纳他霉素高产菌株Streptomyces gilvosporeus F607基因组及其生物合成基因簇分析

【背景】纳他霉素(Natamycin)是一种天然、广谱、高效的多烯大环内酯类抗真菌剂,褐黄孢链霉菌(Streptomyces gilvosporeus)是一种重要的纳他霉素产生菌。目前S. gilvosporeus基因组序列分析还未有报道,限制了该菌中纳他霉素及其他次级代谢产物合成及调控的研究。【目的】解析纳他霉素高产菌株S. gilvosporeus F607的基因组序列信息,挖掘其次级代谢产物基因资源,为深入研究该菌株的纳他霉素高产机理及生物合成调控机制奠定基础。【方法】利用相关软件对F607菌株的基因组序列进行基因预测、功能注释、进化分析和共线性分析,并预测次级代谢产物合成基因簇;对纳他霉素生物合成基因簇进行注释分析,比较分析不同菌种中纳他霉素生物合成基因簇的差异;分析预测S.gilvosporeusF607中纳他霉素生物合成途径。【结果】F607菌株基因组总长度为8482298bp,(G+C)mol%为70.95%,分别在COG、GO、KEGG数据库提取到5 062、4 428、5063个基因的注释信息。同时,antiSMASH软件预测得到29个次级代谢产物合成基因簇,其中纳他霉素基因簇与S.natalensis、S. chattanoogensis等菌株的纳他霉素基因簇相似性分别为81%和77%。除2个参与调控的sngT和sgnH基因和9个未知功能的orf基因有差异外,S. gilvosporeus F607基因簇中其他纳他霉素生物合成基因及其排列顺序与已知的纳他霉素基因簇高度一致。【结论】分析了S. gilvosporeus全基因组信息,预测了S. gilvosporeus F607中纳他霉素生物合成的途径,为从基因组层面上解析S. gilvosporeus F607菌株高产纳他霉素的内在原因提供了基础数据,为揭示纳他霉素高产的机理及工业化生产和未来新药的发现奠定了良好的基础。     

金霉素生物合成基因簇中调控基因ctcB的功能

【目的】研究金霉素产生菌中SARP家族转录调控基因ctc B的作用。【方法】利用大肠杆菌、链霉菌的属间接合转移和同源重组双交换的方法,构建ctc B基因缺失突变株。通过c DNA在相邻同转录方向的基因间隔进行PCR验证,确定金霉素生物合成基因簇中的转录单元。利用荧光定量RT-PCR方法进行突变株金霉素生物合成基因簇的转录水平检测。随后,生物信息学预测分析了金霉素生物合成基因簇内Ctc B与DNA的结合位点。【结果】获得了ctc B基因缺失的双交换突变株。发酵结果显示,该突变株失去产生金霉素与四环素的能力。金霉素生物合成基因簇内有6个共转录单元,其中4个共转录单元在ctc B基因缺失突变株中转录水平明显下降。软件分析预测到一致性较高的Ctc B结合重复序列。【结论】ctc B正调控金霉素生物合成结构基因ctc G-D、ctc H-K、ctc N-P、ctc W-T 4个转录单元和ctc Q,为进一步研究ctc B调控机制奠定了基础。     

雄烯二酮高产菌新金分枝杆菌MN4的全基因组测序及序列分析北大核心CSCD

【目的】新金分枝杆菌(Mycobacterium neoaurum)MN4是1株经诱变育种获得的高产雄烯二酮,并且能够耐受高浓度底物植物甾醇的突变菌株。为深入研究MN4菌株耐底物的机制及雄烯二酮的生物合成途径,有必要解析MN4菌株的全基因组序列信息。【方法】本研究采用高通量测序技术对MN4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装、基因预测与功能注释、COG聚类分析以及次级代谢产物合成基因簇预测等。【结果】新金分枝杆菌MN4基因组装获得33个Contigs,整个基因组大小为5.39 Mb,GC含量为66.9%,编码4920个蛋白基因,序列提交至Gen Bank数据库,登录号为JXYZ00000000。【结论】本研究首次报道了1株高产雄烯二酮菌株MN4的全基因组序列,分析了基因组的基本特征,初步解析了该菌株降解植物甾醇生产雄烯二酮的关键基因,将为MN4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。     

嗜热链球菌IMAU20246胞外多糖基因簇及其表达分析北大核心

【目的】嗜热链球菌IMAU20246是一株具有良好发酵特性且高产胞外多糖(exopolysaccharides,EPS)的菌株,但其EPS基因簇及合成途径尚不清晰。因此可通过全基因组测序及生物信息学分析菌株基因组序列,探究EPS合成及调控机制。【方法】本实验对嗜热链球菌IMAU20246进行全基因组测序并进行生物信息学分析,解析EPS生物合成相关基因簇及EPS合成途径,同时采用实时荧光定量PCR技术(quantitative real-time PCR,qRT-PCR)对其不同时间点EPS基因簇的表达进行定量分析。【结果】嗜热链球菌IMAU20246基因组中有一个18.1 kb的EPS生物合成基因簇,编码15个与EPS生物合成相关的基因。嗜热链球菌IMAU20246通过转运葡萄糖、甘露糖、果糖、半乳糖、乳糖、海藻糖、纤维二糖及蔗糖合成UDP-葡萄糖、dTDP-葡萄糖、dTDP-鼠李糖、UDP-半乳糖、UDP-呋喃半乳糖、UDP-N-乙酰葡萄糖胺和UDP-N-乙酰半乳糖胺等7种糖核苷酸。qRT-PCR的结果表明,EPS基因簇中的基因在细胞生长阶段均能表达,特别是糖基转移酶基因epsE、epsF、epsH和epsJ在培养6 h时表达量最高,此时EPS产量达到最高。【结论】本研究从基因组解析了嗜热链球菌IMAU20246 EPS基因簇及其合成途径,为菌株的进一步开发提供了理论依据。     

一株橡胶降解菌Rhizobacter gummiphilus NBRC109400的全基因组测序及功能挖掘

Rhizobacter gummiphilus NBRC 109400是一种新发现的具有降解天然橡胶能力的革兰氏阴性菌,为进一步探究该菌株降解天然橡胶的作用机制,挖掘菌株可能存在的功能特性,本研究使用第三代高通量测序技术对R. gummiphilus NBRC 109400进行全基因组测序,基于完成图进行基因预测、功能注释以及次级代谢产物合成基因簇预测,并对其橡胶降解蛋白进行挖掘。该菌株基因组大小为6 398 100 bp,GC含量为69.72%。该基因组共预测得到9个次级代谢产物合成基因簇,其中2号基因簇与来自菌株Delftia acidovorans SPH-1的delftibactin金生物矿化基因簇同源并进行了探究。定位了该菌株的橡胶降解关键蛋白LatA橡胶加氧酶,同时,预测到一个可能与菌株降解橡胶途经相关的同工蛋白CPZ87_07230。全基因组序列已提交至美国国立生物技术信息中心(NCBI)的GenBank数据库,登录号为CP024645。以上研究将为菌株NBRC 109400的功能基因组学研究及橡胶降解特性研究提供基础数据。     

环状芽孢杆菌泛基因组分析及次级代谢通路挖掘

旨为对环状芽孢杆菌基因组进行更深入的了解,并探索其次级代谢通路。从NCBI数据库下载了9个环状芽孢杆菌的基因组,利用系统发育分析软件、泛基因组分析软件和次级代谢产物挖掘软件对其进行了分析。9株菌的基因组大小在5.01-9.63Mb之间,在进化树上被归为了两个分支。通过泛基因组和核心基因组分析,发现其泛基因组含有9 572个基因家族,核心基因组由3 622个基因家族组成;共鉴定出4 593个特有基因,其中菌株NCTC2610的特有基因最多(3 030个),而菌株NBRC 13626的特有基因最少(39个)。通过次级代谢产物合成基因簇分析,9个环状芽孢杆菌基因组中共发现6类、32个次级代谢基因簇,重复出现最多的代谢通路是羊毛硫肽、套索肽和萜烯类化合物合成通路。通过本研究,明确了环状芽孢杆菌的泛基因组和核心基因组大小,预测了其次级代谢通路,有助于我们全面了解环状芽孢杆菌,为进一步更好地利用该菌株提供线索。     

Streptomyces sp.NO1W98中杀黑星菌素的分离和生物合成基因簇的鉴定

[目的] 分离Streptomyces sp.NO1W98中的杀黑星菌素并鉴定其生物合成基因簇。[方法] 利用有机溶剂萃取法对Streptomyces sp.NO1W98放大规模发酵产物进行提取;以正向、反向色谱柱层析进行化合物的分离纯化;借助波谱学手段进行单体化合物的结构鉴定;采用Illumina Hiseq技术进行基因组序列测定,对得到的序列进行生物信息学分析、注释并定位杀黑星菌素的生物合成基因簇vtd,利用基于PCR-targeting的遗传操作系统构建vtd内相关基因的阻断突变株,同时利用pSET152AKE进行基因回补,并分析与野生菌株的发酵产物差异。[结果] 从NO1W98发酵产物提取物中初步分离鉴定了2个大环内酯类化合物杀黑星菌素A（1）和B（2）;NO1W98的基因组大小约为11.6 Mb,蕴涵49个次级代谢产物生物合成基因簇,其中scaffold 3上的Region 3.3可能负责杀黑星菌素的生物合成;基因阻断和回补实验初步鉴定了杀黑星菌素的生物合成基因簇,包含6个骨架基因、5个转运基因、2个调控基因以及9个后修饰基因。[结论] 杀黑星菌素的分离、结构鉴定和基因簇的鉴定以及生物合成途径的推导为其遗传改造和工程菌株的构建奠定了分子基础。     

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。     

链霉菌Streptomyces antibioticus NRRL 8167中Naphthgeranine A生物合成基因簇的分析鉴定

【背景】微生物来源的天然产物是小分子药物或药物先导物的重要来源。对链霉菌Streptomyces antibioticus NRRL 8167的基因组分析显示,其包含多个次级代谢产物的生物合成基因簇,具有产生多种新化合物的潜力。【目的】对链霉菌S. antibioticus NRRL 8167中次级代谢产物进行研究,以期发现结构新颖或生物活性独特的化合物,并对相应产物的生物合成基因簇和生物合成途径进行解析。【方法】利用HPLC图谱结合特征性紫外吸收和LC-MS方法,排除S. antibioticus NRRL 8167产生的已知化合物,确定具有特殊紫外吸收的化合物作为挖掘对象,然后利用正、反相硅胶柱色谱、高效液相色谱等技术对次级代谢产物进行分离纯化,分离化合物。利用质谱及核磁共振光谱技术对化合物结构进行解析和鉴定;提取链霉菌S. antibioticus NRRL 8167基因组DNA,利用PacBio测序平台进行基因组测序;利用生物信息学对基因组进行注释,并对合成该化合物的基因簇进行定位分析,推导其生物合成途径。【结果】确定这个化合物是NaphthgeranineA,属于聚酮类化合物。全基因组序列分析发现S.antibioticusNRRL8167基因组含有28个次级代谢产物生物合成基因簇,其中基因簇20可能负责Naphthgeranine A的生物合成,并对其生物合成途径进行了推导。【结论】基于紫外吸收光谱和质谱特征,从S. antibioticus NRRL 8167菌株的发酵提取物中分离鉴定了一个聚酮类化合物Naphthgeranine A。该菌株的全基因组测序为其生物合成基因簇的鉴定提供了前提,对Naphthgeranine A生物合成基因簇和生物合成途径的推测为进一步研究这个化合物的生物合成机制奠定了基础。     

植物内生链霉菌Streptomyces sp. SAT1的基因组测序和比较基因组分析

【背景】一直以来,链霉菌都是活性物质的主要生产者,近年来随着抗生素滥用引起的环境和微生物抗药性问题越发严重,挖掘高效生物防治因子和新型抗生素成为了解决以上问题的重要手段。【目的】通过获得植物内生链霉菌SAT1全基因组序列和次级代谢基因簇信息,利用比较基因组学和泛基因组学分析SAT1菌株的特殊性以及与其他链霉菌的共性,为阐明SAT1抑菌和内生机制提供理论基础,为揭示链霉菌的生态功能提供可靠数据。【方法】通过三代测序平台PacBio Sequel完成SAT1基因组测序,利用生物信息学技术进行注释和功能基因分类;分别利用RAxML和PGAP软件进行系统发育树的构建和泛基因组分析;次级代谢基因簇的预测和分析通过antiSMASH网站完成。【结果】获得SAT1菌株的全基因组完成图,该菌线性染色体长度约7.47 Mb,包含有4个质粒,GC含量近73%,共预测到7 550个蛋白编码基因,含有37个次级代谢基因簇,分属29个类型,其中默诺霉素基因簇与加纳链霉菌具有较高相似性。42株代表链霉菌中,单个菌株次级代谢基因簇数量为20-55个,主要类型为PKS类、Terpene类和Nrps类,而且含有大量杂合基因簇,各个菌株中特有基因数目较为庞大。【结论】链霉菌SAT1菌株在基因组特点以及次级代谢基因簇的数量和类型上与其余41株链霉菌具有一定的共性,其中潮霉素B基因簇和默诺霉素基因簇合成的相关物质可能与SAT1抑菌活性密切相关。42株链霉菌中次级代谢基因簇数量的多少与基因组大小成正相关,同时大量杂合基因簇以及庞大的特有基因数目的存在说明链霉菌在长期进化过程中存在了很高程度的水平基因转移现象,可能具有重要的生态功能。     

Mechanism of the incidental production of a melanin-like pigment during 6-demethylchlortetracycline production in Streptomyces aureofaciens

The secondary metabolite 6-demethylchlortetracycline (6-DCT), which is produced by Streptomyces aureofaciens, is used as a precursor of semisynthetic tetracyclines. Strains that produce 6-DCT also produce a melanin-like pigment (MP). The correlation between MP production and 6-DCT production was investigated by using S. aureofaciens NRRL 3203. Production of both MP and 6-DCT was repressed by phosphate or ammonium ions, suggesting that syntheses of these compounds are controlled by the same regulators. Ten chlortetracycline-producing recombinants were derived from 6-DCT-producing mutant NRRL 3203 by gene replacement. All of the recombinants produced chlortetracycline but not MP, indicating that MP production is the results of a defect in the 6-methylation step and suggesting that the polyketide nonaketideamide is a common intermediate leading to MP as well as 6-DCT. To further examine the possibility that MP might be synthesized via the 6-DCT-biosynthetic pathway, mutants defective in 6-DCT biosynthesis were derived from a 6-DCT producer. Some of these mutants were able to produce MP, while others, including mutants with mutations in the gene encoding anhydrotetracycline oxygenase, an enzyme catalyzing the penultimate step in the pathway, produced neither 6-DCT nor MP. Production of 6-DCT and production of MP were restored simultaneously by integrative transformation with the corresponding 6-DCT-biosynthetic genes, indicating that some of 6-DCT-biosynthetic enzymes are indispensable for MP production. These findings suggest that a defect in the 6-methylation step results in redirection of carbon flux from a certain intermediate in the 6-DCT-biosynthetic pathway to a shunt pathway and results in MP production.     

Identification and cloning of the gene involved in the final step of chlortetracycline biosynthesis in Streptomyces aureofaciens

For chlortetracycline biosynthesis in Streptomyces aureofaciens, the final reduction step is essential to give an antibiotic activity to its intermediate, which is catalyzed by tetracycline dehydrogenase with 7,8-dedimethyl-8-hydroxy-5-deazariboflavin (FO) as a cofactor. We identified and cloned the gene, which is essential for the biosynthesis of 6-demethyltetracycline and participates in the final step of its biosynthesis, from the genomic DNA of the 6-demethyltetracycline producer S. aureofaciens HP77. DNA sequence analysis revealed that the gene (tchA) had an open reading frame of 455 amino acids with an estimated molecular mass of 48.1 kDa. Southern hybridization analysis revealed that the tchA gene was located external to the chlortetracycline biosynthetic gene cluster in the genome. A conserved domain search of protein sequence databases indicated that TchA showed a similarity to FbiB, which is involved in the modification of FO in Mycobacterium bovis.     

Complete genome sequence and analysis of the<Emphasis Type="Italic">Streptomyces aureofaciens</Emphasis> phage μ1/6

The entire double-stranded DNA genome of the Streptomyces aureofaciens phage mu1/6 was sequenced and analyzed. Its size is 38.194 kbp with an overall molar G+C content of 71.2 %. Fifty-two potential open reading frames (orfs) were identified, divided into two oppositely transcribed regions. In the left arm of the mu1/6 genome, an identified putative integrase and possible regulation proteins were identified. The rightwards transcribed region contains genes organized into apparently four functional units responsible for: (i) replication, (ii) DNA packaging and head assembly, (iii) tail morphogenesis, and (iv) lysis. Putative functions were assigned to twelve orfs based on bioinformatic analysis or experimental substantiation. Comparative analysis with three complete genomes of streptomycete phages revealed resemblance with respect to the organization of their genes into functional modules. Closer relationship was observed only between mu1/6 and S. venezuelae phage VWB.     

Fate of the biological control agent Pseudomonas aureofaciens TX-1 after application to turfgrass

The fate and impact of Pseudomonas aureofaciens TX-1 following application as a biocontrol agent for fungi in turfgrass were studied. The organism was applied with a modified irrigation system by using a preparation containing 1 x 10(6) P. aureofaciens TX-1 CFU ml(-1) about 100 times between May and August. We examined the impact of this repeated introduction of P. aureofaciens TX-1 (which is known to produce the antimicrobial compound phenazine-1-carboxylic acid) on the indigenous microbial community of the turfgrass system and on establishment of introduced bacteria in the soil system. A PCR primer-DNA hybridization probe combination was developed to accurately monitor the fate of P. aureofaciens TX-1 following application in irrigation water. To assess the impact of frequent P. aureofaciens TX-1 applications on the indigenous bacterial community, turfgrass canopy, thatch, and rhizosphere samples were obtained during the growing season from control and treated plots and subjected to DNA extraction procedures and denaturing gradient gel electrophoresis (DGGE). PCR amplification and hybridization of extracted DNA with the P. aureofaciens TX-1-specific primer-probe combination revealed that P. aureofaciens TX-1 not only became established in the rhizosphere and thatch but also was capable of overwintering. Separation of PCR-amplified partial 16S rRNA genes by DGGE showed that the repeated application of P. aureofaciens TX-1 in irrigation water resulted in transient displacement of a leaf surface bacterial community member. There was no obvious alteration of any dominant members of the thatch and rhizosphere microbial communities.     

透明颤菌血红蛋白基因表达对金色链霉菌生长代谢的影响

利用四环素抗性基因启动子在金色链霉菌中表达透明颤菌血红蛋白基因。在1m3发酵罐中研究了工程菌株的生长代谢特性。在溶解氧充足的条件下,透明颤菌血红蛋白表达,对金色链霉菌生长代谢未产生明显影响,工程菌株与参比菌株的生长代谢特性基本一致,工程菌株和参比菌株金霉素最终浓度分别为22905u/mL、22896u/mL。在低溶解氧条件下,透明颤菌血红蛋白的表达,可促进金色链霉菌菌体生长、菌丝活力保持和金霉素的合成：工程菌菌体浓度比参比菌株高5％～10％,产物合成提高11.4％。     

Tryptophan 7-halogenase from Pseudomonas aureofaciens ACN strain: gene cloning and sequencing and the enzyme expression

The gene of tryptophan 7-halogenase was isolated from the Pseudomonas aureofaciens ACN strain producing pyrrolnitrin, a chlorocontaining antibiotic, and sequenced. A high homology degree (over 95%) was established for the genes and the corresponding halogenases from P. aureofaciens ACN and P. fluorescens BL915. The tryptophan 7-halogenase gene was amplified by PCR, and the corresponding enzyme was expressed in Escherichia coli cells using the pBSII SK+ vector.     

Molecular cloning and sequencing of a non-haem bromoperoxidase gene from Streptomyces aureofaciens ATCC 10762.

A bromoperoxidase gene (bpoT), recently cloned from Streptomyces aureofaciens Tü24, was used as a probe in Southern blot hybridization of total DNA from S. aureofaciens ATCC 10762. A single SstI fragment of 5.4 kb was detected, which was cloned via an enriched gene library into Escherichia coli. The functional bromoperoxidase gene was located on a 2.1 kb BamHI-HindIII fragment by subcloning into S. lividans TK64, using the multicopy plasmid pIJ486. The enzyme was overproduced in S. lividans TK64 (up to 30,000 times compared to S. aureofaciens ATCC 10762) and showed the same electrophoretic and immunological properties as the bromoperoxidase BPO-A2 purified from S. aureofaciens ATCC 10762. DNA sequence analysis revealed an open reading frame encoding a predicted polypeptide with the same M(r) and N-terminal amino acid sequence as the purified subunit of BPO-A2.