生物活性的化合物,包括抗生素、抗炎和抗肿瘤分子。然而,由于各种技术困难,我们只能获得这些化合物的一小部分。我们在此开发了一种新颖而有效的方法来获取编码土壤细菌天然产物的生物合成基因簇(bgc)。该流水线使用长读测序、用于BGC鉴定的anti - smash和用于克隆BGC的转化相关重组(TAR)的组合。我们假设使用牛津纳米孔技术(ONT)测序的基因组组装可以以相对快速和低成本的DNA测序方式促进大bgc的检测。尽管在含有BGC的细菌中经常发现由于高GC含量和序列重复而导致的相对较低的准确性和序列错误,但我们证明了ONT长读测序和反smash对于鉴定新的BGC和使TAR克隆能够在所需载体中分离BGC是有效的。我们将该管道应用于先前未测序的粘杆菌束状乙杆菌SBSr002。我们的方法使我们能够将以前未知的BGC克隆成基因组工程就绪的载体,说明了这种强大且具有成本效益的策略的能力。
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来源期刊
Microbial Biotechnology
Microbial Biotechnology Immunology and Microbiology-Applied Microbiology and Biotechnology
CiteScore
11.20
自引率
3.50%
发文量
162
审稿时长
1 months
期刊介绍: Microbial Biotechnology publishes papers of original research reporting significant advances in any aspect of microbial applications, including, but not limited to biotechnologies related to: Green chemistry; Primary metabolites; Food, beverages and supplements; Secondary metabolites and natural products; Pharmaceuticals; Diagnostics; Agriculture; Bioenergy; Biomining, including oil recovery and processing; Bioremediation; Biopolymers, biomaterials; Bionanotechnology; Biosurfactants and bioemulsifiers; Compatible solutes and bioprotectants; Biosensors, monitoring systems, quantitative microbial risk assessment; Technology development; Protein engineering; Functional genomics; Metabolic engineering; Metabolic design; Systems analysis, modelling; Process engineering; Biologically-based analytical methods; Microbially-based strategies in public health; Microbially-based strategies to influence global processes
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