Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery

Large-scale genome-mining analyses have identified an enormous number of cryptic biosynthetic gene clusters (BGCs) as a great source of novel bioactive natural products. Given the sheer number of natural product (NP) candidates, effective strategies and computational methods are keys to choosing appropriate BGCs for further NP characterization and production. This review discusses genomics-based approaches for prioritizing candidate BGCs extracted from large-scale genomic data, by highlighting studies that have successfully produced compounds with high chemical novelty, novel biosynthesis pathway, and potent bioactivities. We group these studies based on their BGC-prioritization logics: detecting presence of resistance genes, use of phylogenomics analysis as a guide, and targeting for specific chemical structures. We also briefly comment on the different bioinformatics tools used in the field and examine practical considerations when employing a large-scale genome mining study.     

鱼源致病菌皮特不动杆菌Ap-W20的全基因组序列及其毒力特征分析

皮特不动杆菌是一种新兴的鱼源致病菌,为了对该菌的致病机理进行研究并为该菌引起的鱼类疾病防治提供技术储备,实验选取皮特不动杆菌菌株Ap-W20进行了全基因组测序,并对其毒力特征进行了分析。结果发现,Ap-W20全基因组序列总长为4 399 705 bp,GC含量为38.78%,共预测到4 230个编码序列(CDS),存在4个质粒,GenBank数据库登录号为CP027658～CP027662。ANI分析结果证实,Ap-W20属于皮特不动杆菌,且ApW20与已知人源皮特不动杆菌AP₈82(96.69%)和环境源皮特不动杆菌PHEA-2(96.55%)相似度较高。Ap-W20与AP₈82、PHEA-2的比较基因组学分析发现,Ap-W20中的基因岛、前噬菌体和质粒数量最多,这很可能与它们各自的分离环境和致病力有关。通过与毒力因子数据库(VFDB)比对,在Ap-W20全基因组中预测到286个毒力基因,主要与黏附和抗吞噬等有关。Ap-W20中还存在Ⅰ、Ⅱ和Ⅵ型分泌系统、多套双组分调控系统以及细菌素合成基因簇等,表明鱼源皮特不动杆菌可能存在复杂的致病机制。...     

耐盐芽孢杆菌SF-18的生防潜能与基因组学分析

为从极端环境中分离具有优良抗菌活性的生物防治菌剂,采用稀释涂布平板法从新疆阿克苏盐碱地土样中分离筛选到1株具有明显抑菌作用的耐盐菌株SF-18;以大丽轮枝菌为指示菌,利用牛津杯法测定该菌株发酵液拮抗活性的稳定性,并利用2代和3代测序技术获得该菌株完整的基因组序列,对测序数据进行基因组装、预测、功能注释及次级代谢产物合成基因簇预测。结果显示,该菌株对金黄色葡萄球菌和大丽轮枝菌具有明显的抑制作用,能在18% NaCl的条件下生长;SF-18菌体发酵液在-20~80 ℃均具有较强的抑菌活性,能耐受pH 5~12的酸碱度环境;通过16S rDNA基因和gyrB基因序列分析,鉴定SF-18菌株隶属于芽孢杆菌属（Bacillus）;全基因序列分析结果显示菌株有480个基因参与了多种碳源的代谢,含有编码亚精胺和海藻糖等与菌株抗逆性相关化合物合成的基因,以及能够降解病原菌细胞壁的葡聚糖酶、几丁质酶等酶的相关基因;次生代谢产物预测分析SF-18含有合成bacillaene、bacillibactin等多种抗性化合物的基因簇,推测菌株SF-18可能通过产生抑菌性的次生代谢产物以及相关降解酶来达到抑菌的效果,在农业生物防治中具有较好的应用前景。     

昆虫病原真菌基因组学及多组学研究进展

昆虫病原真菌是重要的生物防治资源,利用昆虫病原真菌防治农业害虫具有不易产生抗性、易造成昆虫病害流行、生态安全环保等优势,推广应用昆虫病原真菌控制害虫是今后生态农业的发展趋势.现代测序技术的飞速发展促进了真菌基因组学的研究,在全基因组测序、系统发育基因组学、比较基因组学以及多组学(转录组学、蛋白组学、代谢组学)联合分析等...     

Multi-omics-driven development of alternative crops for natural rubber production

Natural rubber (NR) is an irreplaceable biopolymer of economic and strategic importance owing to its unique physical and chemical properties.  The Pará rubber tree (Hevea brasiliensis (Willd. ex A. Juss.) Müll. Arg.) is currently the exclusive commercial source of NR, and it is primarily grown in plantations restricted to the tropical and subtropical areas of Southeast Asia.  However, current Pará rubber production barely meets the sharply increasing global industrial demand for rubber.  Petroleum-based synthetic rubber (SR) has been used to supplement the shortage of NR but its industrial performance is not comparable to that of NR.  Thus, there is an urgent need to develop new productive rubber crops with broader environmental adaptability.  This review summarizes the current research progress on alternative rubber-producing plants, including horticultural plants (Taraxacum kok-saghyz Rodin and Lactuca L. species), woody plants (Parthenium argentatum A. Gray and Eucommia ulmoides Oliv.), and other plant species with potential for NR production.  With an emphasis on the molecular basis of NR biosynthesis revealed by a multi-omics approach, we highlight new integrative strategies and biotechnologies for exploring the mechanism of NR biosynthesis with a broader scope, which may accelerate the breeding and improvement of new rubber crops.      

芽孢杆菌蛋白酶基因的比较基因组学分析

【目的】研究芽孢杆菌产蛋白酶能力与携带的蛋白酶基因的关系，探寻影响芽孢杆菌产蛋白酶能 力的重要基因。【方法】通过 筛选培养基筛选能够产生蛋白酶的菌株，采用福林酚法 检测菌株产生的蛋白酶的活 性，对 15 株芽孢杆菌分离株进行全基因组测序，获得菌株染色体上携带的蛋白酶基因情况并将其分类；采用实 时荧光定量 PCR 方法检测蛋白酶基因 mRNA 的转录水平；通过比较基因组学和细菌全基因组关联分析（BGWAS）， 探讨影响细菌产蛋白酶能力高低的原因。【结果】根据菌株染色体上携带的蛋白酶基因情况，可分为 7 种基因 型（G1~G7）。比较基因组学和 BGWAS 分析发现，细菌染色体上携带的蛋白酶基因种类的多寡与其产蛋白酶能 力的高低有直接关系，且缺少 aprX 和 aprE 基因菌株的产蛋白酶能力明显下降。进一步研究基因 mRNA 水平发现， 芽孢杆菌产蛋白酶能力的差异与 aprX 的表达水平有关。【结论】 菌株染色体上携带的蛋白酶基因情况与菌株产 蛋白酶能力之间存在关联。aprX 是影响芽孢杆菌属细菌产胞外蛋白酶能力的重要基因。