负调节基因nsdA在链霉菌中同源性及激活沉默抗生素合成基因簇的研究

nsdA基因是在天蓝色链霉菌中发现的抗生素合成负调控基因。以nsdA基因片段为探针,通过Southern杂交发现nsdA存在于多种链霉菌中。根据天蓝色链霉菌和阿维链霉菌的nsdA序列设计PCR引物,扩增多种链霉菌中nsdA基因并测序。发现在不同链霉菌中nsdA基因的相似性高达77%～100%。其中变铅青链霉菌与天蓝色链霉菌A3(2)的nsdA序列100%一致。变铅青链霉菌通常不合成放线紫红素,中断nsdA获得的突变菌株WQ2能够合成放线紫红素;在WQ2中重新引入野生型nsdA,又失去产抗生素能力。表明nsdA的中断可以激活变铅青链霉菌中沉默的放线紫红素生物合成基因簇的表达;nsdA的广泛存在及其序列高度保守则提示可以尝试用于这些菌种的抗生素高产育种。     

利迪链霉菌nsdA基因的克隆及其阻断载体的构建

[目的]构建nsdA基因的敲除载体和表达载体,获得阳性转化子。[方法]根据GenBank中报道的天蓝色链霉菌nsdA基因序列设计引物,在利迪链霉菌产纳他霉素菌株A01、A02和G117中扩增到预期目的片段,进一步克隆nsdA基因全长序列;经BLAST比对,其核苷酸序列及其编码蛋白的氨基酸序列与天蓝色链霉菌均有较高同源性,据此判断利迪链霉菌A01、A02、G117中含有nsdA基因;进一步构建nsdA基因的敲除载体pLM103和表达载体pIBN139,转入大肠杆菌ET12567(puz8002)。[结果]nsdA基因全长序列1 407 bp,编码468个氨基酸,构建了nsdA基因的敲除载体pLM103和表达载体pIBN139。[结论]成功构建nsdA基因的敲除载体pLM103和表达载体pIBN139,并获得阳性转化子,为后续构建利迪链霉菌nsdA基因阻断突变株,以进一步探究nsdA基因在利迪链霉菌纳他霉素生物合成中的调控作用奠定了基础。     

大肠杆菌甲基转移酶dcm基因的表达对变铅青链霉菌的多效性影响

【目的】大肠杆菌的dcm基因编码的DNA甲基转移酶可以特异性地将5′CCWGG3′(W=A/T)序列中第二个胞嘧啶变成5-甲基胞嘧啶。Dcm甲基转移酶发现已有37年了,但其确切的功能不明,本篇主要研究其对变铅青链霉菌的影响。【方法】通过构建克隆、接合转移、异源表达及HPLC、酶切、Southern杂交等方法研究dcm基因的表达对变铅青链霉菌的多效性影响。【结果】首次发现变铅青链霉菌基因组中不含5-甲基胞嘧啶修饰,将dcm基因导入变铅青链霉菌后,接合子菌落比正常菌落小很多,并有放线紫红素产生。【结论】基因组的表观遗传修饰能激活沉默放线紫红素基因簇的表达这一现象,为基因组挖掘隐藏的活性天然产物提供了一条新途径。     

terC基因对天蓝色链霉菌抗生素合成和菌丝体生长的影响

【目的】研究天蓝色链霉菌中terC (SCO2366)基因的功能。【方法】通过敲除天蓝色链霉菌中terC基因,检测其对放线紫红素合成和菌丝体生长的影响。【结果】敲除天蓝色链霉菌中的terC基因后,放线紫红素提前合成,同时菌丝体长度变短。【结论】terC在天蓝色链霉菌中对放线紫红素的合成有负调控作用,同时影响菌丝体生长发育。     

5-甲基胞嘧啶修饰对沉默抗生素基因的激活

对真核生物的表观遗传学研究表明,5-甲基胞嘧啶修饰参与了多种重要生理功能。虽然在原核生物中也存在5-甲基胞嘧啶修饰,但其具体功能尚未确定。大肠杆菌编码的Dcm甲基转移酶负责DNA的5-甲基胞嘧啶修饰[1],有研究报道显示,Dcm与细菌的限制修饰系统相关[2];也有研究报道dcm基因能影响大肠杆菌中核糖体基因的表达,从而影响初级代谢和次级代谢[3]。本期介绍了高婕、贺新义等发表的论文"大肠杆菌甲基转移酶dcm基因的表达对变铅青链霉菌的多效性影响"[4],作者巧妙地利用变铅青链霉菌的DNA无甲基化修饰这一特点,将大肠杆菌dcm基因导入变铅青链霉菌,研究了5-甲基胞嘧啶修饰在变铅青链霉菌中的功能。结果发现,DNA的5-甲基胞嘧啶修饰不仅可影响变铅青链霉菌的形态和生理分化,而且还能激活放线紫红素沉默基因的表达。论文作者以变铅青链霉菌为材料,拓展了对原核生物DNA5-甲基胞嘧啶修饰的生理功能的认识。以此为基础的深入研究,不仅有助于揭示5-甲基胞嘧啶修饰在原核生物中的功能,而且有可能为沉默抗生素基因的表达或抗生素产量的提高提供一个新的途径。     

刺糖多孢菌中铵载体蛋白基因amtS的克隆及功能研究

目的:铵离子是细胞内合成各种核酸、氨基酸和辅助因子等含氮化合物的重要原料之一。微生物细胞膜上的铵载体蛋白介导了铵离子的转运。通过异源表达刺糖多孢菌中铵载体蛋白基因,研究其对链霉菌产孢能力和次级代谢产物产量的影响。方法:从刺糖多孢菌S04-41菌株中克隆铵载体蛋白基因amt S,通过接合转移导入天蓝色链霉菌M145和变铅青链霉菌TK24中,分析比较amt S基因的异源表达对其产孢能力和次级代谢产物产量的影响。结果:天蓝色链霉菌重组菌株M145/p MF-amt S和变铅青链霉菌重组菌株TK24/p MF-amt S中放线紫红素的产量分别提高了2.85倍和30.02倍。结论:刺糖多孢菌中的铵载体蛋白能够提高链霉菌中次生代谢产物的产量,为进一步研究该基因的功能与对刺糖多孢菌中多杀菌素合成的作用奠定了重要基础。     

力达霉素产生菌球孢链霉菌C-1027中atrA同源基因的克隆及分析

目的:在天蓝色链霉菌Streptomyces coelicolor A3(2)中多效性调节因子AtrA(AtrA-c)可通过激活放线紫红素途径特异性的调节因子ActII-ORF4的转录来控制放线紫红素的产生。在灰色链霉菌Streptomyces griseus NBRC13350和阿维链霉菌Streptomyces avermitilis MA-4680中也发现了AtrA-c编码基因(atrA-c)的同源基因,分别影响链霉素和阿维菌素的生物合成。为探索球孢链霉菌C-1027(Streptomyces globisporus C-1027)中是否存在AtrA,克隆球孢链霉菌C-1027中atrA基因并进行生物信息学分析,为进一步确定其对力达霉素产生的调控作用及调控机制奠定基础。方法:采用在球孢链霉菌C-1027中异源表达AtrA-c,来确定AtrA-c对力达霉素产量的影响;通过Southern blot分析来判断在球孢链霉菌C-1027基因组中是否有atrA-c同源基因;PCR扩增方法获得球孢链霉菌C-1027 atrA基因(atrA-gl)并测序;通过多种生物信息学软件来分析atrA-gl及其与旁侧基因的组织结构、对已发现的AtrA蛋白进行同源性比对及亲缘关系分析。结果:在球孢链霉菌C-1027中异源表达天蓝色链霉菌AtrA-c蛋白,发现其对力达霉素的产量有影响。以atrA-c为探针,通过Southern blot分析显示球孢链霉菌C-1027基因组中存在atrA-c的同源基因。PCR扩增得到球孢链霉菌C-1027的atrA基因的全序列以及该基因上下游的旁侧序列(GenBank/EMBL/DDBJ登录号GU723707)。通过对球孢链霉菌C-1027、天蓝色链霉菌A3(2)、灰色链霉菌NBRC13350以及阿维链霉菌MA-4680 AtrA蛋白序列进行同源性分析发现,4种AtrA蛋白编码氨基酸序列一致性达到65%～87%,相似性高达70%～89%。并且,球孢链霉菌C-1027 atrA基因与相邻基因形成的组织结构与天蓝色链霉菌和灰色链霉菌完全一致。根据蛋白质同源性绘制进化树,发现球孢链霉菌AtrA蛋白与灰色链霉菌AtrA蛋白亲缘关系最近。结论:确定在球孢链霉菌C-1027中存在atrA同源基因并影响力达霉素的产量,克隆了首个力达霉素生物合成基因簇外的调节基因——atrA基因,通过生物信息学分析初步推测了该基因的功能,为进一步研究AtrA-gl对力达霉素途径特异性级联调控网络的调控关系奠定了基础。     

异源表达afsRScla全局性调控基因提高工业菌株纳他霉素产量

前期研究表明棒状链霉菌的全局性调控基因afsRScla异源表达可以激活变铅青链霉菌中两种抗生素的合成。本研究将包含afsRScla基因的质粒pHL851整合到纳他霉素工业生产菌株褐黄孢链霉菌TZ1401的基因组中,使纳他霉素产量提高38%,达到3.56g/L。qRT-PCR检测6个纳他霉素生物合成基因的转录情况,发现其转录水平提高1.9-2.7倍,表明afsRScla通过正调控纳他霉素生物合成基因的转录,从而提高纳他霉素的产量。本研究结果对afsRScla在抗生素工业生产菌株的高产育种应用具有借鉴意义。     

麦迪霉素聚酮缩合酶基因的亚克隆及表达

利用与麦迪霉素生物合成有类似途径的放线紫红素聚酮缩台酶基因ActⅠ作为探针,将来源于麦迪霉素产生菌基因文库的与ActⅠ有同源性的阳性初级克隆pcN8812进一步缩小,亚克隆获得了2．4kb的麦迪霉素聚酮缩台酶基因,将其插入pwHM3载体中构建了重组质粒pcG2 DNA。pcG2 DNA在放线紫红素聚酮缩合酶基因缺陷型变株天蓝色链霉菌TKl7及螺旋霉素产生菌S．Ambofaciens中均获得表达。前者所得产物不同于麦迪霉素和放线紫红素,可能为新的杂合抗生素,后者能使螺旋霉素产量得到提高。另外pcG2 DNA在道诺红霉素产生菌调节变株S.peucetiusH6101中的表达产物经TLC及HPLC分析表明为紫红霉酮。pcG2 DNA在Tetracenomycin C产生菌S．Glaucescens中亦有一定的功能表达,而在红霉素产生菌红霉内酯阻断变株Saccharapolyspara erythraea WMH 15,26l中未观察到活性表达。推测pCG2 DNA具有一定调节或在某些聚酮类抗生素产生菌变株中超互补的功能。     

NsdB——天蓝色链霉菌A3(2)中一个负调控抗生素产量蛋白的研究

TPR(tetratricopeptide repeat)是在很多蛋白中均被发现到的一个含有34个氨基酸的蛋白重复序列,其基本功能是参与蛋白间的相互作用。天蓝色链霉菌A3(2)中有70个蛋白含有类TPR结构域,NsdA是其中的一个,研究发现该蛋白对天蓝色链霉菌的产孢和产素都有负调控作用。本研究中发现基因SCO7252和SCO1593编码含TPR结构的蛋白,中断SCO7252基因后菌株放线紫红素和钙依赖抗生素产量均提高,但形态分化没有明显变化,基因SCO1593中断后菌株在产孢产素及形态等各方面均未受到影响。基因SCO7252被命名为nsdB,RT-PCR分析表明,该基因在生长30h时开始表达。通过生物信息分析表明,天蓝色链霉菌的70个含类TPR结构的蛋白中有32个仅含该结构域,有25个另外含有DNA结合区域,这些暗示着它们可能直接控制基因的表达。     

Identification of a gene negatively affecting antibiotic production and morphological differentiation in Streptomyces coelicolor A3(2)

SC7A1 is a cosmid with an insert of chromosomal DNA from Streptomyces coelicolor A3(2). Its insertion into the chromosome of S. coelicolor strains caused a duplication of a segment of ca. 40 kb and delayed actinorhodin antibiotic production and sporulation, implying that SC7A1 carried a gene negatively affecting these processes. The subcloning of SC7A1 insert DNA resulted in the identification of the open reading frame SCO5582 as nsdA, a gene negatively affecting Streptomyces differentiation. The disruption of chromosomal nsdA caused the overproduction of spores and of three of four known S. coelicolor antibiotics of quite different chemical types. In at least one case (that of actinorhodin), this was correlated with premature expression of a pathway-specific regulatory gene (actII-orf4), implying that nsdA in the wild-type strain indirectly repressed the expression of the actinorhodin biosynthesis cluster. nsdA expression was up-regulated upon aerial mycelium initiation and was strongest in the aerial mycelium. NsdA has DUF921, a Streptomyces protein domain of unknown function and a conserved SXR site. A site-directed mutation (S458A) in this site in NsdA abolished its function. Blast searching showed that NsdA homologues are present in some Streptomyces genomes. Outside of streptomycetes, NsdA-like proteins have been found in several actinomycetes. The disruption of the nsdA-like gene SCO4114 had no obvious phenotypic effects on S. coelicolor. The nsdA orthologue SAV2652 in S. avermitilis could complement the S. coelicolor nsdA-null mutant phenotype.     

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.     

Alteration of the synthesis of the Clp ATP-dependent protease affects morphological and physiological differentiation in Streptomyces

The genes of Streptomyces coelicolor A3(2) encoding catalytic subunits (ClpP) and regulatory subunits (ClpX and ClpC) of the ATP-dependent protease family Clp were cloned, mapped and characterized. S. coelicolor contains at least two clpP genes, clpP1 and clpP2, located in tandem upstream from the clpX gene, and at least two unlinked clpC genes. Disruption of the clpP1 gene in S. lividans and S. coelicolor blocks differentiation at the substrate mycelium step. Overexpression of clpP1 and clpP2 accelerates aerial mycelium formation in S. lividans, S. albus and S. coelicolor. Overproduction of ClpX accelerates actinorhodin production in S. coelicolor and activates its production in S. lividans.     

Cloning of a pleiotropic gene that positively controls biosynthesis of A-factor, actinorhodin, and prodigiosin in Streptomyces coelicolor A3(2) and Streptomyces lividans.

A-factor (2S-isocapryloyl-3S-hydroxymethyl-gamma-butyrolactone), an autoregulating factor originally found in Streptomyces griseus, is involved in streptomycin biosynthesis and cell differentiation in this organism. A-factor production is widely distributed among actinomycetes, including Streptomyces coelicolor A3(2) and Streptomyces lividans. A chromosomal pleiotropic regulatory gene of S. coelicolor A3(2) controlling biosynthesis of A-factor and red pigments was cloned with a spontaneous A-factor-deficient strain of S. lividans HH21 and plasmid pIJ41 as a host-vector system. The restriction endonuclease KpnI-digested chromosomal fragments were ligated into the plasmid vector and introduced by transformation into the protoplasts of strain HH21. Three red transformants thus selected were found to produce A-factor and to carry a plasmid with the same molecular weight, and a 6.4-megadalton fragment was inserted in the KpnI site of pIJ41. By restriction endonuclease mapping and subcloning, a restriction fragment (1.2 megadaltons, approximately 2,000 base pairs) bearing the gene which causes concomitant production of A-factor and red pigments was determined. The red pigments were identified by thin-layer chromatography and spectroscopy to be actinorhodin and prodigiosin, both of which are the antibiotics produced by S. coelicolor A3(2). The cloned fragment was introduced into the A-factor-negative mutants (afs) of S. coelicolor A3(2) by using pIJ702 as the vector, where it complemented one of these mutations, afsB, characterized by simultaneous loss of A-factor and red pigment production. We conclude that the cloned gene pleiotropically and positively controls the biosynthesis of A-factor, actinorhodin, and prodigiosin.