Wheat germ systems for cell-free protein expression

Cell-free protein expression plays an important role in biochemical research. However, only recent developments led to new methods to rapidly synthesize preparative amounts of protein that make cell-free protein expression an attractive alternative to cell-based methods. In particular the wheat germ system provides the highest translation efficiency among eukaryotic cell-free protein expression approaches and has a very high success rate for the expression of soluble proteins of good quality. As an open in vitro method, the wheat germ system is a preferable choice for many applications in protein research including options for protein labeling and the expression of difficult-to-express proteins like membrane proteins and multiple protein complexes. Here I describe wheat germ cell-free protein expression systems and give examples how they have been used in genome-wide expression studies, preparation of labeled proteins for structural genomics and protein mass spectroscopy, automated protein synthesis, and screening of enzymatic activities. Future directions for the use of cell-free expression methods are discussed.     

锥虫早老素蛋白亲水区的克隆和表达纯化

目的体外表达锥虫早老素蛋白亲水区肽段,以制备抗血清用于功能研究。方法根据锥虫早老素蛋白二级结构特性,设计引物分别扩增N端及C端片段的亲水区肽段基因,装入原核表达载体进行表达,并通过变性纯化方法获得足够量表达蛋白,制备兔抗血清。结果成功扩增并克隆锥虫早老素蛋白亲水区片段L2及L7．并分别采用变性磁珠法和变性树脂法进行大量蛋白产物纯化,浓缩纯化产物制备兔抗血清经Westem blot杂交验证,出现目的蛋白大小阳性条带。结论成功表达锥虫早老素蛋推测N端及C端亲水肽段,并成功制备抗血清．可用于锥虫早老素蛋白功能分析。     

Gene technology-based antimetabolite design: the use of an in vitro protein expression system to facilitate antimetabolite design for virally-induced human diseases and malignant conditions

A precondition for the chemotherapeutic treatment of a variety of virally-induced human diseases and malignant conditions is a highly selective interaction of the drug molecule to be used with it's biological target. To ensure the development of novel, effective drugs, it is essential that the biological target is well characterised with regard to it's structure and activity. Such characterisation relies upon adequate amounts of pure target being available. One of the most important enzymatic importers for antimetabolites is the enzyme thymidine kinase. In this article an in vitro protein expression system is described which facilitates the production of milligram amounts of pure and biologically active thymidine kinase, from a number of important biological sources. Results have shown that the in vitro produced enzyme has the exact biochemical propeties of the in vivo enzyme. Thus the in vitro protein expression system is an ideal vechicle to facilitate an in depth investigation of the enzyme's biological properties.     

vMIP-II-TfN融合蛋白在毕赤酵母中的表达和纯化

目的:构建pPIC-vMIP-II-TfN酵母表达载体,表达纯化vMIP-II-TfN融合蛋白。方法:利用PCR方法扩增编码人转铁蛋白N端半分子的基因片段,通过酶切、连接、转化等分子克隆方法构建pPIC-vMIP-II-TfN酵母表达载体;电击法转化X33酵母菌;用甲醇诱导重组酵母菌表达融合蛋白,利用硫酸铵沉淀、透析、Ni-NTA层析等技术进行蛋白纯化,SDS-PAGE和Western blot检测蛋白表达和纯化情况,利用趋化实验进行纯化蛋白活性检测。结果:经过两次PCR扩增了一个长约1.1kb的包含Xba I酶切位点的IgG3-TfN基因片段,插入pPIC-vMIP-II的Xba I酶切位点,经菌液PCR鉴定获得重组子,测序结果表明构建载体pPIC-vMIP-II-TfN的表达框正确无误,转化X33酵母菌,用甲醇诱导表达出48kDa的vMIP-II-TfN融合蛋白,经硫酸铵沉淀、透析、Ni-NTA纯化后得到纯度约为95%的vMIP-II-TfN融合蛋白。Western印迹结果表明融合蛋白能与转铁蛋白抗体特异性结合。活性检测表明经过诱导表达的vMIP-II-TfN融合蛋白具有趋化抑制活性。结论:成功构建pPIC-vMIP-II-TfN酵母表达载体,重组酵母工程菌经甲醇诱导成功表达出vMIP-II-TfN融合蛋白,纯化后的vMIP-II-TfN融合蛋白具有趋化抑制活性。     

HBV preS/S基因克隆及其在酿酒酵母中的表达

目的:探索利用酿酒酵母系统表达乙型肝炎病毒(HBV)preS／S基因。方法:利用PCR技 术,以HBV病毒DNA为模板,体外扩增HBV preS／S基因。然后构建重组表达载体pESC-preS／S。 用LiAc法转化酿酒酵母YPH50,选取重组菌进行培养,并诱导表达外源蛋白。提取蛋白浓缩后 进行SDS-PAGE分析,并经Western blot分析鉴定。结果:实验结果表明重组菌能够表达HBV preS／S蛋白。结论:利用酿酒酵母系统可成功表达HBV preS／S基因,为制备新型预防性疫苗提供 条件。     

重组人卵透明带ZP3蛋白在毕赤酵母中的表达

利用P.pastoris表达人卵透明带ZP3蛋白。设计特定引物从全长hZP3 cDNA上扩增含跨膜区序列的人卵透明带ZP3基因片段,并在N末端接上串联组氨酸编码序列的重组基因序列;扩增片段插入表达载体pPIC9K中;线性化后的重组质粒转入P.pastoris中,用高浓度G418筛选高拷贝菌株,然后甲醇诱导目的蛋白表达。用SDS-PAGE和Western blot分析表达产物。结果发现P.pastoris表达的人ZP3蛋白可以分泌到培养液中,并且可溶性好。纯化前后的重组人ZP3蛋白均能与兔抗猪ZP3蛋白抗体发生交叉反应,证实表达的目的蛋白具有反应原性。     

Community-Wide Experimental Evaluation of the PROSS Stability-Design Method

Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins. Here, we benchmark the application of PROSS as a stand-alone tool for protein scientists with no or limited experience in modeling. Twelve laboratories from the Protein Production and Purification Partnership in Europe (P4EU) challenged the PROSS algorithm with 14 unrelated protein targets without support from the PROSS developers. For each target, up to six designs were evaluated for expression levels and in some cases, for thermal stability and activity. In nine targets, designs exhibited increased heterologous expression levels either in prokaryotic and/or eukaryotic expression systems under experimental conditions that were tailored for each target protein. Furthermore, we observed increased thermal stability in nine of ten tested targets. In two prime examples, the human Stem Cell Factor (hSCF) and human Cadherin-Like Domain (CLD12) from the RET receptor, the wild type proteins were not expressible as soluble proteins in E. coli, yet the PROSS designs exhibited high expression levels in E. coli and HEK293 cells, respectively, and improved thermal stability. We conclude that PROSS may improve stability and expressibility in diverse cases, and that improvement typically requires target-specific expression conditions. This study demonstrates the strengths of community-wide efforts to probe the generality of new methods and recommends areas for future research to advance practically useful algorithms for protein science.     

High level soluble production of functional ribonuclease inhibitor in Escherichia coli by fusing it to soluble partners

Ribonuclease inhibitor (RI) is a 50-kDa cytosolic scavenger of pancreatic-type ribonucleases which inhibits ribonucleolytic activity. Expression of recombinant RI is extremely difficult to reach high levels in soluble form in the cytoplasm of Escherichia coli. Here, we utilized five N-terminal fusion partners to improve the soluble expression of RI. Among these five fusion partners which have been screened, maltose-binding protein (MBP), N-utilization substance A (NusA) and translation initiation factor 2 domain I (IF2) have greatly improved the soluble expression level of recombinant murine RI under the drive of T7 promoter, while glutathione S-transferase (GST) and small ubiquitin modifying protein (SUMO) were much less efficient. All these RI-fusion proteins remained to be highly active in inhibiting RNase A activity. Furthermore, all fusion tags can be efficiently removed by enterokinase digestion to generate native RI which results the highest yield to date (>30mg of native RI per liter culture). And a convenient two-step immobilized metal affinity chromatography (IMAC) method has been implemented in our study, comparing with the traditional RNase A affinity chromatography method.     

Enzyme Free Cloning for high throughput gene cloning and expression

Structural and functional genomics initiatives significantly improved cloning methods over the past few years. Although recombinational cloning is highly efficient, its costs urged us to search for an alternative high throughput (HTP) cloning method. We implemented a modified Enzyme Free Cloning (EFC) procedure, a PCR-only method that eliminates all variables other than PCR efficiency by circumventing enzymatic treatments. We compared the cloning efficiency of EFC with that of Ligation Independent Cloning (LIC). Both methods are well suited for HTP cloning, but EFC yields three times more transformants and a cloning efficiency of 91%, comparable with recombinational cloning methods and significantly better than LIC (79%). EFC requires only nanogram amounts of both vector and insert, does not require highly competent cells and is, in contrast to LIC, largely insensitive to variations in PCR product concentration. Automated protein expression screening of expression strains directly transformed with EFC reactions showed, that the traditional preceding step via a cloning strain can be circumvented. EFC proves an efficient and robust HTP cloning method, that is compatible with existing Ligation Independent Cloning vectors, and highly suitable for automation.     

Pilot studies on the parallel production of soluble mouse proteins in a bacterial expression system

We investigated the parallel production in medium throughput of mouse proteins, using protocols that involved recombinatorial cloning, protein expression screening and batch purification. The methods were scaled up to allow the simultaneous processing of tens or hundreds of protein samples. Scale-up was achieved in two stages. In an initial study, 30 targets were processed manually but with common protocols for all targets. In the second study, these protocols were applied to 96 target proteins that were processed in an automated manner. The success rates at each stage of the study were similar for both the manual and automated approaches. Overall, 15 of the selected 126 target mouse genes (12%) yielded soluble protein products in a bacterial expression system. This success rate compares favourably with other protein screening projects, particularly for eukaryotic proteins, and could be further improved by modifications at the cloning step.     

Matrix layer sample preparation: an improved MALDI-MS peptide analysis method for proteomic studies

The analytical performance of MALDI-MS is highly influenced by sample preparation and the choice of matrix. Here we present an improved MALDI-MS sample preparation method for peptide mass mapping and peptide analysis, based on the use of the 2,5-dihydroxybenzoic acid matrix and prestructured sample supports, termed: matrix layer (ML). This sample preparation is easy to use and results in a rapid automated MALDI-MS and MS/MS with high quality spectra acquisition. The between-spot variation was investigated using standard peptides and statistical treatment of data confirmed the improvement gained with the ML method. Furthermore, the sample preparation method proved to be highly sensitive, in the lower-attomole range for peptides, and we improved the performance of MALDI-MS/MS for characterization of phosphopeptides as well. The method is versatile for the routine analysis of in-gel tryptic digests thereby allowing for an improved protein sequence coverage. Furthermore, reliable protein identification can be achieved without the need of desalting sample preparation. We demonstrate the performance and the robustness of our method using commercially available reference proteins and automated MS and MS/MS analyses of in-gel digests from lung tissue lysate proteins separated by 2-DE.     

Efficient production of active and mutated ADP-ribosyltransferase (S1) of pertussis toxin using affinity expression cassette polymerase chain reaction

Abstract We describe an efficient, general approach for cloning, expression and purification of heterologous proteins in Escherichia coli host strains. The affinity expression cassette polymerase chain reaction (AEC-PCR) allows the insertion of virtually any coding sequence in suitable expression vectors. For ease of purification of the (over)produced protein the gene expression cassettes are engineered by specifically designed oligonucleotide primers in the polymerase chain reaction (PCR) to contain either 3′ or 5′ additional nucleotides coding for a short amino acid sequence constituting an ‘affinity block’ fused to either end of the protein. This allows a one-step purification by affinity chromatography. In combination with PCR-mediated site-specific mutagenesis this approach is a highly efficient way for the expression and isolation of proteins and for the analysis and dissection of functional domains. The application of AEC-PCR is demonstrated by the cloning, production and purification of the native, active and the mutagenized, inactive ADP-ribosyltransferase (S1 subunit) of pertussis toxin. In this example, a string of six histidines has been engineered to either the N-terminal or the C-terminal end of the protein to serve as ‘affinity block’ for the isolation of the recombinant protein by immobilized metal ion affinity chromatography (IMAC). Thus, the S1 subunit can now be produced in sufficient quantities to facilitate further studies on its immunological and molecular properties.     

Fully automated protein purification

Obtaining highly purified proteins is essential to begin investigating their functional and structural properties. The steps that are typically involved in purifying proteins can include an initial capture, intermediate purification, and a final polishing step. Completing these steps can take several days and require frequent attention to ensure success. Our goal was to design automated protocols that would allow the purification of proteins with minimal operator intervention. Separate methods have been produced and tested that automate the sample loading, column washing, sample elution and peak collection steps for ion exchange, metal affinity, hydrophobic interaction, and gel filtration chromatography. These individual methods are designed to be coupled and run sequentially in any order to achieve a flexible and fully automated protein purification protocol.     

Tuning different expression parameters to achieve soluble recombinant proteins in E. coli: advantages of high-throughput screening

Proteins are the main reagents for structural, biomedical, and biotechnological studies; however, some important challenges remain concerning protein solubility and stability. Numerous strategies have been developed, with some success, to mitigate these challenges, but a universal strategy is still elusive. Currently, researchers face a plethora of alternatives for the expression of the target protein, which generates a great diversity of conditions to be evaluated. Among these, different promoter strength, diverse expression host and constructs, or special culture conditions have an important role in protein solubility. With the arrival of automated high-throughput screening (HTS) systems, the evaluation of hundreds of different conditions within reasonable cost and time limits is possible. This technology increases the chances to obtain the target protein in a pure, soluble, and stable state. This review focuses on some of the most commonly used strategies for the expression of recombinant proteins in the enterobacterium Escherichia coli, including the use of HTS for the production of soluble proteins.     

Immunostaining with dissociable antibody microarrays

The availability of a large number of biological materials such as cDNA, antibodies, recombinant proteins, and tissues has promoted the development of microarray technologies that make use of these materials in high-throughput screening assays. However, because microarray technologies have been less successful in examining proteins than DNA and mRNA, there is a need for improved protein microarray systems. To address this need, we developed an antibody microarray-based immunostaining method that can analyze the properties of a large number of proteins simultaneously. In this method, antibodies are arrayed and immobilized on a solid support and cells bearing antigens of interest are attached to a second support. Apposition of the two supports allows the antibodies to dissociate from the array support and bind to the cellular antigens. After separation of the supports, antigen-bound antibodies can be detected by standard secondary antibody techniques. These "dissociable" antibody arrays were used to detect both the expression and subcellular localization of a large number of specific proteins in various cultured cell types.     

重组高原鼠兔瘦素原核表达载体的构建、蛋白表达及纯化

瘦素(leptin)由ob 基因编码,对调节能量代谢起着重要作用。本研究建立了高原鼠兔瘦素的原核表达系统,并对其进行了原核表达。研究中作者从高原鼠兔瘦素基因的cDNA 文库中,扩增编码高原鼠兔瘦素的核酸序列,并利用DNA 基因重组技术将其克隆到原核表达载体pET30a(+ )中,构建了高原鼠兔瘦素原核表达载体pET30a(+ )/ ppleptin。对目的片段进行测序确认后,将其转化到大肠杆菌BL21 中,并利用IPTG 诱导外源性目的蛋白表达。表达的包涵体蛋白经溶解及变性后上柱纯化。重组质粒经测序检测后,表明原核载体构建正确。同时,SDS - PAGE 凝胶电泳结果显示,重组菌在16KD 处有明显新增条带,纯化后的目的蛋白条带纯度较高。该结果为高原鼠兔瘦素的后续基础研究提供了基础资料。     

Screening methods to determine biophysical properties of proteins in structural genomics

We have developed and tested a simple and efficient protein purification method for biophysical screening of proteins and protein fragments by nuclear magnetic resonance (NMR) and optical methods, such as circular dichroism spectroscopy. The method constitutes an extension of previously described protocols for gene expression and protein solubility screening [M. Hammarstr?m et al., (2002), Protein Science 11, 313]. Using the present purification scheme it is possible to take several target proteins, produced as fusion proteins, from cell pellet to NMR spectrum and obtain a judgment on the suitability for further structural or biophysical studies in less than 1 day. The method is independent of individual protein properties as long as the target protein can be produced in soluble form with a fusion partner. Identical procedures for cell culturing, lysis, affinity chromatography, protease cleavage, and NMR sample preparation then initially require only optimization for different fusion partner and protease combinations. The purification method can be automated, scaled up or down, and extended to a traditional purification scheme. We have tested the method on several small human proteins produced in Escherichia coli and find that the method allows for detection of structured proteins and unfolded or molten globule-like proteins.     

人源蛋白酪氨酸磷酸酶SHP-2基因克隆与原核表达

目的:构建蛋白酪氨酸磷酸酶SHP-2的原核表达载体并在大肠杆菌中表达。方法:以人脑组织mRNA为模板,通过RT-PCR扩增出目标cDNA,构建蛋白酪氨酸磷酸酶SHP-2-pEASY-E1重组质粒。将重组质粒转化进E.coli TOP10感受态细胞中,通过菌落PCR和测序进行阳性克隆的筛选和验证,将正确的质粒转化E.coli Transetta感受态细胞中,通过SDS-PAGE和western-blot进行蛋白检测和验证,酶促动力学分析SHP-2可溶性蛋白的活性。结果:成功克隆SHP-2功能域,构建SHP-2-pEASY-E1原核表达载体,完成可溶性蛋白的表达;酶促动力学分析结果为:米氏常数Km=0.97mmol/L,Vmax为13.57mmol/L/s。结论:本研究成功构建SHP-2的原核表达载体,重组表达的SHP-2蛋白具有较高的磷酸酶活性。     

Methods and Results for Semi-automated Cloning Using Integrated Robotics

The Joint Center for Structural Genomics (JCSG) has emphasized automation and parallel processing approaches. Here, we describe automated methods used across the cloning process with results from JCSG projects. The protocols for PCR, restriction digests and ligations, as well as for gel electrophoresis and microtiter plate assays have all been automated. The system has the capacity to routinely process 384 clones a week. This throughput can adequately supply our expression and purification pipeline with expression-ready clones, including novel targets and truncations. The utility of our system is demonstrated by our results from three diverse projects. In summary, 94% of the PCR amplicons generated to date have been successfully cloned and verified by sequencing (83% of the total attempted targets). Our results demonstrate the capabilities of this robotic platform to provide an avenue to high-throughput cloning which requires little manpower and is rapid and cost-effective while providing insights for method optimization.