slnN基因在盐霉素生物合成中的调控功能分析

【目的】研究盐霉素生物合成基因簇上游潜在调控基因slnN的功能。【方法】本实验利用遗传操作技术,分别对白色链霉菌出发菌株Streptomyces albus BK3-25中的slnN基因进行敲除和过表达,然后利用抑菌圈实验和发酵实验,分别检测不同衍生菌株中盐霉素生物合成产量的变化。同时利用qRT-PCR分析衍生菌株与原始出发菌株之间的结构基因表达差异。【结果】结果表明在slnN基因缺失株(slnNDM)中,盐霉素的表达水平提高了35%左右;而在slnN基因过表达株(slnNOE)中,盐霉素产量下降达43%左右。qRT-PCR分析进一步发现slnN基因缺失,会引起slnO和slnA1基因的上调;而slnN基因过表达后,一方面会下调slnO与slnA1基因的表达,另一方面引起slnT1、slnF基因上调。【结论】本研究证实slnN基因对盐霉素的生物合成具有明显的负调控作用,其机制有待进一步研究。     

卡西霉素生物合成基因簇中调控基因calR1的功能

【背景】卡西霉素(calcimycin)是重要的离子载体抗生素,其生物合成基因簇已从教酒链霉菌NRRL3882的基因组DNA中成功克隆,但基因簇内的部分生物合成基因及调控基因的功能有待研究。【目的】研究卡西霉素产生菌教酒链霉菌NRRL3882中编码TylR家族同源转录调控蛋白的calR1基因的功能。【方法】通过PCR-targeting的方法,构建calR1基因敲除突变株及回补菌株,对突变菌株及回补菌株进行发酵,通过HPLC分析其代谢产物。利用荧光定量PCR检测ΔcalR1突变菌株和野生菌株的生物合成基因转录水平。【结果】calR1基因敲除突变株丧失产生卡西霉素的能力,但仍有中间产物噻唑霉素的积累,回补菌株中卡西霉素的产量有一定程度的恢复。RT-qPCR结果表明,卡西霉素合成相关的一些重要基因calC、calG、calU3等基因的表达量明显改变。【结论】TylR家族转录调控基因calR1是卡西霉素生物合成的调控基因。     

卡西霉素生物合成调控基因calR2的功能

【背景】卡西霉素(Calcimycin)是由教酒链霉菌NRRL3882产生的吡咯聚醚类抗生素,结构独特且具有广泛的生物活性,但其生物合成调控机制尚不清楚。【目的】研究卡西霉素生物合成基因簇上编码LuxR家族同源蛋白的潜在调控基因calR2的功能。【方法】通过PCR-targeting的方法对卡西霉素基因簇上的calR2基因进行中断,HPLC对突变株及回补菌株的代谢产物进行分析。利用荧光定量RT-PCR分析ΔcalR2突变菌株和野生菌株的基因转录水平差异。【结果】calR2基因中断的突变株不能产生卡西霉素,回补菌株则恢复产生卡西霉素的能力。RT-PCR结果表明卡西霉素生物合成的一些重要骨架基因在ΔcalR2突变株中的转录水平明显降低。【结论】LuxR家族转录调控基因calR2在卡西霉素生物合成过程中起正调控作用。     

杀念菌素/FR-008生物合成途径中转运基因fscTI与fscTII的功能

摘要:【目的】分析杀念菌素/FR-008 生物合成途径中转运基因fscTI和fscTII的功能。【方法】构建转运基因fscTI和fscTII的敲除质粒pJTU4137,并通过接合转移和同源重组双交换的方法得到转运基因缺失突变株。转运基因fscTI和fscTII也被克隆到高拷贝质粒pJTU1278上用于在链霉菌FR-008(Streptomyces sp．FR-008)的衍生菌株ZYJ-6中进行转运蛋白的过量表达。【结果】获得了转运蛋白缺失的双交换突变株LX10,发酵结果显示该突变株不再产生杀念菌素及其衍生物;过量表达转运蛋白的基因工程菌株LX11,其杀念菌素的产量约是对照菌株的1.5倍。【结论】体内遗传实验进一步证实FR-008生物合成途径中的fscTI和fscTII是ATP依赖的ABC转运基因,fscTI与fscTII的过量表达增加了杀念菌素的产量,为利用此方法提高其它多烯类抗生素的产量提供了例证。     

适用于链霉菌大片段基因组DNA 克隆和异源表达的细菌人工染色体(BAC)载体的构建及应用

【目的】很多链霉菌来源的天然产物的生物合成基因簇往往很大,用传统的cosmid载体很难完整的克隆和异源表达。本研究通过载体改造,成功构建出一个新的细菌人工染色体(BAC)载体,用于链霉菌来源的天然产物生物合成基因簇的克隆及异源表达实验。【方法】从复合型载体pCUGIBAC1出发,通过λRED介导的PCR-targeting方法,用链霉素抗性基因替换掉原有的氯霉素抗性基因标记,同时插入链霉菌中常用的安普拉霉素抗性标记、转移起始位点oriT、φC31整合酶基因int、整合位点attP等元件。【结果】成功构建出可装载链霉菌大片段DNA的BAC载体pMSBBACs。使用pMSBBACs构建出链霉菌U27的基因组BAC文库,平均插入片段大小为100 kb。选取其中一个大小为140 kb的BAC质粒进行功能验证,实验证明通过接合转移和原生质体转化的方法都能够将这个大型BAC质粒导入链霉菌模式菌株,并通过位点特异性重组整合到染色体中进行异源表达。【结论】BAC载体pMSBBACs可成功用于放线菌大片段基因组DNA的克隆和异源表达实验。     

林可链霉菌NRRL 2936中帕马霉素生物合成基因簇的异源 表达及调控基因功能研究

【背景】帕马霉素属于大环内酯类抗生素,具有较好的抗感染活性。该类化合物独特的化学结构和显著的生理活性受到了许多研究者的关注。同时,本实验室在林可链霉菌NRRL2936的全基因组序列中发现了帕马霉素的生物合成基因簇。【目的】尽管其生物合成途径已经得到了解析,但其生物合成基因簇中的2个调控基因功能尚不清楚。本研究从林可链霉菌NRRL2936的基因组文库中克隆了含有帕马霉素生物合成完整基因簇的质粒pJQK450,开展了质粒pJQK450在链霉菌中的异源表达,实现了帕马霉素的异源合成,并初步确定该生物合成基因簇中两个调控基因的功能。【方法】利用聚合酶链式反应递缩基因组文库筛选的方法,从林可链霉菌(Streptomyces lincolnensis)NRRL 2936基因组文库中筛选到了含有帕马霉素生物合成完整基因簇的Fosmid质粒pJQK450。然后,将该质粒转化到E.coli ET12567/pUZ8002中,利用大肠杆菌-链霉菌双亲接合转移的方法将pJQK450转入异源宿主中。对获得的异源表达菌株进行发酵产物的制备,采用耻垢分枝杆菌mc2155作为指示菌株进行帕马霉素生物活性测试,并结合LC-MS的分析确定帕马霉素的产生情况。最后,通过基因失活与回补的方法,考察帕马霉素生物合成基因簇中调控蛋白PamR1和PamR2对帕马霉素生物合成的影响。【结果】帕马霉素生物合成基因簇在天蓝色链霉菌M1154中实现了表达,证明PamR1和PamR2负调控了帕马霉素生物合成的过程。【结论】帕马霉素完整基因簇的成功异源表达,一方面便于其生物合成途径的遗传改造,为帕马霉素的生物合成及优产改造研究奠定了基础;另外,调控基因功能的研究为帕马霉素的产量优化提供了改造的目标。     

春雷霉素低产和高产菌株的比较基因组分析

氨基糖苷类抗生素春雷霉素由春雷链霉菌和小金色链霉菌产生,广泛应用于农业病害的防治。本研究利用二代和三代测序技术相结合的策略对低产的春雷链霉菌BCRC12349(Streptomyces kasugaensis BCRC12349,LY)和高产的小金色链霉菌XM301(S.microaureus XM301,HY)进行了全基因组测序,发现高产菌株染色体比低产菌株小了将近200 kb。比较基因组分析发现,与低产菌株相比,高产菌株中存在41个插入缺失(In Del)和164个单碱基突变位点(SNV)。基于RNA-seq的比较转录组分析发现,高产菌株中的一些初级代谢关键基因、春雷霉素前体合成相关基因、春雷霉素生物合成基因簇内部基因的转录发生了上调。同时发现基因组中调控基因有44个显著上调、16个显著下调,转运蛋白基因有32个显著上调、11个显著下调。高产菌株和低产菌株基因组和转录组的比较分析为春雷霉素产生菌的进一步高产改造提供了理论基础。     

圈卷产色链霉菌san7324和san7324L基因阻断对形态分化和尼可霉素产生的影响

【目的】圈卷产色链霉菌全局性调控基因wblA阻断突变后,尼可霉素不再产生。RNA-seq和转录分析表明san7324基因在野生型菌株中可以正常转录,而在wblA阻断突变株(ΔwblA)中不能转录,为此本文旨在揭示san7324与尼可霉素产生的关系。【方法】利用同源双交换策略对san7324进行基因阻断,而后通过基因遗传回补及对尼可霉素生物合成相关基因的转录分析等方法研究san7324的功能。【结果】在相同培养条件下,阻断突变株Δsan7324与野生型菌株相比失去了合成尼可霉素的能力。我们通过同源比对发现圈卷产色链霉菌中还存在一个与san7324同源的基因san7324L,该基因的阻断导致尼可霉素产量降低。当san7324和san7324L两个基因同时被阻断后,得到的突变株Δsan7324-san7324L生长稀疏而且不能正常发育分化形成灰色表型的孢子或孢子链,只能形成白色表型的气生菌丝,同时也丧失了合成尼可霉素的能力。当这两个基因(san7324-san7324L)回补双突变株后,则恢复了野生型的表型(能形成孢子链并恢复尼可霉素的产生)。进一步的研究初步表明san7324和san7324L的阻断主要影响了尼可霉素生物合成基因簇中途径特异性调控基因sanG的转录水平,从而影响圈卷产色链霉菌的发育分化和尼可霉素的产生。【结论】该结果为链霉菌形态分化与生理代谢关系的研究提供了更多的证据,同时为多效调控基因wblA作用机制的阐明奠定了基础。     

黄脂菌素生物合成基因簇中调控基因xanR3的功能

【目的】研究黄脂菌素产生菌灰黄链霉菌中编码ArsR家族转录调控蛋白(Arsenical resistance regulator)的xanR3基因的功能。【方法】利用大肠杆菌和链霉菌双亲本接合转移的方法,构建xanR3基因缺失突变株及回补突变株。利用cDNA在相邻同方向的基因间隔区进行PCR确定黄脂菌素生物合成基因簇中的转录单元。利用荧光定量RT-PCR方法进行突变株中黄脂菌素生物合成基因簇转录水平的检测。【结果】对得到的xanR3基因缺失突变株及回补突变株进行发酵,发现xanR3基因缺失突变株产黄脂菌素能力下降,回补菌株中黄脂菌素产量相比缺失突变株有一定程度的恢复,但仍未达到野生型水平。经鉴定,黄脂菌素生物合成基因簇中共有18个共转录单元,其中4个共转录单元在?xanR3突变株中转录水平明显下降。【结论】ArsR家族转录调控基因xanR3是黄脂菌素生物合成的正调控基因。     

ABC转运蛋白SgnA/B促进纳他霉素胞外转运与高产

纳他霉素是一种天然、广谱、高效的多烯大环内酯类还原性抗真菌剂,广泛应用于食品真菌污染的防治和临床真菌感染的治疗。纳他霉素胞外转运效率可能是限制褐黄孢链霉菌(Streptomyces gilvosporeus)发酵高产纳他霉素的重要因素。通过生物信息学及分子对接技术分析纳他霉素胞外转运蛋白SgnA/B,发现SgnA和SgnB两个异源二聚体组成的ABC转运蛋白是内向开口构象的转运蛋白,且2个结合位点与纳他霉素结合能力有强弱差异,更有利于纳他霉素的胞外转运。本研究以纳他霉素生产菌株——褐黄孢链霉菌F607为出发菌株,构建了sgnA/B基因超表达菌株F-EX,以分析sgn A/B基因超表达对纳他霉素合成及胞外转运的影响。研究发现,纳他霉素对数合成期的F-EX菌株不仅提高了纳他霉素胞外/胞内比,其120 h发酵总产量也提高了12.5%,达到7.38 g/L。最后,通过转录组测序发现,sgnA/B基因超表达除提高纳他霉素胞外转运效率外,还影响了与多种氨基酸、丙酸盐、糖、五碳化合物代谢和TCA循环相关基因的表达。研究表明,强化纳他霉素胞外转运有利于纳他霉素的合成,是提高褐黄孢链霉菌纳他霉素产量的有效...     

变铅青链霉菌广谱胁迫蛋白对氧化压力响应的研究

【目的】广谱胁迫蛋白(USP)是一种古老的蛋白家族,在链霉菌属细菌中其功能研究尚未报道。以变铅青链霉菌USP蛋白为对象对其功能进行解析。【方法】使用序列比对的方法分析同源性及保守结构域。纯化USP蛋白,用圆二色谱分析蛋白与环腺苷酸(cAMP)的结合对usp(SLI_7517)进行基因中断。检测野生型和usp基因缺失株对偶氮二甲酰胺造成的氧化压力的耐受能力。使用qPCR荧光定量分析技术,检测野生型菌株与usp缺失株在氧化环境中谷胱甘肽过氧化物酶及巯基过氧化物酶基因转录量的差异。【结果】同源序列分析表明链霉菌属来源的USP蛋白序列相互之间相似性较高,USP-like结构域高度保守。USP蛋白在体外结合cAMP引起CD谱的变化。usp基因缺失株对偶氮二甲酰胺更耐受,同时菌株中谷胱甘肽过氧化物酶基因转录量上升。【结论】变铅青链霉菌中USP蛋白能够结合cAMP。usp参与菌体应对氧化环境的调控,对谷胱甘肽过氧化物酶基因的转录有阻遏作用。     

Improved Production of Mannanase by Streptomyces lividans

Replacement of the natural promoter of the (beta)-mannanase gene of Streptomyces lividans by lacp resulted in a 15-fold increase in enzyme production over that of the previously reported clone S. lividans IAF36, a clone carrying multiple copies of manA, and a 350-fold increase over that of the wild-type strain S. lividans 1326. In addition, the use of lacp in the shuttle vector pIAF199 allowed synthesis of the enzymes on carbon sources that did not contain mannan, such as xylan and whey, which offers interesting possibilities for industrial production of the enzyme.     

Molecular cloning of streptomyces genes encoding vanillate demethylase

The vanillate demethylase genes from Streptomyces sp. NL15-2K were cloned and sequenced. The vanA and vanB gene homologs, which encode the terminal oxygenase subunit (VanA) and the ferredoxin-type reductase subunit (VanB) of the enzyme respectively, were found in the sequenced 7.5-kb DNA region. Expression of the vanAB genes in Streptomyces lividans 1326 resulted in in vivo demethylation of veratric acid to vanillic acid.     

华癸根瘤菌外膜孔蛋白编码基因MCHK_1326突变株的构建与共生固氮表型分析

【目的】Mesorhizobium huakuii 7653R的MCHK_1326基因编码一种外膜孔蛋白,可能参与根瘤菌侵染宿主植物以及结瘤固氮过程,本研究旨在探索该基因在共生固氮中的功能。【方法】生物信息学分析MCHK_1326蛋白的结构特征及生物学功能,启动子原位表达技术检测MCHK_1326共生时空表达特征,利用Cre-loxp系统构建MCHK_1326缺失突变株,考察其共生固氮表型及早期侵染事件,通过植物盆栽并额外添加无机氮源,检测突变株接种紫云英后的共生固氮表型变化。【结果】MCHK_1326基因在侵染早期如侵染线的延伸等过程中表达,在成熟根瘤的侵染区表达,与野生型相比,突变体△1326侵染线和根瘤原基数量显著减少;植株地上部分鲜重与固氮酶活性极显著降低,根瘤数量和根瘤重量显著降低;额外添加无机氮源能恢复其共生缺陷表型。【结论】MCHK_1326基因参与根瘤菌早期侵染和结瘤,在根瘤发育与共生固氮过程中发挥作用。     

Cloning and characterization of the polyether salinomycin biosynthesis gene cluster of Streptomyces albus XM211

Salinomycin is widely used in animal husbandry as a food additive due to its antibacterial and anticoccidial activities. However, its biosynthesis had only been studied by feeding experiments with isotope-labeled precursors. A strategy with degenerate primers based on the polyether-specific epoxidase sequences was successfully developed to clone the salinomycin gene cluster. Using this strategy, a putative epoxidase gene, slnC, was cloned from the salinomycin producer Streptomyces albus XM211. The targeted replacement of slnC and subsequent trans-complementation proved its involvement in salinomycin biosynthesis. A 127-kb DNA region containing slnC was sequenced, including genes for polyketide assembly and release, oxidative cyclization, modification, export, and regulation. In order to gain insight into the salinomycin biosynthesis mechanism, 13 gene replacements and deletions were conducted. Including slnC, 7 genes were identified as essential for salinomycin biosynthesis and putatively responsible for polyketide chain release, oxidative cyclization, modification, and regulation. Moreover, 6 genes were found to be relevant to salinomycin biosynthesis and possibly involved in precursor supply, removal of aberrant extender units, and regulation. Sequence analysis and a series of gene replacements suggest a proposed pathway for the biosynthesis of salinomycin. The information presented here expands the understanding of polyether biosynthesis mechanisms and paves the way for targeted engineering of salinomycin activity and productivity.     

The very large amplifiable element AUD2 from Streptomyces lividans 66 has insertion sequence-like repeats at its ends.

In a spontaneous, chloramphenicol-sensitive (Cms), arginine-auxotrophic (Arg-) mutant of Streptomyces lividans 1326, two amplified DNA sequences were found. One of them was the well-characterized 5.7-kb ADS1 sequence, amplified to about 300 copies per chromosome. The second one was a 92-kb sequence called ADS2. ADS2 encoding the previously isolated mercury resistance genes of S. lividans was amplified to around 20 copies per chromosome. The complete ADS2 sequence was isolated from a genomic library of the mutant S. lividans 1326.32, constructed in the phage vector lambda EMBL4. In addition, the DNA sequences flanking the corresponding amplifiable element called AUD2 in the wild-type strain were isolated by using another genomic library prepared from S. lividans 1326 DNA. Analysis of the ends of AUD2 revealed the presence of an 846-bp sequence on both sides repeated in the same orientation. Each of the direct repeats ended with 18-bp inverted repeated sequences. This insertion sequence-like structure was confirmed by the DNA sequence determined from the amplified copy of the direct repeats which demonstrated a high degree of similarity of 65% identity in nucleic acid sequence to IS112 from Streptomyces albus. The recombination event leading to the amplification of AUD2 occurred within these direct repeats, as shown by DNA sequence analysis. The amplification of AUD2 was correlated with a deletion on one side of the flanking chromosomal region beginning very near or in the amplified DNA. Strains of S. lividans like TK20 and TK21 which are mercury sensitive have completely lost AUD2 together with flanking chromosomal DNA on one or both sides.     

Relationship of an unstable argG gene to a 5.7-kilobase amplifiable DNA sequence in Streptomyces lividans 66.

The relationship between an unstable argG gene and a 5.7-kilobase (kb) amplifiable DNA sequence in Streptomyces lividans 66 was investigated. Spontaneous, high-frequency Arg mutants deleted for this gene typically contain 200 to 300 copies of the tandemly reiterated sequence. A library of S. lividans 66 (strain 1326) wild-type genomic DNA was prepared in the vector lambda Charon 35. Chromosome walking over 44 kb established that argG is located 25 kb distant from a duplicated amplifiable DNA structure. A sequence was characterized, located farther distal from the amplifiable structure, containing strong homology with an internal sequence of the amplifiable DNA, which may have a role in the deletion of argG. Genetic mapping showed that argG and the 5.7-kb amplifiable sequence are linked to another unstable gene, determining chloramphenicol resistance (Camr) and that together these genes may be located in a silent chromosomal arc.     

Streptomyces coelicolor A3(2) lacks a genomic island present in the chromosome of Streptomyces lividans 66

Streptomyces lividans ZX1 has become a preferred host for DNA cloning in Streptomyces species over its progenitor, the wild-type strain 66 (stock number 1326 from the John Innes Center collection), especially when stable DNA is crucial for in vitro electrophoresis, because DNA from strain 66 contains a novel modification that makes it sensitive to oxidative double-strand cleavage during electrophoresis. Detailed analysis of this modification-deficient mutant (ZX1) revealed that it has several additional phenotypic traits associated with a chromosomal deletion of ca. 90 kb, which was cloned and mapped by using a cosmid library. Comparative sequence analysis of two clones containing the left and right deletion ends originating from strain 66 and one clone with the deletion and fused sequence cloned from strain ZX1 revealed a perfect 15-bp direct repeat, which may have mediated deletion and fusion to yield strain ZX1 by site-specific recombination. Analysis of AseI linking clones in the deleted region in relation to the published AseI map of strain ZX1 yielded a complete AseI map for the S. lividans 66 genome, on which the relative positions of a cloned phage phiHAU3 resistance (phiHAU3r) gene and the dnd gene cluster were precisely localized. Comparison of S. lividans ZX1 and its progenitor 66, as well as the sequenced genome of its close relative, Streptomyces coelicolor M145, reveals that the ca. 90-kb deletion in strain ZX1 may have originated from an insertion from an unknown source.