Simple Method for Markerless Gene Deletion in Multidrug-Resistant Acinetobacter baumannii

The traditional markerless gene deletion technique based on overlap extension PCR has been used for generating gene deletions in multidrug-resistant Acinetobacter baumannii. However, the method is time-consuming because it requires restriction digestion of the PCR products in DNA cloning and the construction of new vectors containing a suitable antibiotic resistance cassette for the selection of A. baumannii merodiploids. Moreover, the availability of restriction sites and the selection of recombinant bacteria harboring the desired chimeric plasmid are limited, making the construction of a chimeric plasmid more difficult. We describe a rapid and easy cloning method for markerless gene deletion in A. baumannii, which has no limitation in the availability of restriction sites and allows for easy selection of the clones carrying the desired chimeric plasmid. Notably, it is not necessary to construct new vectors in our method. This method utilizes direct cloning of blunt-end DNA fragments, in which upstream and downstream regions of the target gene are fused with an antibiotic resistance cassette via overlap extension PCR and are inserted into a blunt-end suicide vector developed for blunt-end cloning. Importantly, the antibiotic resistance cassette is placed outside the downstream region in order to enable easy selection of the recombinants carrying the desired plasmid, to eliminate the antibiotic resistance cassette via homologous recombination, and to avoid the necessity of constructing new vectors. This strategy was successfully applied to functional analysis of the genes associated with iron acquisition by A. baumannii ATCC 19606 and to ompA gene deletion in other A. baumannii strains. Consequently, the proposed method is invaluable for markerless gene deletion in multidrug-resistant A. baumannii.     

IRDL Cloning: A One-Tube,Zero-Background,Easy-to-Use,Directional Cloning Method Improves Throughput in Recombinant DNA Preparation

Rapid and efficient construction of expression vectors and subsequent transformation are basic recombinant methods for the investigation of gene functionality. Although novel cloning methods have recently been developed, many laboratories worldwide continue to use traditional restriction digestion-ligation methods to construct expression vectors owing to financial constraints and the unavailability of appropriate vectors. We describe an improved restriction digestion-ligation (IRDL) cloning method that combines the advantage of directional cloning from double digestion-ligation with that of a low background observed by using a positive selection marker gene ccdB to facilitate digestion and ligation in a single tube. The IRDL cloning overcomes the time-consuming and laborious limits of traditional methods, thereby providing an easy-to-use, low-cost, and one-step strategy for directional cloning of target DNA fragments into an expression vector. As a proof-of-concept example, we developed two yeast vectors to demonstrate the feasibility and the flexibility of the IRDL cloning method. This method would provide an effective and easy-to-use system for gene cloning and functional genomics studies.     

TMV复制酶基因靶向的RNA干涉载体构建

以TMV复制酶基因作为RNAi的靶向序列,应用RT－PCR法获得目的DNA序列。依据RNAi机制,以酶切后连接的方法将目的DNA序列正向、反向锚定连接到pUCCRNAi载体质粒,构建含目的序列反向重复结构的RNA干涉中间载体;反向重复结构酶切后插入含超强启动子的pC2300-35s-OCS表达载体,重组的表达载体质粒经冻融法转化到只含辅助质粒的根癌农杆菌中,完成双元载体系统的构建。每步的重组子经特异引物PCR验证和酶切验证有相应的特异条带存在,且测序鉴定序列正确。确认成功构建了TMV复制酶基因靶向的RNAi双元载体,为RNAi技术在植物病毒病害防治中的应用奠定基础。     

Overexpressions of dihydroxyacetone synthase and dihydroxyacetone kinase in chloroplasts install a novel photosynthetic HCHO-assimilation pathway in transgenic tobacco using modified Gateway entry vectors

Dihydroxyacetone synthase (DAS) and dihydroxyacetone kinase (DAK) are two key enzymes for formaldehyde assimilation in methylotrophic yeasts. In order to using a Gateway LR recombination reaction to construct a plant expression vector that contains the expression cassettes for the das and dak genes and allow the proteins encoded by the two target genes to be localized to the chloroplasts of transgenic plants, the entry vector pEN-L4*-PrbcS-*T-gfp-L3* contained the tomato rbcS 3C promoter (PrbcS) with its transit peptide sequence (*T) and a GFP reporter gene (gfp) was constructed in this study. To verify the applicability of pEN-L4*-PrbcS-*T-gfp-L3*, we generated an entry vector for the dak gene by replacing the gfp gene in this entry vector with the dak gene. We also generated an entry vector for the das gene by replacing the gus gene in another entry vector (pENTR*-PrbcS-*T-gus) with the das gene. Using these entry vectors and pK7m34GW2-8m21GW3, we successfully constructed the pKm-35S-PrbcS-*T-gfp-PROLD-PrbcS-*T-gus and the pKm-35S-PrbcS-*T-dak-PROLD-PrbcS-*T-das expression vectors. Our results showed that high expression of GUS was achieved in leaves, and the expressed GFP, DAS and DAK proteins could be targeted to the chloroplasts after the two expression vectors were used to transform tobacco. The overexpressions of DAS and DAK in the chloroplasts successfully created a novel photosynthetic HCHO-assimilation pathway in transgenic tobacco. By utilizing these expression vectors, we not only successfully expressed two target genes with one transformation but also localized the expressed proteins to chloroplasts via the transit peptide sequence (*T). Therefore, the construction of pEN-L4*-PrbcS-*T-gfp-L3* establishes a technique platform that provides a convenient means for chloroplast genetic engineering.     

PCR依赖型方法构建高质量酵母基因突变文库

针对定向进化中利用亚克隆的方法建立酵母突变文库建库周期长、效率低、库容量低、丰度低等问题,建立了一种基于体内同源重组构建酵母整合型基因突变文库的新方法。步骤为：构建目标基因的重组表达质粒;以此为模版,设计长引物片段,PCR/易错PCR/DNA Shuffling等方法扩增得到两端带有与表达载体40~70 bp同源序列的突变基因;再利用PCR扩增得到表达载体;将扩增得到的目标基因和表达载体以一定的摩尔比混合电转化酵母,目标基因和表达载体在酵母体内同源重组成为完整的表达盒,整合入酵母基因组,获得基因突变文库。对构建的突变文库进行筛选,分别得到了酶活、蛋白表达量及热稳定性提高的突变株。该方法为完全PCR依赖型 (PDM),在体内构建表达盒,效率高,操作方便,将建库周期由2周缩短为3 d,将库容量从传统的103~104提高到105以上,库阳性率达到95％。     

A New Large-DNA-Fragment Delivery System Based on Integrase Activity from an Integrative and Conjugative Element

During the past few decades, numerous plasmid vectors have been developed for cloning, gene expression analysis, and genetic engineering. Cloning procedures typically rely on PCR amplification, DNA fragment restriction digestion, recovery, and ligation, but increasingly, procedures are being developed to assemble large synthetic DNAs. In this study, we developed a new gene delivery system using the integrase activity of an integrative and conjugative element (ICE). The advantage of the integrase-based delivery is that it can stably introduce a large DNA fragment (at least 75 kb) into one or more specific sites (the gene for glycine-accepting tRNA) on a target chromosome. Integrase recombination activity in Escherichia coli is kept low by using a synthetic hybrid promoter, which, however, is unleashed in the final target host, forcing the integration of the construct. Upon integration, the system is again silenced. Two variants with different genetic features were produced, one in the form of a cloning vector in E. coli and the other as a mini-transposable element by which large DNA constructs assembled in E. coli can be tagged with the integrase gene. We confirmed that the system could successfully introduce cosmid and bacterial artificial chromosome (BAC) DNAs from E. coli into the chromosome of Pseudomonas putida in a site-specific manner. The integrase delivery system works in concert with existing vector systems and could thus be a powerful tool for synthetic constructions of new metabolic pathways in a variety of host bacteria.     

快速构建CRISPR/Cas9基因组靶向编辑系统

CRISPR/Cas9核酸酶作为一种新的基因组靶向编辑技术,已成功应用于多种动植物基因组修饰研究. CRISPR/Cas9作用后的阳性细胞筛选和富集是该技术的关键之一. 本研究以鸡EAV-HP（endogenous avian retrovirus-HP）基因和MSTN（myostatin）基因为例,从靶位点的选择、表达载体构建、双基因报告载体构建和核酸酶活性验证4个方面,系统研究了CRISPR/Cas9核酸酶技术平台. 结果表明,利用寡聚核苷酸直接退火方法,构建表达载体和报告载体的阳性率分别高达100%和89.5%. 报告载体的PuroR（puromycin resistant gene）和eGFP（enhanced green fluorescent protein）基因的成功表达表明,构建的CRISPR/Cas9系统能有效切割靶序列,并用于后续阳性克隆的筛选和富集. 本方法摒弃了传统分子克隆的PCR扩增和酶切处理目标基因的方法,而是利用寡聚核苷酸直接退火获得含有黏性末端的目标DNA,简化了载体构建过程,低成本且快速获得CRISPR/Cas9基因组靶向编辑系统.     

一步法快速构建多片段连接的同源臂载体

目的：建立一种简便、高效,可一步完成多个片段连接,从而构建含同源臂的载体的方法。方法：按照酶切后可产生前后片段相匹配的粘性末端接头的原则设计PCR引物,在目的片段两端均引入BsaⅠ酶切位点。以G160基因为例,PCR扩增打靶用左右同源臂片段、示踪基因CMV-EGFP片段、载体骨架pMD19－T等4个片段,纯化后一起加入一个反应管中,并加入BsaⅠ限制性内切酶和T7DNA连接酶及相应缓冲液,进行酶切、酶连接共10～50个循环反应,一步构建含同源臂载体的质粒;产物经高温处理后,直接转化感受态细胞,并进行重组子PCR鉴定;对pMD19－T载体进行优化,突变载体上的BsaⅠ酶切位点,把示踪基因CMV-EGFP片段引入pHSG298－T载体,再选择不同的G160基因同源臂片段组合对构建系统进行验证。结果：重组质粒酶切和PCR结果表明,应用一步法可成功连接多个片段来构建含同源臂及示踪基因的克隆载体;用优化后的pMD19－T－O载体体系,在2d内即完成了6种各含4个片段的载体的构建。结论：多个基因片段一步无缝连接的方法简便、易行、可靠,不仅可快速构建某类载体系统,还可对基因进行精确的点突变,该系统可用于快速构建基因打靶载体。     

MicroRNA-based RNA Interference Vector for Gene Silencing in Plants

RNA interference (RNAi) is a powerful tool for functional gene analysis, which has been successfully used to down-regulate the levels of specific target genes. In this study a microRNA 159a-based binary vector was constructed which can be used for hpRNA expression. Hairpin (hp) RNA expression cassettes carrying the gene sequences are typically constructed on binary plasmid and delivered into plant cells by Agrobacterium-mediated genetic transformation. This system allows simple insertion of 21- nt target gene sequences into microRNA backbone, to facilitate the processing of microRNA hpRNA by the endogenous machinery of host, thereby producing artificial microRNA carrying the sequence of target gene(s). The functionality of new vector system was tested by silencing viral gene in transgenic plants. Strong down regulation of viral gene was observed in virus infected tobacco plants transformed with pAmiR₁₅₉ vector. The processing of amIRNA leading to viral-specific sIRNA was confirmed by northern blotting. This vector system provides an important addition to the plant molecular biologists’ toolbox, which will significantly facilitate the use of RNAi technology for analyses of various gene functions in plant cells.     

A novel approach for the construction of plant amiRNA expression vectors

Artificial microRNA (amiRNA) technology has been applied in Arabidopsis thaliana and other plants to efficiently silence target genes of interest. Here we described a novel approach to construct plant amiRNA expression vectors with seamless enzyme-free cloning (SEFC) and mating-assisted genetically integrated cloning (MAGIC). Two pairs of primers were designed when the loop of amiRNA precursor was longer than 60 bp while three oligonucleotides were used to amplify the linearized vector containing the amiRNA precursor whose loop was smaller than 60 bp. The PCR products were transformed into Escherichia coli to generate the donor plasmid containing the amiRNA expression cassette through homologous recombination in vivo. The amiRNA expression cassette was then transferred to the recipient plasmid via MAGIC and an amiRNA expression plasmid was created. More than 200 amiRNA expression vectors were generated with this approach, three of which have been transformed into A. thaliana and successfully silence the target genes. Given its low-cost and simplicity, this novel approach of plant amiRNA expression vectors construction will benefit the study of individual gene function and establishment of plant amiRNA libraries.     

几种新型植物基因表达载体的构建方法

利用基因工程技术手段研究基因功能过程中,构建基因表达载体处于转基因植物的主导地位,采用合适的构建方法会使实验效果事半功倍。植物基因表达载体的构建方法除了传统构建法、Gateway技术、三段T-DNA法、一步克隆法等,还有近年来出现的几种新型的载体构建方法:基于竞争性连接原理快速构建小片段基因表达载体;MicroRNA前体PCR置换法适用于构建小分子RNA表达载体;重组融合PCR法特别适用于插入片段中含有较多限制性酶切位点的载体构建;利用In-Fusion试剂盒可以将任何目的片段插入一个线性化载体的某个区域;构建多片段复杂载体可采用不依赖序列和连接的克隆方法(Sequence and ligation-independent cloning,SLIC)法;Gibson等温拼接法;Golden Gate拼接法。本文将在总结分析前人工作的基础上,结合自己工作的体会和经验分析这7种新方法的特点,期望通过这几种新的方法给植物基因工程表达载体的构建提供新的思路。     

Construction of pDESTR, a GATEWAY Vector for Gene Disruption in Filamentous Fungi

We have constructed pDESTR, a destination vector of gateway system especially for gene targeting and disruption in filamentous fungi. The vector was constructed by removing the multicloning site of pGEM-T easy vector, and inserting hygromycin phosphotransferase gene construct from pCB1004, and a gateway vector conversion cassette. In order to construct a DNA for gene disruption, only an inverse-polymerase chain reaction (PCR) amplification of the restricted, target sequence is needed. After the amplification with a 5′CACC-tagged primer and an ordinary primer, the DNA fragment will be inserted into pENTR/D-TOPO vector and then transferred into pDESTR through LR-recombination reaction. The resulting vector has the disruption construct, after being digested with the restriction enzyme used for the inverse-PCR. The effectiveness of this vector was assessed in Neurospora crassa. The use of pDESTR will therefore simplify the construction of a targeting vector, where multiple ligation steps are usually needed     

金花茶FLS基因的克隆及其植物表达载体的构建

利用RT-PCR和RACE技术,从我国珍稀濒危植物金花茶花瓣中获得了黄酮醇合成酶（Flavonol synthase,FLS）基因的cDNA全长,命名为CnFLS,GenBank登录号JF343560.1。根据该基因序列设计全长扩增引物P3/P4进行PCR扩增,将扩增产物插入PMD18-T载体并转化克隆菌株DH5α,提取质粒DNA酶切鉴定,通过酶切连接的方法将该基因与改造后的pCAMBIA1300表达载体连接,成功构建了该基因的正义表达载体pCAM-CnFLS。根据该基因的保守序列设计了含有酶切位点的特异引物G1/G2,扩增出250 bp的干扰片段并将其克隆到PMD18-T载体,在中间载体pUCCRNAi及表达载体pCAMBIA1300的基础上,通过多次酶切连接,成功构建了金花茶FLS基因的干扰表达载体pCAMRNAi-CnFLS。金花茶正义及干扰植物表达载体的成功构建,为进一步研究该基因的功能及其对花色的调控效应奠定了基础。     

用于筛选shRNA的新型双萤光素酶报告基因载体的构建及应用

目的:构建一个新型双萤光素酶报告基因载体用于准确高效地筛选有效抑制靶基因表达的shRNA。方法:采用PCR、定向克隆、基因重组等分子生物学方法,将双萤光素酶报告基因系统中需要的报告基因载体、shRNA真核表达载体和内参载体三个功能,整合于一个新型的双萤光素酶报告基因载体pFLuc-C-TK-RLuc-shRNA之中。应用该载体对靶向人PD1基因以及Furin基因的shRNA进行干涉效果比较。结果:应用p FLuc-C-TK-RLuc-shRNA载体进行单质粒转染方法与传统的三质粒转染方法均提示shRNA#1对靶基因PD1的抑制效果最优;但是使用新型双萤光素酶报告基因载体检测结果的标准差数值显著低于传统方法。以pFLuc-C-TK-RLuc-shRNA单质粒转染方法得到的各组样品结果的均一性显著提高,能够准确地反映出shRNA#3较shRNA#2具有更强的Furin基因抑制作用;而传统方法未能有效判断二者的差异。结论:新型双萤光素酶报告基因载体简化了操作步骤,降低了传统三质粒共转染方法所引起的检测结果大幅波动,进一步增强了双萤光素酶报告基因系统的信噪比,提高了筛选抑制靶基因表达shRNA的准确性。     

Selectable in-vivo recombination to increase antibody library size — an improved phage display vector system

Phage display technology permits the display of libraries of random combinations of light (LC) and heavy chain (HC) antibody genes. Maximizing the size of these libraries would enable the isolation of antibodies with high affinity and specificity. In this study, the loxP/Cre system of in-vivo recombination has been employed to construct an improved vector system for the display of antibodies. In this system, the chloramphenicol acetyl transferase (CAT) gene is linked to a HC library in a donor plasmid, pUX. This CAT gene is `silent' before recombination but active after recombination. A second acceptor phagemid, pMOX, is used for cloning the LC repertoire. Following infection with a Cre producing phage, pMOX accepts the CAT/HC library from pUX via site-specific recombination at the loxP sites. Recombinants can then be selected via chloramphenicol resistance. Using this vector system, we have generated libraries of 4×10⁹ recombinants. Restriction analysis and Fab expression confirmed that 100% of the colonies in the library were recombinants. This system provides a stable selectable mechanism for the generation of large libraries and avoids the isolation of non-recombinants encountered with earlier in-vivo recombination systems.     

Size unlimited markerless deletions by a transconjugative plasmid-system in Bacillus licheniformis

Conjugative shuttle vectors of the pKVM series, based on an IncP transfer origin and the pMAD vector with a temperature sensitive replication were constructed to establish a markerless gene deletion protocol for Bacilli without natural competence such as the exoenzyme producer Bacillus licheniformis. The pKVM plasmids can be conjugated to strains of B. licheniformis and B. subtilis. For chromosomal gene deletion, regions flanking the target gene are fused and cloned in a pKVM vector prior to conjugative transfer from Escherichia coli to B. licheniformis. Appropriate markers on the vector backbone allow for the identification of the integration at the target locus and thereafter the vector excision, both events taking place via homologous recombination. The functionality of the deletion system was demonstrated with B. licheniformis by a markerless 939 bp in-frame deletion of the yqfD gene and the deletion of a 31 kbp genomic segment carrying a PBSX-like prophage.