在变铅青链霉菌基因组中定域克隆外源DNA的置换性载体及通过反选择获得重组体的模式方法

ΦHAU3^R是变铅青链霉菌66中对噬菌体ΦHAU3显示抗性的基因,已从基因组中获得分离。将基因组中邻近于该基因两侧的一个3.5kb和另一个3.8kb的DNA片段分别以其在染色体上的天然取向插入到一个由pIJ101衍生的质粒pIJ653上,构建成pHZ806。然后在pHZ806上对应于pIJ101复制子的区域中插入一个spc/str抗性基因,同时在3.5kb和3.8kb片段之间插入一个潮霉素抗性基因(hyg),衍生出一个新质粒pHZ808。由于pHZ808中不具有完整的pIJ101复制功能区,所以它不能在链霉菌中复制。然而,在该质粒3.5kb和3.8kb片段之间插入的任何DNA片段,在导入到变铅青链霉菌中后都可借助于3.5kb和3.8kb两个片段与内源染色体的同源区域所发生的双交换而稳定地整入到内源染色体的特定区域(3.5kb和3.8kb片段之间),同时置换出染色体上的ΦHAU3-R基因。发生了这种基因置换的重组子菌株会对噬菌体ΦHAU3变得敏感,这种反选择方法可用来浓缩和初选携带定域插入片段的重组子。已利用潮霉素抗性基因(hyg)作为一个模式基因片段阐明了这种载体和这种在染色体上定域克隆外源基因片段的方法学和适用性。同时,用pHZ808作载体克隆另外的基因片段时还有另一个优越性：hyg可作为报告基因一同参与外源基因片段的定域整合,携带插入片段的重组子除了对噬菌体ΦHAU3显示敏感性以外,还对潮霉素显示抗性。     

类产碱假单胞菌耐热碱性脂肪酶基因的克隆

将类产碱假单胞菌(Pseudomonas pseudoalcaligene)总DNA经Sau3AI部分酶解后的35～50kbDNA片段与经BamHI线性化及CIAP处理过的粘粒pIJ285连接,以大肠杆菌LE392为受体,构建类产碱假单胞菌的基因文库。通过三丁酸甘油酯平板和橄榄油平板法检测克隆子,获得一株具有耐热碱性脂肪酶活性的菌株LE392(pHZ1401)。随后将pHZ1401上的外源DNA片段进行亚克隆,从而获得了具有脂肪酶活性的菌株HB101(pHZ1402)和HB101(pHZ1403),它们分别携带有2.9kb和3.0kb的外源片段。两外源片段约有2kb的重叠区。HB101(pHZ1403)所分泌的脂肪酶活性比HB101(pHZ1402)高4倍,是出发菌的5倍。     

转座子Tn5-Mob对菜豆根瘤菌共生基因的诱变、转移和初步定位

转座子Tn5-Mob在质粒RP4-4配合下能诱动(Mobilization)菜豆根瘤菌RCR3622内源质粒的诱动转移。在种间根瘤菌杂交过程中,二个巨型质粒的转移频率均大于10~(-3);分子量约为285kb的psym3622是带有结瘤(nod)和产黑素(mel)基因的共生质粒(Symbiotic plasmid);这二个基因的最大距离不超过70kb左右。另一个分子量约为135kb的质粒在试验中为不具结瘤功能的隐蔽质粒。将psym3622共生质粒导入不结瘤(Nod-)的豌豆根瘤菌菌株B151,能够使后者在菜豆植物上表达结瘤的特性,形成无效根瘤。将psym3622共生质粒导入不结瘤的菜豆根瘤菌菌株JI8400,能够在菜豆植物上形成正常发育的有效根瘤。     

水稻植物内生链霉菌中线型和环型质粒的检测

以广东番禺和五山地区水稻植株中分离到的内生链霉菌为对象,调查可能存在的内源质粒.利用脉冲电泳技术从8个菌株中检测到大小在60 kb～410 kb的线型质粒,其中4个菌株的线型质粒可能有保守的端粒复制基因.该结果与土壤链霉菌中检测到线型质粒和具有保守端粒复制基因的比例相似,表明水稻植物组织内部的独特环境不会造成链霉菌线型质粒的多样性分布产生大的变化.此外,从13个菌株中检测到6 kb～60 kb的环型质粒.     

尼泊尔马桑根瘤内生菌纯培养物的质粒检测

采用胶内裂解法快速检测了21株马桑根瘤内生菌纯培养物和4株弗兰克氏菌参考菌株的质粒,其中有5株马桑分离菌株和1株参考菌株含有质粒。除马桑菌株和参考菌株各有1株携带2个质粒外,其它菌株均只含有1个质粒。这些质粒的分子量约为13～20kb。根据所含质粒的大小和数目,将21株马桑分离菌株划分成4个质粒类群。实验还对菌丝体生长,细胞酶解和裂解等条件对质粒检测效果的影响进行了探讨。     

24株产不同抗生素的放线菌质粒的分离和鉴定

分离鉴定了中国微生物菌种保藏管理委员会保藏的24株产不同抗生素的放线菌的质粒。按改进的Kado和Liu快速法提取质粒DNA,经电泳、电镜的检测,在24株检测菌中的7株菌里分离出10个质粒,携带质粒的菌株约占检测菌株的29％。质粒DNA的分子量约为1.8—61.6 kb。通过消除质粒试验和致死接合(Ltz)反应,研究了质粒和抗生素产生的关系。     

庆丰链霉菌的致死接合现象

庆丰链霉菌各种衍生菌株的平板或斜面能自发产生麻点现象(pock),而当种内或种间杂交时,这种现象出现得更频繁。从麻点中心和周围孢子中可分别分离到具有产生麻点能力的菌株(Ltz~+)和本身虽然不能产生麻点但却可以作为检测麻点产生的指示菌株(Ltz~-)。 本文的研究结果表明,庆丰链霉菌的麻点现象是Ltz~+菌株和作为指示菌的Ltz~-菌株细胞之间在接合过程中的一种致死接合作用(lethal zygosis),致死率可达99％以上。决定这种致死能力的遗传因子能感染转移,可用已知质粒消除因子(如吖啶黄、高温预培养)处理及原生质体再生过程诱发消除。据此,我们认为庆丰链霉菌中产生麻点的能力很可能由质粒基因所决定。对于这种质粒的可能来源进行了讨论。     

嗜温性乳链球菌质粒的分离及其DNA同源性的研究

分离10株嗜温性乳链球菌的质粒,DNA的电泳图表明,不同菌株中有2至9个质粒,其分子量从 2.8到80k6不等。用”p标记已知的质粒pUCL22(55kb）和pUCL22的1.3kb,4.4kb DNA片段分 子探针,分别与被研究的乳链球菌的质粒杂交,放射自显影结果证明,一些菌株的某些质粒与pUCL22 探针和其DNA片段探针有同源性。质粒pUCL22探针检验出菌株L72, D47中的80kb的质粒,该 质粒在电泳图中没有看到。     

质粒研究与载体构建

922365 甲基营养细菌中新质粒的鉴别[英]/Brenner,V.…∥Antonie Leeuwenhoek J.Microbiol.-1991,60(1).-43～48[译自DBA,1991,10(25),91-14504] 从50种甲基营养菌菌株(其中30种来自土壤)中筛选质粒DNA。用碱性清除溶菌物法从专性甲基营养型甲基单胞菌属(Methylomonas sp.)菌株R103a中分离出36kb质粒pIH36,并构建了其限制性图谱。检测了甲基杆菌属(Methylobacterium)桃红色色素的兼性甲基营养菌中的4种质粒;菌株R15d中的质粒plB200(200kb)和pIB14(14kb),菌株M17中的pWU14(14kb)和     

黑暗链霉菌DNA转移系统的建立

研究了黑暗链霉菌的基因转移系统,探索了通过PEG介导的原生质体转化、接合转移向黑暗链霉菌中转入外源DNA的可能性。多次尝试用质粒pIJ702转化黑暗链霉菌9904原生质体均未成功。对原生质体进行“热处理”后转化、利用单链DNA转化等都不能将质粒导入黑暗链霉菌中,表明黑暗链霉菌对外源DNA有很强的限制修饰作用。利用接合转移将具有oriT的大肠杆菌链霉菌穿梭质粒pHZ132转入大肠杆菌ET12567(pUZ8002)中,获得供体菌ET12567(pUZ8002,pHZ132)。将供体菌与预萌发的黑暗链霉菌9904的孢子进行接合转移,成功地将pHZ132转入黑暗链霉菌9904中。质粒pHZ132经黑暗链霉菌自身修饰后也可转入黑暗链霉菌9904菌株的原生质体中,转化率约为103/μg DNA(pHZ132)。     

A linear plasmid temperature-sensitive for replication in Streptomyces hygroscopicus 10-22

Streptomyces hygroscopicus 10-22 harbors a conjugative, autonomously replicating linear plasmid pHZ6 of ca. 70 kb, which shows no obvious homology with chromosomal DNA and is temperature-sensitive for replication, being stable in the host at 28 degrees C but easily lost at 37 degrees C. On a lawn of the wild-type S. hygroscopicus 10-22 cured of pHZ6, pHZ6 elicit pocks. Temperature sensitivity seemed to be a unique property for pHZ6 among six linear plasmids tested, including the well-known linear plasmids SLP2 in Streptomyces lividans 1326 and SCP1 in Streptomyces coelicolor A3(2). The distinct identity of pHZ6 from previously identified pHZ1-pHZ5 was demonstrated by the profile of relevant plasmids in six well-defined strains originated from S. hygroscopicus 10-22.     

Interspecific transfer of Streptomyces giant linear plasmids in sterile amended soil microcosms

The interspecific transfer of two giant linear plasmids was investigated in sterile soil microcosms. Plasmids pRJ3L (322 kb) and pRJ28 (330 kb), both encoding mercury resistance, were successfully transferred in amended soil microcosms from their streptomycete hosts, the isolates CHR3 and CHR28, respectively, to a plasmidless and mercury-sensitive strain, Streptomyces lividans TK24. Transconjugants of S. lividans TK24 were first observed after 2 to 3 days of incubation at 30 degrees C, which corresponded to the time taken for the formation of mycelia in soil. Transfer frequencies were 4.8 x 10(-4) and 3.6 x 10(-5) CFU/donor genome for pRJ3L and pRJ28, respectively. Transconjugants were analyzed by pulsed-field gel electrophoresis for the presence of plasmids, and plasmid identity was confirmed by restriction digests. Total genomic DNA digests confirmed that transconjugants were S. lividans TK24. The mercury resistance genes were shown to be on the plasmid in the transconjugants by hybridization analysis and were still functional. This is the first demonstration of transfer of giant linear plasmids in sterile soil microcosms. Giant linear plasmids were detected in many Streptomyces spp. isolated from mercury-contaminated sediments from Boston Harbor (United States), Townsville Harbor (Australia), and the Sali River (Tucuman, Argentina). Mercury resistance genes were shown to be present on some of these plasmids. Our findings that giant linear plasmids can be transferred between Streptomyces spp. and are common in environmental Streptomyces isolates suggest that these plasmids are important in gene transfer between streptomycetes in the environment.     

Characterization of plasmids from Haemophilus parainfluenzae and Haemophilus haemolyticus.

The laboratory strains of Haemophilus parainfluenzae and Haemophilus haemolyticus that are commonly used as restriction enzyme sources carry several small multicopy plasmids. H. parainfluenzae carries plasmids pKC1, pKC2, and pKC3 of sizes 1.50, 2.86, and 3.84 kb, respectively, as determined by gel electrophoresis and electron microscopy. H. haemolyticus carries plasmids pKC4 and pKC5 of sizes 1.3 and 1.7 kb as determined by gel electrophoresis. At least two of the plasmids pKC1 and pKC4 were successfully transferred into E. coli by cotransfection with plasmid pBR322. They are compatible with pBR322 and have a comparable copy number.     

侧孢芽孢杆菌质粒提取方法的探究

以能够降解有机磷农药的两株侧孢芽孢杆菌BL-21和BL-22为研究对象,分别采用碱裂解法、试剂盒提取法和SDS法对侧孢芽孢杆菌BL-21和BL-22的质粒进行提取,并通过凝胶电泳和紫外分光光度法对提取结果进行分析,试验结果证明,适合侧孢芽孢杆菌BL-21和BL-22的质粒提取方法是SDS裂解法,该方法提取的质粒大小为10kb,且该方法提取的结果稳定,质粒的产量和质量均符合分子生物学实验的要求。     

Plasmid analysis in pink facultative methylotrophic bacteria using a modified acetone-alkaline hydrolysis method

Routine screening of indigenous and recombinant plasmids in pink facultative methylotrophic bacteria has been difficult, time-consuming, and yields variable results. We report a modified alkaline hydrolysis method for rapid plasmid isolation from these organisms that reproducibly results in good yields of closed circular plasmid DNA which can be readily digested with restriction enzymes. This method greatly facilitates direct screening of indigenous and introduced recombinant plasmids in the methylotrophic host strain. We have confirmed earlier findings that the original NCIB wild-type strain of Methylobacterium sp. strain AM1 (NCIB 9133) contains three cryptic plasmids. However, sizing of these plasmids by comparison to standards and by restriction fragment analysis suggests that they are larger than previously reported. We have designated these plasmids pAM1-1 (65 kb), pAM1-2 (40 kb) and pAM1-3 (33 kb). We have also shown that a rifamycin-resistant strain of Methylobacterium sp. strain AM1 used routinely in our laboratory lacks pAM1-2, although no phenotype has been associated with its loss. Finally, we have shown that another pink facultative methylotroph, Methylobacterium isolate (#YK1), contains three cryptic plasmids of approximately 43, 37 and 22 kb, respectively.     

酵母杂交系统在CRISPR/Cas9基因编辑系统脱靶率研究中的应用*

目的:为提高CRISPR/Cas9(clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9)靶向性奠定基础,同时证明酵母杂交系统在研究CRISPR/Cas9脱靶效应中的应用价值。方法:以实验室前期构建成功的activase基因编辑水稻株为研究对象,先采用T7核酸内切酶Ⅰ法初步预测30株基因编辑水稻株的脱靶率。随后以酵母杂交系统进一步预测脱靶率以及研究sgRNA结构对脱靶率的影响。首先,将activase靶向基因的标准sgRNA(standard sgRNA)和短sgRNA(truncated sgRNA)分别克隆至CRISPR/Cas9系统表达载体pDW3769中,构建对应的重组载体pHZ2和pHZ4,转化至YPH499酵母单倍体形成重组酵母YpHZ2和YpHZ4;其次,根据脱靶位点预测选择7组脱靶序列A、B、C、D、E、F、G以及靶向序列,分别克隆至包含报告基因mCherry的高拷贝载体pDW3133和低拷贝载体pDW3134,构建相应的高拷贝重组载体pHZ5、pHZ7、pHZ9、pHZ11、pHZ13、pHZ15、pHZ17和pHZ19,以及对应的低拷贝重组载体pHZ6、pHZ8、pHZ10、pHZ12、pHZ14、pHZ16、pHZ18和pHZ20,转化至YPH500酵母单倍体,构建重组酵母YpHZ5-20。随后,重组酵母YpHZ2和YpHZ4与重组酵母YpHZ5-20分别杂交,挑取双倍体酵母菌落,在不同的时间段下检测荧光数值,根据荧光值定量预测脱靶率。结果:酵母培养144~192 h时荧光最为显著,脱靶序列sgRNA与靶向基因sgRNA同源性越高,越易造成脱靶,但短sgRNA较标准sgRNA脱靶率低。根据水稻植株的脱靶检测显示脱靶率约20%,基于酵母杂交的检测结果显示脱靶率为20%~28%。结论:酵母细胞进入稳定期时荧光值最为显著,且与载体的拷贝数量成正比。sgRNA序列以及长短结构可影响CRISPR/Cas9的基因靶向性。两种方法的脱靶率预测结果相当,表明酵母杂交系统在评价CRISPR/Cas9系统的脱靶率以及研究脱靶影响因素中具有良好的应用价值。     

Physical characterisation of plasmids in a morpholine-degrading mycobacterium

The plasmid content of an environmental mycobacterium (MorG) which degrades morpholine (Mor+ phenotype) was investigated. The combination, in what appears to be a novel way, of restriction endonuclease digestion, gel electrophoresis and scanning densitometry permitted the resolution of mixed plasmid preparations into four distinct plasmids with sizes of 54 (approximately), 27.7, 22.8 and 22.6 kb. These plasmids were named pMOR1, 2, 3 and 4, respectively. The Mor+ phenotype was found to be unstable during acriflavin treatment. In four independently isolated Mor- mutants, plasmid pMOR2 was found to have acquired an insert of approximately 1.8 kb within a specific 5.9 kb BamHI fragment. It is concluded that pMOR2 is involved in the coding of the Mor+ phenotype.     

A BlnI restriction map of the Salmonella typhimurium LT2 genome.

BlnI or AvrII (5'-CCTAGG) sites are very rare in the Salmonella typhimurium LT2 genome. BlnI was used to construct a physical map which was correlated with the genetic map by using three methods. First, Tn10 carries BlnI sites, and the extra restriction sites produced by 34 genetically mapped Tn10 insertions were physically mapped by using pulsed-field gel electrophoresis. Second, six genetically mapped Mud-P22 prophage insertions were used to assign BlnI fragments. Integration of Mud-P22 introduces 30 kb of DNA that can easily be detected by a "shift up" in all but the largest BlnI fragments. Finally, induced Mud-P22 insertions package more than 100 kb of genomic DNA adjacent to one side of the insertion. Some of the smaller BlnI fragments were localized by hybridization to a dot blot array of 52 lysates from induced Mud-P22 insertions. Of the 10 BlnI sites mapped, 6 probably occur in or near the 16S rRNA genes at about 55, 71, 83, 86, 88.5, and 89.5 min. There is one BlnI site in the 90-kb pSLT plasmid. Two additional BlnI fragments of about 7 and 4 kb have not been localized. The size of the genome was estimated as 4.78 Mb (+/- 0.1 Mb) excluding pSLT but including prophages Fels-1 and Fels-2. One BlnI fragment that maps between 55 and 59 min showed a 40-kb reduction in size in a strain cured of the approximately 40-kb Fels-2 prophage.     

Large plasmids in ruminal strains of Selenomonas ruminantium

The plasmid content of six different isolates of Selenomonas ruminantium from the rumen of sheep, cows or goats was examined by electron microscopy. In addition to small plasmids (< 12 kb) studied previously, all six strains contained at least one plasmid larger than 20 kb. Plasmid sizes of 1·4, 2·1, 2·4, 5·0, 6·2, 20·4, 20·8, 22·7, 23·3, 29·3, 30·7, 34·4 and 42·6 kb were estimated from contour length measurements. DNA-DNA hybridization experiments revealed homology among the large plasmids from five strains, while the 20·8 kb plasmid from a sixth isolate showed no apparent relationship with the plasmids of the other strains.