Gene silencing in Escherichia coli using antisense RNAs expressed from doxycycline‐inducible vectors

Here, we report on the construction of doxycycline (tetracycline analogue)‐inducible vectors that express antisense RNAs in Escherichia coli. Using these vectors, the expression of genes of interest can be silenced conditionally. The expression of antisense RNAs from the vectors was more tightly regulated than the previously constructed isopropyl‐β‐D‐galactopyranoside‐inducible vectors. Furthermore, expression levels of antisense RNAs were enhanced by combining the doxycycline‐inducible promoter with the T7 promoter‐T7 RNA polymerase system; the T7 RNA polymerase gene, under control of the doxycycline‐inducible promoter, was integrated into the lacZ locus of the genome without leaving any antibiotic marker. These vectors are useful for investigating gene functions or altering cell phenotypes for biotechnological and industrial applications.

Significance and Impact of the Study

A gene silencing method using antisense RNAs in Escherichia coli is described, which facilitates the investigation of bacterial gene function. In particular, the method is suitable for comprehensive analyses or phenotypic analyses of genes essential for growth. Here, we describe expansion of vector variations for expressing antisense RNAs, allowing choice of a vector appropriate for the target genes or experimental purpose.     

Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli

In this study, we describe a method of simultaneous conditional gene silencing of up to four genes in Escherichia coli by using antisense RNAs. We used antisense RNAs with paired termini, which carried flanking inverted repeats to create paired double-stranded RNA termini; these RNAs have been proven to have high silencing efficacy. To express antisense RNAs, we constructed four IPTG-inducible vectors carrying different but compatible replication origins. When the lacZ antisense RNA was expressed using these vectors, lacZ expression was successfully silenced by all the vectors, but the expression level of the antisense RNA and silencing efficacy differed depending on the used vectors. All the vectors were co-transformable; the antisense RNAs against lacZ, ackA, pta and pepN were co-expressed, and silencing of all the target genes was confirmed. Furthermore, when antisense RNAs were targeted to the mutator genes mutS, mutD (dnaQ) and ndk, which are involved in DNA replication or DNA mismatch repair, spontaneous mutation frequencies increased over 2000-fold. The resulting mutator strain is useful for random mutagenesis of plasmids. The method provides a robust tool for investigating functional relationships between multiple genes or altering cell phenotypes for biotechnological and industrial applications.     

Alterations in tumorigenicity of embryonal carcinoma cells by IGF-I triple-helix induced changes in immunogenicity and apoptosis

IGF-I antisense gene therapy has been applied successfully to animal models of glioma, hepatoma and teratocarcinoma. The antisense strategy has shown that tumor cells transfected with vectors encoding IGF-I antisense RNA lose tumorigenicity, become immunogenic and are associated with tumor specific immune response involving CD8+ lymphocytes. An IGF-I triple helix approach to gene therapy for glioma was recently described. The approach we have taken is to establish parameters of change using the IGF-I triple helix strategy. PCC-3 embryonal carcinoma cells derived from murine teratocarcinoma which express IGF-I were used as a model. The cells were transfected with vector which encodes an oligoribonucleotide that forms RNA-IGF-I DNA triple-helix structure. The triple-helix stops the production of IGF-I. Cells transfected in this manner underwent changes in phenotype and an increase in MHC-I and B-7 cell surface molecules. They also showed enhancement in the production of apoptotic cells (60-70%). The "triple helix" transfected cells lost the ability to induce tumor when injected subcutaneously in syngeneic 129 Sv mice. When co-transfected in vitro with expression vectors encoding both MHC-I and B-7 cDNA in antisense orientation, the "triple-helix" transfected cells were down-regulated in expression of MHC-I and B-7 and the number of apoptotic cells was significantly decreased. Injection of the doubly co-transfected cells into 129 Sv mice was associated with induction of teratocarcinoma. Comparison between antisense and triple-helix transfected cells strategies showed similar immunogenic and apoptotic changes. The findings suggest that triple-helix technology may offer a new clinical approach to treatement of tumors expressing IGF-I.     

A family of lambda phage cDNA cloning vectors, lambda SWAJ, allowing the amplification of RNA sequences

This paper describes the construction and characterization of a family of lambda phage cDNA cloning vectors that allows high-efficiency directional cDNA cloning and selective amplification of either sense or antisense cRNA sequences. These vectors contain several unique restriction sites (EcoRI, XbaI, and SacI) positioned between two specific phage promoters, SP6 and T7. This system facilitates the in vitro preparation of single-stranded (ss) RNA molecules that should be useful in subtractive hybridization and in situ hybridization procedures. Using subtractive hybridization and this vector system, it should be possible to identify sequences present in one cDNA library and not another. In addition, it should be possible to construct subtracted cDNA libraries in these vectors and to generate high specific activity, ss, antisense cRNA probes directly from DNA prepared from the whole subtracted library or from individual clones.     

Antisense RNA does not significantly affect expression of the galK gene of Escherichia coli or the N gene of coliphage lambda

The effect of antisense RNA on the expression of genes galK and N was studied in vivo. These two genes were either present in the Escherichia coli chromosome, as single copies, or were cloned on plasmid vectors. Antisense RNA was supplied from multicopy vectors where the entire galK or N gene, or only their N-proximal portions, were cloned in the antisense orientation downstream from the strong PL, PR or lacZp promoters. In all of the experiments there was no significant inhibition of the galK or N expression by up to a 50-fold excess of the specific antisense RNAs, for both the in cis and in trans experimental designs. The excess of the antisense RNA was calculated as based on respective copy numbers, but was not experimentally measured. The apparent five-fold regulatory effect observed in one of the experiments was found to be artifactually caused by unexpected creation of a terminator in one of our constructs. To avoid such artifacts, all our constructs were equipped with the nut-N antitermination system. We conclude that the reported antimessenger-mediated inhibition of gene expression is not a general phenomenon, but must require some special features which are not present in the galK and N systems.     

Antisense inhibition of the renin-angiotensin system in brain and peripheral organs

Antisense inhibition is a method of attenuating the target at the gene expression level. There are two main groups of molecular tools for this goal. The first includes the use of short synthetic stretches of DNA-antisense oligodeoxynucleotides. The second tool is the use of vectors (plasmids or viruses) containing the gene of interest subcloned in the antisense orientation, which in the cells produces the antisense RNA. Both antisense DNA and RNA can bind to the complementary sense mRNA and interfere with its translation. Effects are usually short lasting (days) for oligodeoxynucleotides and longer lasting (weeks or months) for vectors. In this article we briefly describe techniques of antisense inhibition in the context of the renin-angiotensin system.     

猪瘟病毒反义基因在培养细胞上的效应研究——反义基因对猪瘟病毒的抑制作用

应用免疫荧光抗体技术检测了整合有猪瘟病毒反义基因的PK-15细胞克隆对猪瘟病毒的抑制效应。结果表明,五个不同的反义基因片段对猪瘟病毒的抑制效率存在很大差异,其中A片段的抑制效率最高(94％～98％),B片段次之(58％～76％),C片段再次(～64％),D片段和E片段未见明显的抑制效应。抑制效率的差异可能与反义基因片段的位置、长短以及反义RNA表达质粒载体的差异有关。     

A Vector Library for Silencing Central Carbon Metabolism Genes with Antisense RNAs in Escherichia coli

We describe here the construction of a series of 71 vectors to silence central carbon metabolism genes in Escherichia coli. The vectors inducibly express antisense RNAs called paired-terminus antisense RNAs, which have a higher silencing efficacy than ordinary antisense RNAs. By measuring mRNA amounts, measuring activities of target proteins, or observing specific phenotypes, it was confirmed that all the vectors were able to silence the expression of target genes efficiently. Using this vector set, each of the central carbon metabolism genes was silenced individually, and the accumulation of metabolites was investigated. We were able to obtain accurate information on ways to increase the production of pyruvate, an industrially valuable compound, from the silencing results. Furthermore, the experimental results of pyruvate accumulation were compared to in silico predictions, and both sets of results were consistent. Compared to the gene disruption approach, the silencing approach has an advantage in that any E. coli strain can be used and multiple gene silencing is easily possible in any combination.     

Plasmodium falciparum: generation of a cDNA library enriched in sporozoite-specific transcripts by directional tag subtractive hybridization

We have adapted the "directional tag subtractive hybridization" technique as a means of investigating stage-specific gene expression in Plasmodium falciparum. This technique utilizes unidirectional cDNA libraries cloned into separate lambda vectors and involves hydroxyapatite chromatographic separation of target antisense cDNA and driver sense strand cRNA followed by PCR amplification of cDNA sequences specific to the target stage. This technique enabled efficient subtraction of asexual blood stage sequences from a P. falciparum sporozoite cDNA library and led to identification of novel sporozoite sequences. This technique can be applied to study gene expression in parasite stages that are difficult to obtain routinely.     

Prediction of antisense oligonucleotides using structural and thermodynamic motifs

Specific gene expression regulation strategy using antisense oligonucleotides occupy significant space in recent clinical trials. The therapeutical potential of oligos lies in the identification and prediction of accurate oligonucleotides against specific target mRNA. In this work we present a computational method that is built on Artificial Neural Network (ANN) which could recognize and predict oligonucleotides effectively. In this study first we identified 11 major parameters associated with oligo:mRNA duplex linkage. A feed forward multilayer perceptron ANN classifier is trained with a set of experimentally proven feature vectors. The classifier gives an exact prediction of the input sequences under 2 classes – oligo or non-oligo. On validation, our tool showed comparatively significant accuracy of 92.48% with 91.7% sensitivity and 92.09% specificity. This study was also able to reveal the relative impact of individual parameters we considered on antisense oligonucleotide predictions.     

Epitope-tagging vectors for the expression and detection of recombinant proteins in mycobacteria

New tools are required to study the growing number of uncharacterised genes derived from genome sequence projects that are specific to bacterial pathogens such as Mycobacterium tuberculosis. We have developed a series of vectors that permit the specific detection of recombinant proteins expressed in mycobacterial species. Gene expression in these vectors is driven by the strong hsp60 promoter of Mycobacterium bovis BCG and detection of expressed products is facilitated by C-terminal fusion of residues 409-419 of the human c-myc proto-oncogene. Using the M. tuberculosis Ag85B as a reporter of gene expression, we demonstrate that the vectors permit the specific detection of recombinant products expressed in the host species M. bovis BCG. BCG over-expressing Ag85B was a potent inducer of Ag85B-specific T cells in immunised mice, indicating that the C-terminal c-myc tag did not alter the characteristics of the recombinant protein. The versatility of the epitope-tagging vectors was demonstrated by the efficient secretion and detection of recombinant products in BCG. The vectors described in this study will facilitate the expression of foreign proteins in mycobacterial host systems.     

小鼠Prx2正义和反义真核表达载体的构建与表达

目的：构建小鼠Prx2正义及反义真核表达载体pEGFP-N1-sPrx2、pEGFP-N1-aPrx2并在小鼠卵巢颗粒细胞中表达。方法：应用RT—PCR技术,从小鼠卵巢颗粒细胞提取的总RNA中,获得Prx2基因编码序列的正义及反义片段,克隆至真核表达载体pEGFP—N1中,对重组质粒进行酶切和测序鉴定后,以脂质体介导法转染至体外培养的未成熟小鼠颗粒细胞,通过荧光显微镜观察和Westernblot检测其在颗粒细胞中的表达改变。结果：酶切和测序证明重组真核衰达载体pEGFP—N1一sPrx2、pEGFP—N1-aPrx2构建成功,荧光显微镜观察及Westernblot确认目标蛋白在颗粒细胞中表达增强或减弱。结论：成功构建小鼠Prx2基因正义及反义真核表达载体pEGFP-N1-sPrx2、pEGFP-N1．aPrx2并在小鼠卵巢颗粒细胞中表达。     

Stably Transfected Antisense Granzyme B and Perforin Constructs Inhibit Human Granule-Mediated Lytic Ability

In human NK cells and CTL it has been shown that release of lytic molecules is, at least in part, responsible for the lysis of target cells (TC). Of the various types of molecules thought to be involved in cell-mediated cytotoxicity (CMC), perforin and the serine proteases (granzymes A and B) are the best described. Using mammalian expression vectors (pRSV-neo and pSV₂-neo), antisense constructs for perforin and granzyme B were independently electroporated into YT-INDY, a human non-MHC-restricted, IL-2-independent, cytotoxic lymphocyte. Transfected YT-INDY was then selected for expression of the plasmid by antibiotic G418 resistance. The presence of plasmid was confirmed by detection of the integrated plasmid G418 resistance gene using PCR. The presence of antisense perforin in YT-INDY (YT-xPFP) inhibited lytic ability by >95% compared to YT-INDY transfected with plasmid alone or plasmid with unrelated antisense (YT-neo, YT-ctrl, respectively). Likewise, the presence of antisense GrB (YT-xGrB) inhibited the lytic ability of YT-INDY by >95%. Western analysis revealed a 30% decrease in the level of perlatin and a 55% decrease in granzyme B protein levels compared to YT-neo. Northern analysis using oligo probes complementary to perforin and granzyme B mRNA showed a decrease in their respective message levels. In conclusion, stably transfected antisense constructs for perforin and granzyme B essentially eliminated the lytic ability of YT-INDY. These results strongly indicate that both perforin and granzyme B are required by this human cytotoxic lymphocyte for effective TC lysis.     

Short-term and long-term modulation of gene expression by antisense therapeutics

To achieve effective modulation of gene expression by antisense oligonucleotides, novel oligonucleotide chemistries that do not promote RNase H degradation of target RNA are needed. In addition to short-term oligonucleotide effects, long-term gene regulation can be accomplished by intracellularly expressed antisense RNAs delivered by viral vectors.