Draft genome sequence of the marine bacterium Streptomyces griseoaurantiacus M045, which produces novel manumycin-type antibiotics with a pABA core component

Streptomyces griseoaurantiacus M045, isolated from marine sediment, produces manumycin and chinikomycin antibiotics. Here we present a high-quality draft genome sequence of S. griseoaurantiacus M045, the first marine Streptomyces species to be sequenced and annotated. The genome encodes several gene clusters for biosynthesis of secondary metabolites and has provided insight into genomic islands linking secondary metabolism to functional adaptation in marine S. griseoaurantiacus M045.     

海洋放线菌Streptomyces sp.大片段DNA基因组文库的构建

目的:构建稀有海洋放线菌Streptomyces sp.基因组文库.方法:以稀有海洋放线菌Streptomyces sp.为实验材料,随机剪切提取的总DNA,5'-磷酸末端补平回收40kb左右的DNA片段,与pWEBTM载体连接,经包装蛋白包装成噬菌体后侵染宿主细胞E.coli EPI100,构建该菌株的基因组文库,并对该文库进行质量鉴定.结果:成功构建了稀有海洋放线菌Streptomyces sp.的基因组文库,效价达9.0×104CFU/mL,得到4000个阳性克隆子,远远大于按覆盖率为99%计算至少所需的837个阳性克降子数,且平均插入片段长度为36kb,重组率100%.阳性克隆子保存于96孔板中,-80℃保存.结论:所构建文库的各项指标均达到要求,为了进一步评估Streptomyces sp.所能合成的所有潜在天然产物,还需要进一步检测该文库中包含有生物合成基因簇的大肠杆菌的表达情况.     

Genome sequence of Streptomyces sp. strain Tü6071

Streptomyces sp. Tü6071 is a soil-dwelling bacterium which has a highly active isoprenoid biosynthesis. Isoprenoids are important precursors for biopharmaceutical molecules such as antibiotics or anticancer agents, e.g., landomycin. Streptomyces sp. Tü6071 produces the industrially important terpene glycosides phenalinolactones, which have antibacterial activity against several Gram-positive bacteria. The availability of the genome sequence of Streptomyces sp. Tü6071 allows for understanding the biosynthesis of these pharmaceutical molecules and will facilitate rational genome modification to improve industrial use.     

Streptomyces sp. 173, an insecticidal micro-organism from marine

AIMS: To find new insecticidal antibiotics from marine micro-organisms. METHODS AND RESULTS: Strains isolated from seawater and sea sediments from Beidiahe and Dagang of the east coast of China were screened for their insecticidal qualities. The screening was carried out using bioassay of brine shrimp and the insect pest Helicoverpa armigera. The fermentation, preliminary extraction and isolation of Streptomyces sp.173 were carried out. CONCLUSIONS: In total 331 isolates were examined through bioassay of brine shrimp and 40 isolates (12.08%) showed potential insecticidal activities. Of the 40 isolates, one isolate, designated Streptomyces sp.173, was found to have strong insecticidal activity against both brine shrimp and H. armigera, similar to that of avermectin B1. SIGNIFICANCE AND IMPACT OF THE STUDY: The isolated Streptomyces sp.173 has great insecticidal potency. This work indicated that marine micro-organisms could be an important source of insecticidal antibiotics and the improved anti-brine shrimp bioassay is suitable for primary screening.     

Cloning and analysis of the simocyclinone biosynthetic gene cluster of <Emphasis Type="Italic">Streptomyces antibioticus</Emphasis> Tü 6040

The biosynthetic gene cluster of the aminocoumarin antibiotic simocyclinone D8 was cloned by screening a cosmid library of Streptomyces antibioticusTü 6040 with a heterologous probe from a gene encoding a cytochrome P450 enzyme involved in the biosynthesis of the aminocoumarin antibiotic novobiocin. Sequence analysis of a 39.4-kb region revealed the presence of 38 ORFs. Six of the identified ORFs showed striking similarity to genes from the biosynthetic gene clusters of the aminocoumarin antibiotics novobiocin and coumermycin A(1). Simocyclinone also contains an angucyclinone moiety, and 12 of the ORFs showed high sequence similarity to biosynthetic genes of other angucyclinone antibiotics. Possible functions within the biosynthesis of simocyclinone D8 could be assigned to 23 ORFs by comparison with sequences in GenBank. Experimental proof for the function of the identified gene cluster was provided by a gene inactivation experiment, which resulted in the abolishment of the formation of the aminocoumarin moiety of simocyclinone. Feeding of the mutant with the aminocoumarin moiety of novobiocin led to a new, artificial simocyclinone derivative.     

Draft genome sequence of the marine Streptomyces sp. strain PP-C42, isolated from the Baltic Sea

Streptomyces, a branch of aerobic Gram-positive bacteria, represents the largest genus of actinobacteria. The streptomycetes are characterized by a complex secondary metabolism and produce over two-thirds of the clinically used natural antibiotics today. Here we report the draft genome sequence of a Streptomyces strain, PP-C42, isolated from the marine environment. A subset of unique genes and gene clusters for diverse secondary metabolites as well as antimicrobial peptides could be identified from the genome, showing great promise as a source for novel bioactive compounds.     

Molecular basis for chloronium-mediated meroterpene cyclization: cloning, sequencing, and heterologous expression of the napyradiomycin biosynthetic gene cluster

Structural inspection of the bacterial meroterpenoid antibiotics belonging to the napyradiomycin family of chlorinated dihydroquinones suggests that the biosynthetic cyclization of their terpenoid subunits is initiated via a chloronium ion. The vanadium-dependent haloperoxidases that catalyze such reactions are distributed in fungi and marine algae and have yet to be characterized from bacteria. The cloning and sequence analysis of the 43-kb napyradiomycin biosynthetic cluster (nap) from Streptomyces aculeolatus NRRL 18422 and from the undescribed marine sediment-derived Streptomyces sp. CNQ-525 revealed 33 open reading frames, three of which putatively encode vanadium-dependent chloroperoxidases. Heterologous expression of the CNQ-525-based nap biosynthetic cluster in Streptomyces albus produced at least seven napyradiomycins, including the new analog 2-deschloro-2-hydroxy-A80915C. These data not only revealed the molecular basis behind the biosynthesis of these novel meroterpenoid natural products but also resulted in the first in vivo verification of vanadium-dependent haloperoxidases.     

芽孢杆菌SK007的分类鉴定及其拮抗植物病原菌的功能分析

【背景】农业生产中,发掘和利用具有生防功能的微生物资源是保障粮食安全和提高作物产量的重要举措。【目的】明确土壤中芽孢杆菌SK007的分类地位,验证其对多种植物病原菌的拮抗作用,挖掘潜在的生防功能。【方法】通过16SrRNA基因和基因组分析方法确定分离菌株SK007的分类地位;采用平板对峙法研究该菌株对番茄灰霉病菌、白菜黑斑病菌、烟草赤星病菌、小麦赤霉病菌、马铃薯干腐病菌等植物病原菌的拮抗作用;采用AntiSMASH分析和预测菌株SK007的抗生素相关基因。【结果】基于16SrRNA基因、全基因组序列、平均核苷酸一致性和DNA同源性分析,结果表明菌株SK007属于Bacillus velezensis,并且具有产生脂肽类抗生素和聚酮类抗生素的基因,对多种植物病原真菌有较强的抗性。此外,菌株SK007基因组中抗生素基因簇数目较多,丰富度高。【结论】芽孢杆菌SK007在拮抗植物病原菌方面有许多优良性状,具有促进作物抗病和增产的潜力。     

海洋放线菌Streptomyces variabilis strain 6-1次级代谢产物的研究

目的:对来自海洋软珊瑚的链霉菌6-1(Streptomyces variabilis strain 6-1)进行次级代谢产物的分离和鉴定,寻找具有生物活性的化合物,为人类健康服务。方法:采用液体培养基对分自海洋软珊瑚Scleronephthya sp中的链霉菌6-1(Streptomyces variabi-lis strain 6-1)进行发酵培养,用乙酸乙酯对发酵液进行萃取;采用半制备高效液相色谱(semi-preparative HPLC)分离方法对乙酸乙酯萃取物进行分离纯化,得到单体化合物;运用电喷雾质谱(ESI-MS)、核磁共氢振(1H NMR)、核磁共振碳谱(13C NMR)和物理性质对所得单体化合物进行结构鉴定。结果:从海洋链霉菌6-1(strain 6-1)发酵液的乙酸乙酯萃取物中分离得到3个单体化合物,分别鉴定为:7,4'-二羟基异黄酮(1)、5,7,4'-三羟基异黄酮(2)和丁烯酸内酯-Ⅰ(3)。结论:丁烯酸内酯-Ⅰ是从链霉菌属首次分离得到,化合物1和2均是从Streptomyces variabilis中首次分离得到;变异链霉菌6-1(Streptomyces variabilis strain 6-1)可以作为活性化合物3(丁烯酸内酯-Ⅰ)的重要来源。     

东乡野生稻内生放线菌Streptomyces sp. PRh5的全基因组测序及序列分析

【目的】Streptomyces sp. PRh5是从东乡野生稻(Oryza rufipogon Griff.)中分离获得的一株对细菌和真菌都具有较强抗菌活性的内生放线菌。为深入研究PRh5菌株抗菌机制及挖掘次级代谢产物基因资源,有必要解析PRh5菌株的基因组序列信息。【方法】采用高通量测序技术对PRh5菌株进行全基因组测序,然后使用相关软件对测序数据进行基因组组装、基因预测与功能注释、直系同源簇(COG)聚类分析、共线性分析及次级代谢产物合成基因簇预测等。【结果】基因组组装获得290 contigs,整个基因组大小约11.1 Mb,GC含量为71.1%,序列已提交至GenBank数据库,登录号为JABQ00000000。同时,预测得到50个次级代谢产物合成基因簇。【结论】将为Streptomyces sp. PRh5的功能基因组学研究及相关次级代谢产物的生物合成途径与异源表达研究提供基础。     

Genome Sequence of a New Streptomyces coelicolor Generalized Transducing Bacteriophage, ?CAM

Streptomyces coelicolor is a model system for the study of Streptomyces, a genus of bacteria responsible for the production of many clinically important antibiotics. Here we report the genome sequence of ϕCAM, a new S. coelicolor generalized transducing bacteriophage, isolated from a soil sample originating from Lincolnshire, United Kingdom. Many open reading frames within ϕCAM shared high levels of similarity to a prophage from Salinispora tropica and a putative prophage in Streptomyces sp. strain C.     

Microbial growth and production kinetics of Streptomyces antibioticus Tü 6040

Streptomyces antibioticus Tü 6040 is the producer of simocyclinones, which belong to a novel family of angucyclinone antibiotics some of which show antitumor activities. Growth and antibiotic production is dependent on the medium composition, especially on the carbon and nitrogen source, and on the fermentation conditions. The best results with respect to antibiotic productivity were achieved using a chemically defined medium with glycerol and L-lysine as carbon and nitrogen source, respectively, in an airlift fermenter with minimised shear stress at low gas flow rates withour oxygen limitation. These conditions led to a homogeneous formation of pellets of 1–2 mm in diameter and guaranteed reproducible product yields of the main compound, simocyclinone D8, in the range of 300 mg/l.     

海洋放线菌Streptomyces variabilisstrain 6-1次级代谢产物的研究

目的：对来自海洋软珊瑚的链霉菌6-1（Streptomyces variabilisstrain6-1）进行次级代谢产物的分离和鉴定,寻找具有生物活性的化合物,为人类健康服务。方法：采用液体培养基对分自海洋软珊瑚Scleronephthya sp中的链霉菌6．1（Streptomyces vafiabilisstrain6-1）进行发酵培养,用乙酸乙酯对发酵液进行萃取;采用半制备高效液相色谱（semi-preparative HPLC）分离方法对乙酸乙酯萃取物进行分离纯化,得到单体化合物;运用电喷雾质谱（ESI—MS）、核磁共氢振（1HNMR）、核磁共振碳谱（13C NMR）和物理性质对所得单体化合物进行结构鉴定。结果：从海洋链霉菌6-1（strain6-1）发酵液的乙酸乙酯萃取物中分离得到3个单体化合物,分别鉴定为：7,4’-二羟基异黄酮（1）、5,7,4’-三羟基异黄酮（2）和丁烯酸内酯-I（3）。结论：丁烯酸内酯．I是从链霉菌属首次分离得到,化合物1和2均是从Streptomyces variabilis中首次分离得到;变异链霉菌6-1（Stmptomyces variabilis strain6-1）可以作为活性化合物3（丁烯酸内酯-I）的重要来源。     

Bioconversion capacity ofStreptomyces sp GE44282, a producer of the antibiotics heneicomycin and aurodox

Streptomyces sp GE44282 was isolated in the course of a screening program for novel antibiotics. It co-produces heneicomycin and aurodox, two kirromycin-type antibiotics, which differ by the presence of an hydroxyl group at the C30 position of aurodox. Heneicomycin is converted into aurodox both by growing and resting cells ofStreptomyces sp GE44282 and by the producer of aurodox,Streptomyces goldiniensis ATCC 21386. This bioconversion of heneicomycin is substrate-specific and is not observed using the producer of heneicomycin,Streptomyces filippiniensis NRRL 11044. The three strains show very similar taxonomic characteristics. These results suggest that heneicomycin is a precursor of aurodox, the production of which depends on the bioconversion capability expressed by the strain.     

Isolation, characterization and antifungal activity of Streptomyces sampsonii GS 1322

For new antifungal antibiotics from actinomycetes, a strain of Streptomyces GS 1322 was isolated from a sample of garden soil. The strain was found to possess antagonistic activity against four fungi i.e., Candida albicans, Aspergillus niger, Microsporum gypseum and Trichophyton sp. The strain was identified as Streptomyces sampsonii and the antifungal compound produced by it was found to be the heptaene group of polyene antibiotics.     

Draft genome sequence of Streptomyces clavuligerus NRRL 3585, a producer of diverse secondary metabolites

Streptomyces clavuligerus is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics.     

Gephyromycin, the first bridged angucyclinone, from Streptomyces griseus strain NTK 14

The new, highly oxygenated angucyclinone gephyromycin was isolated from an extract of a Streptomyces griseus strain. Its unprecedented ether-bridged structure was elucidated by NMR methods and substantiated by single crystal X-ray analysis. The absolute configuration was evidenced by quantum chemical CD calculations. Gephyromycin exhibits glutaminergic activity towards neuronal cells. Furthermore, the known compounds fridamycin E and dehydrorabelomycin were identified.     

Streptopyrrolidine, an angiogenesis inhibitor from a marine-derived Streptomyces sp. KORDI-3973

Streptopyrrolidine, a benzyl pyrrolidine derivative, was isolated as an angiogenesis inhibitor from the fermentation broth of a marine Streptomyces sp. isolated from the deep sea sediment. Its structure was elucidated by extensive 2D NMR and mass spectroscopic analyses. Streptopyrrolidine exhibited significant anti-angiogenesis activity.     

阿维菌素的生物合成及代谢工程研究进展

阿维菌素(avermectin)是由除虫链霉菌(Streptomycesavermitilis)产生的一种具有杀虫活性的大环内酯类抗生素,在农业和畜牧业中应用广泛。本文综述了有关除虫链霉菌基因组序列分析、阿维菌素的生物合成以及阿维菌素育种和代谢工程的研究进展。     

Draft genome sequence of the marine sediment-derived actinomycete Streptomyces xinghaiensis NRRL B24674T

Actinobacteria are a rich source of novel natural products. We recently characterized Streptomyces xinghaiensis NRRL B24674(T) as a novel species of marine origin. Here we report the draft genome sequence of this species. This is the first validly published marine streptomycete for which a genome sequence has been presented.