Construction of Mutation Library in Haemophilus parasuis by Inserting Tn5 Transposon and the Screening of Attenuated Strain

[Objective] The study aimed to obtain attenuated strain of Haemophilus parasuis.[Method] Tn5 transposon technology was used to construct a library of mutants.Positive mutants were screened by kanamycin resistance.False positive was identified by PCR and then removed.Mice were infected to detect the virulence of mutants.The bionomics of attenuated strains were detected,too.[Result] The attenuated mutants showed similar reproductive activity to that of wild strain.The virulence of mutants was still stable after 30 passages.[Conclusion] This study provided foundation for exploring the virulence factors and pathogenic mechanism of HPS.

PiggyBac Transposon Mediated Efficient eGFP Expression in Porcine Somatic Cells and Cloned Embryos

PiggyBac transposon has demonstrated its long-term and stable transposition on genomes of various species but lacking of the evidence on farm animal genomes. In this study, we constructed a piggyBac transposon marked with enhanced green fluorescent protein （eGFP） and showed efficient transposition in porcine somatic cells and cloned embryos. Our results demonstrated that piggyBac transposase could efficiently catalyze transposition in porcine fetal fibroblast cells, as well as in embryos. PiggyBac transposition generated 18-fold more eGFP-positive cell colonies compared to pEGFP-C1 random insertion mutagenesis, but excessive transposase might affect the transfection rate. Also piggyBac mediated 4-fold more eGFP expression than random insertion in cells and 17-fold in cloned embryos at mRNA level. When the mutagenized cells were used for somatic cell nuclear transfer （SCNT）, the cleavage rate and blastocyst rate of constructed embryos harboring piggyBac transposition had no difference with random insertion group. This study provides key information on the piggyBac transposon system as a tool for creating transgenic pigs.

Transposon mutagenesis of Psychrobacter cryohalolentis PAMC 21807 by tri-parental conjugation

Random mutagenesis is commonly used to study gene function. The screening of mutants exhibiting specific pheno- types assists in the identification of phenotype-related genes. In the current study, we isolated Antarctic bacteria, and developed a transposon Tn5 mutagenesis system. A total of 26 strains were isolated from seawater and freshwater near Antarctic King Sejong Research Station, King George Island. Six Psychrobacter strains were identified as psychrophilic, with optimal growth tempera- tures of 10~C or 15~C Psychrobacter cryohalolentis PAMC 21807 with a high growth rate at 4~C was selected for transposon mutagenesis. Tri-parental conjugation with a plasmid containing Tn5 produced 13 putative recombinants containing the selectable marker. Genomic Southern hybridization confirmed Tn5 existed as episomes for seven recombinants, and for a single recombinant, Tn5 was integrated into the genome of Psychrobacter cryohalolentis PAMC 21807. The result indicates that the mutagenesis method, although successful, has a relatively low rate. The psychrophilic bacteria isolated in this study may be a useful resource for studying cold adaptation mechanisms, and the mutagenesis method can be applied to genetic analysis.

Epigenetic interventions for brain rejuvenation：anchoring age-related transposons

Highlights：1.Iron and homocysteine accumulation in aging neurons alter genomic methylation.2.The altered methylome reactivates neuronal cell cycle,enabling transposable element mobilization.3.mi R29/p53 axis restores age-related methylation shifts,reactivating neuronal plasticity.4.Augmentation of mi R-29/p53 axis may preempt neurodegenerative disorders.

Potential of transposon-mediated cellular reprogramming towards cell-based therapies

Induced pluripotent stem(iPS)cells present a seminal discovery in cell biology and promise to support innovative treatments of so far incurable diseases.To translate iPS technology into clinical trials,the safety and stability of these reprogrammed cells needs to be shown.In recent years,different non-viral transposon systems have been developed for the induction of cellular pluripotency,and for the directed differentiation into desired cell types.In this review,we summarize the current state of the art of different transposon systems in iPS-based cell therapies.

Effects of intrinsic and extrinsic noises on transposons kinetics

The absolute concentration robustness （ACR） steady state of a biochemical system can protect against changing a large concentration of the system＇s components. In this paper, a minimal model of autonomous-nonautonomous transposons driven by intrinsic and extrinsic noises is investigated. The effects of intrinsic and extrinsic noises on ACR steady state of the transposons kinetics are studied by numerical simulations. It is found that the predator-prey-like oscillations around the ACR steady state are induced by the intrinsic or extrinsic noises. Comparing with the case of intrinsic noises, the extrinsic noises can inhibit the amplitude of oscillations of transposon kinetics. To characterize the predator-prey-like oscillations, we calculate the probability distributions and the normalized correlation functions of a system in the stability domain. With the increasing of noise intensity, the peak of the probability distribution is shifted from the ACR steady state to the trivial steady state. The normalized autocorrelation and cross-correlation functions indicate that the state of the predator-prey oscillator is transmitted to 50 successive generations at least.

Establishment of Real-Time Quantitative PCR Method for the Determination of Transposon Copy Number in Cronobacter sakazakii

[Objective] This study aimed to establish a Real-Time quantitative PCR method for the determination of transposon copy number in C. sakazakii. [ Method ] With single-copy housekeeping gene atpD as the reference gene, recombinant plasmid containing both single-copy housekeeping gene atpD and EZ-TN5 transposon was constructed; based on the established standard curves for real-time quantitative detection of atpD gene and EZ-TN5 transposon, copy number of atpD gene and EZ-TN5 transpason in three C. sakazakii mutants was detected and the ratio was calculated. [ Result] Correlation coefficients of the standard curves for real-time quantitative detection of atpD gene and EZ-TN5 transposon were 0. 999 and 0.998, respectively ; the ratios of copy number of atpD gene and EZ-TN5 transposon in three C. sakazakii mutants were 0.98, 1.17 and 0.91, respectively, which indicates that EZ-TN5 transpeson in C. sakakii mutants is a single-copy. [ Conclusion] Real-time quantitative PCR method established in this study had high availability and could replace the Southern blot method to detect the copy num- ber of EZ-TN5 transposon in different bacteria.

Transformation of dissociation transposon in japonica rice Zhonghua 11 mediated by Agrobacterium

Dissociation (Ds) transposon is one of thetransposable elements in corn. The trans-posons can be transferred into other plantswhere the transposons were not found. Oncethe transposon was inserted into target gene ofthese plants, it could be used as a marker todistinguish and isolate the gene. The object ofthis study is to transfer Ds transposon to riceby Agrobacterium -mediated transformation.The calli of immature embryos, mature

Rationally designed mariner vectors for functional genomic analysis of Actinobacillus pleuropneumoniae and other Pasteurellaceae species by transposon-directed insertion-site sequencing (TraDIS)

Comprehensive identification of conditionally essential genes requires efficient tools for generating high-density transposon libraries that, ideally, can be analysed using next-generation sequencing methods such as Transposon Directed Insertion-site Sequencing (TraDIS). The Himar1 (mariner) transposon is ideal for generating near-saturating mutant libraries, especially in AT-rich chromosomes, as the requirement for integration is a TA dinucleotide, and this transposon has been used for mutagenesis of a wide variety of bacteria. However, plasmids for mariner delivery do not necessarily work well in all bacteria. In particular, there are limited tools for functional genomic analysis of Pasteurellaceae species of major veterinary importance, such as swine and cattle pathogens, Actinobacillus pleuropneumoniae and Pasteurella multocida, respectively. Here, we developed plasmids, pTsodCPC9 and pTlacPC9 (differing only in the promoter driving expression of the transposase gene), that allow delivery of mariner into both these pathogens, but which should also be applicable to a wider range of bacteria. Using the pTlacPC9 vector, we have generated, for the first time, saturating mariner mutant libraries in both A. pleuropneumoniae and P. multocida that showed a near random distribution of insertions around the respective chromosomes as detected by TraDIS. A preliminary screen of 5000 mutants each identified 8 and 14 genes, respectively, that are required for growth under anaerobic conditions. Future high-throughput screening of the generated libraries will facilitate identification of mutants required for growth under different conditions, including in vivo, highlighting key virulence factors and pathways that can be exploited for development of novel therapeutics and vaccines.

Gene Tagging by Activating DNA Transposon nDart in Indica Rice

As International Rice Genome sequencing Project (2005) demonstrated, the rice genome contains various transposons and about 13% of the genome is occupied by DNA transposons. So far, only a few DNA

New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species

Long terminal repeat （LTR） retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferen-tially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well under-stood. In this study, a total of 1.52 Gb of Brassica sequence containing 2020 bacterial artificial chromosomes （BACs） was scanned, and six bacterial artificial chromosome （BAC） clones with extremely nested LTR-TEs （LTR-TEs density： 7.24/kb） were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23 Mya. LTR-TEs also pref-erably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes （3/207） could be matched to the Brassica expressed sequence tag （EST） database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.

热激活的Vg1转基因文昌鱼品系构建及表型分析

[目的] Vg1作为Nodal信号通路的重要配体之一参与了早期胚胎发育过程中的背腹分化调控及左右不对称模式的建立.构建Vg1转基因文昌鱼品系以研究其在文昌鱼胚胎不同发育阶段的功能.[方法]结合Tol2转座子转基因系统和热敏启动子Hsp70构建文昌鱼BbHsp70-BfVg1稳定转基因品系;并用热激实验、表型统计和原位杂交等手段对该转基因品系的有效性进行评估.[结果]热激结果显示,在囊胚晚期热激处理Vg1转基因文昌鱼导致胚胎背腹轴形成异常;在原肠胚中期热激处理Vg1转基因文昌鱼导致胚胎原本左右不对称的器官变为对称分布.基因表达分析结果显示,在囊胚晚期热激F1代胚胎中有部分比例胚胎的Vg1呈现全身性表达,背部中胚层标记基因Gsc表达扩张,腹部标记基因Evx表达下调,神经标记基因SoxB1a向腹侧蔓延;在原肠胚中期热激F1代胚胎中有部分比例胚胎的左侧特异基因Pitx呈现两侧对称表达,左侧口前窝标记基因Pit呈现两侧对称表达.[结论]初步构建了一个能够实现实时热激活Vg1的文昌鱼稳定转基因品系,并为后续在文昌鱼中进行基因功能研究提供了一个新手段.

酿酒酵母转座子介导外源基因的整合效率

为了比较分析酿酒酵母不同转座子对外源基因整合效率的影响,构建了转座子Ty1、Ty2和Ty4介导的G418表达盒及酿酒酵母BY4741重组菌BY-Ty1、BY-Ty2、BY-Ty4。研究发现,Ty2介导的整合型表达G418的BY4741重组菌转化平均菌落数为122,整合效率为93.33%,均高于Ty1和Ty4。Ty2介导的G418抗性重组菌BY-Ty2,比BY-Ty1和BY-Ty4对G418抗耐受性更强,基因拷贝数更高。结果表明,转座子Ty2更适合在酿酒酵母中介导外源基因整合。

鲍曼不动杆菌基因突变文库构建及耐药抑制基因筛查与鉴定

为挖掘鲍曼不动杆菌(Acinetobacter baumannii)耐药性产生的调控基因,以敏感株鲍曼不动杆菌AB43为研究对象,采用Tn5转座突变技术建立突变库并构建亚胺培南(IPM)和四环素(Tet)抗生素筛选模型,通过全基因组测序确认耐药突变株的基因突变位点。结果表明:成功地从突变库的4000余株突变株中筛选出6株对亚胺培南耐药性升高的突变株,1株对四环素耐药性升高的突变株。通过全基因组测序确认,UvrD、LipA、CzcD、OprD等基因突变可导致鲍曼不动杆菌AB43耐药性、生物膜形成能力和生长速率发生改变。这一研究为进一步探索鲍曼不动杆菌耐药调控机制奠定了基础。

IS200/IS605转座子家族编码的核酸酶OgeuIscB基因编辑体系的优化

目的提升来源于IS200/IS605转座子家族的RNA引导的核酸内切酶OgeuIscB的基因编辑效率。方法利用OgeuIscB蛋白已解析的晶体结构,计算氨基酸与核酸之间的原子距离,将距离小于10的非正电荷氨基酸残基突变为精氨酸(arginine,R)以提高OgeuIscB与核酸的亲和力,通过人胚肾293T细胞内源性位点验证不同突变体的基因编辑效率。结果经过两轮迭代突变,发现Q376R-S456R和A401R-S456R这2个双突变体在不同细胞系的多个内源性位点上均能显著提升OgeuIscB的基因编辑效率。结论基于结构对OgeuIscB蛋白进行理性蛋白质工程化改造,能够提升OgeuIscB核酸内切酶活性,为将其作为一种有效的基因编辑工具提供了实验依据。

玉米rMrh/Mrh双元转座系统体细胞转座特性分析

基因组中转座子的插入和剪切都会使插入位点的序列发生改变,包括基因突变,进而导致表型变异或基因组进化。Mrh/rMrh是玉米Mutator超家族中首个经遗传学鉴定的双元转座子系统,其中仅有非自主性转座子rMrh完成了基因克隆及序列测定。通过遗传杂交后代的表型分离比确定Mrh活性系中仅有一个自主性转座子Mrh调控报告基因a1位点的rMrh发生转座。为了明确rMrh转座子在玉米体细胞中的转座剪切修复对宿主a1基因功能的影响,以及分处两个遗传位点的自主性Mrh转座子对同一a1位点rMrh剪切转座后序列修复类型的影响,对转座修复位点的PCR扩增产物进行了分子克隆及测序。结果显示,rMrh在玉米体细胞中a1位点转座后产生两种足迹类型,一种是精确修复,另一种是末端反向重复序列(terminal inverted repeat,TIR)残留。同时,在不同遗传位点的自主性转座子Mrh的调控下,rMrh在玉米体细胞中原初位点发生转座剪切时的修复类型相对单一,既能通过精确修复恢复宿主基因功能,也会因为残留碱基导致宿主基因功能的突变,但是不同遗传位点的自主性转座子Mrh的修复产物序列不尽相同。研究结果明确了经典Mrh/rMrh双元转座子系统中rMrh的转座剪切修复特性,在丰富对Mutator转座子遗传特性认识的同时,也为进一步应用这一转座子系统创制玉米新种质资源和功能基因组学遗传材料奠定了理论基础。

Identification of Two Transposon-like Elements in Rice Wx Gene

Rice Wx genes have been cloned and sequenced from Oryza saliva subsp. japonica (Wx-R-jp) and subsp. indica (Wx-R-id) and wild rice Oryza saliva L. f. spontanea (Wx-R-sp). Comparison of the nucleotide sequences of these three Wx genes indicates that Wx-R-jp and Wx-R-id genes contain two types of transposon-like elements, designated by RTL-1 and RTL-2. in the region of their two introns and 5’ upstream, RTL-1 shares sequence homology with valine tRNA molecules, and contains an internal promoter of RNA polymerase Ⅲ. RTL-2 forms a stem-loop structure. Both RTL-1 and RTL-2 are flanked by direct repetitive sequences. Compared with the elements that have been known transposable, RTL-1 resembles the short interspersed-repeated DNA elements (SINEs) and RTL-2 is similar to the fold-back (FB) element of trahsposon of Drosophila.

Sustained high level transgene expression in mammalian cells mediated by the optimized piggyBac transposon system

Sustained,high level transgene expression in mammalian cells is desired in many cases for studying gene functions.Traditionally,stable transgene expression has been accomplished by using retroviral or lentiviral vectors.However,such viral vector-mediated transgene expression is often at low levels and can be reduced over time due to low copy numbers and/or chromatin remodeling repression.The piggyBac transposon has emerged as a promising nonviral vector system for efficient gene transfer into mammalian cells.Despite its inherent advantages over lentiviral and retroviral systems,piggyBac system has not been widely used,at least in part due to their limited manipulation flexibilities.Here,we seek to optimize piggyBac-mediated transgene expression and generate a more efficient,user-friendly piggyBac system.By engineering a panel of versatile piggyBac vectors and constructing recombinant adenoviruses expressing piggyBac transposase(PBase),we demonstrate that adenovirusmediated PBase expression significantly enhances the integration efficiency and expression level of transgenes in mesenchymal stem cells and osteosarcoma cells,compared to that obtained from co-transfection of the CMV-PBase plasmid.We further determine the drug selection timeline to achieve optimal stable transgene expression.Moreover,we demonstrate that the transgene copy number of piggyBac-mediated integration is approximately 10 times higher than that mediated by retroviral vectors.Using the engineered tandem expression vector,we show that three transgenes can be simultaneously expressed in a single vector with high efficiency.Thus,these results strongly suggest that the optimized piggyBac system is a valuable tool for making stable cell lines with sustained,high transgene expression.

Construction of mini-Tn4001 transposon vector for Mycoplasma gallisepticum

The detailed genetic analysis of mycoplasmas has long been hampered by the lack of appropriate tools for genetic manipulation. In this study, the transposon vector, mini-Tn4001tetM, was constructed containing the tnp gene, encoding a transposase gene in Staphylococcus aureus, two copies of the IS256 inverted repeat sequence (inner and outer) and the tetM gene, from the Enterococcus faecalis Tn916 transposon, conferring resistance to tetracycline. This vector was electro-transformed into Mycoplasma gallisepticum (MG). The recombinant cells were screened by tetracycline selection. The results indicated that the transposon vector could replicate in MG strain R by successive passages, indicating that MG is a potential vector for expressing protective antigens of other pathogens.

Effective Expression-Independent Gene Trapping and Mutagenesis Mediated by Sleeping Beauty Transposon

Expression-independent gene or polyadenylation[poly（A）]trapping is a powerful tool for genome-wide mutagenesis regardless of whether a targeted gene is expressed.Although a number of poly（A）-trap vectors have been developed for the capture and mutation of genes across a vertebrate genome,further efforts are needed to avoid the 3＇-terminal insertion bias and the splice donor（SD） read-through,and to improve the mutagenicity.Here,we present a Sleeping Beauty（SB） transposon-based vector that can overcome these limitations through the inclusion of three functional cassettes required for gene-finding,gene-breaking and large-scale mutagenesis, respectively.The functional cassette contained a reporter/selective marker gene driven by a constitutive promoter in front of a strong SD signal and an AU-rich RNA-destabilizing element（ARE）,which greatly reduced the SD read-through events,except that the internal ribosomal entry site（IRES） element was introduced in front of the SD signal to overcome the phenomenon of 3＇-bias gene trapping.The breaking cassette consisting of an enhanced splicing acceptor（SA）,a poly（A） signal coupled with a transcriptional terminator（TT） effectively disrupted the transcription of trapped genes.Moreover,the Hsp70 promoter from tilapia genome was employed to drive the inducible expression of SB11,which allows the conditional remobilization of a trap insert from a non-coding region.The combination of three cassettes led to effective capture and disruption of endogenous genes in HeLa cells.In addition,the Cre/LoxP system was introduced to delete the Hsp70-SB11 cassette for stabilization of trapped gene interruption and biosafety. Thus,this poly（A）-trap vector is an alternative and effective tool for identification and mutation of endogenous genes in cells and animals.