Autophosphorylation profiling of Arabidopsis protein kinases using the cell-free system

Protein phosphorylation is one of the main process in the signal transduction pathway. In recent years, there has been increasing attention to plant phosphorylation signaling and many laboratories are trying to elucidate pathways using various approaches. Although more than 1000 protein kinase (PK) genes have been annotated in the Arabidopsis genome, biochemical characterization of those PKs is limited. In this work, we demonstrate high-throughput profiling of serine/threonine autophosphorylation activity by a combination of the 759N-terminal biotinylated proteins library, produced using a wheat germ cell-free protein production system, and a commercially available luminescence system. Luminescent analysis revealed that 179 of the 759 PKs had autophosphorylation activity. From these 179 PKs, 67 of the most active PKs were analyzed to determine their function using the PlantP database. This analysis revealed that 35 (53%) of the proteins were classified as non-transmembrane protein kinases, and 15 (23%) were receptor-like protein kinases. Additionally, PKs from Group 4.4-MAP3K, Group 1.6, Group 4.5-MAPK/CDC/CK2/GSK kinases and Group 1.10-receptor like cytoplasmic kinases contained the highest percentage of autophosphorylated activity. Next, to get a better overview of the annotated 67 PKs, we used the gene ontology annotation search on the TAIR website to classify the 67 PKs into functional category. As a result, some of these PKs may be involved in phospho-signaling pathways such as signal transduction, stress response, and the regulation of cell division. Information from this study may shed light on many unknown plant PKs. This study will be a basis for understanding the function of PKs in phosphorylation network for future research.     

High-throughput, genome-scale protein production method based on the wheat germ cell-free expression system

Cell-free protein synthesis systems can synthesize proteins with high speed and accuracy, but produce only a low yield because of their instability over time. Here we review our recent advances in a cell-free protein synthesis system prepared from wheat embryos. We first addressed and resolved the source of the instability of existing systems in light of endogenous ribosome-inactivating proteins. We found that conventional wheat germ extracts contained the RNA N-glycosidase tritin and other inhibitors such as thionin, ribonucleases, deoxyribonucleases, and proteases that originate from the endosperm and inhibit translation. Extensive washing of wheat embryos to eliminate endosperm contaminants has resulted in extracts with a high degree of stability and activity. To maximize the translation yield and throughput of the system, we then focused on developing the following issues: optimization of the ORF flanking regions, a new strategy to construct PCR-generated DNAs for screening, and design of an expression vector for large-scale protein production. The resulting system achieves high-throughput expression, with a PCR-directed system at least 50 genes that can be translated in parallel, yielding between 0.1 and 2.3 mg of protein by one person within 2 days. Under the dialysis mode of reaction, the system with the expression vector can maintain productive translation for 14 days. The cell-free system described here bypasses most of the biological processes and lends itself to robotic automation for high-throughput expression of genetic information, thus opening up many possibilities in the post-genome era.     

A novel way of amino acid-specific assignment in 1H-15N HSQC spectra with a wheat germ cell-free protein synthesis system

For high-throughput protein structural analyses, it is indispensable to develop a reliable protein overexpression system. Although many protein overexpression systems, such as ones utilizing E. coli cells, have been developed, a lot of proteins functioning in solution still were synthesized as insoluble forms. Recently, a novel wheat germ cell-free protein synthesis system was developed, and many of such proteins were synthesized as soluble forms. This means that the applicability of this protein synthesis method to determination of the functional structures of soluble proteins. In our previous work, we synthesized (15)N-labeled proteins with this wheat germ cell-free system, and confirmed this applicability on the basis of the strong similarity between the (1)H-(15)N HSQC spectra for native proteins and the corresponding ones for synthesized ones.In this study, we developed a convenient and reliable method for amino acid selective assignment in (1)H-(15)N HSQC spectra of proteins, using several inhibitors for transaminases and glutamine synthase in the process of protein synthesis. Amino acid selective assignment in (1)H-(15)N HSQC spectra is a powerful means to monitor the features of proteins, such as folding, intermolecular interactions and so on. This is also the first direct experimental evidence of the presence of active transaminases and glutamine synthase in wheat germ extracts.     

A bilayer cell-free protein synthesis system for high-throughput screening of gene products

A high-throughput cell-free protein synthesis method has been described. The methodology is based on a bilayer diffusion system that enables the continuous supply of substrates, together with the continuous removal of small byproducts, through a phase between the translation mixture and substrate mixture. With the use of a multititer plate the system was functional for a prolonged time, and as a consequence yielded more than 10 times that of the similar batch-mode reaction. Combining this method with a wheat germ cell-free translation system developed by us, the system could produce a large amount of protein sufficient for carrying out functional analyses. This novel bilayer-based cell-free protein synthesis system with its simplicity, minimum time and low cost may be useful practical methodology in the post-genome era.     

A wheat germ cell-free system is a novel way to screen protein folding and function

For high-throughput protein structural analysis, it is indispensable to develop a reliable protein overexpression system. Although many protein overexpression systems, such as that involving Escherichia coli cells, have been developed, the number of overexpressed proteins showing the same biological activities as those of the native proteins is limited. A novel wheat germ cell-free protein synthesis system was developed recently, and most of the proteins functioning in solution were synthesized as soluble forms. This suggests the applicability of this protein synthesis method to determination of the solution structures of functional proteins. To examine this possibility, we have synthesized two (15)N-labeled proteins and obtained (1)H-(15)N HSQC spectra for them. The structural analysis of these proteins has already progressed with an E. coli overexpression system, and (1)H-(15)N HSQC spectra for biologically active proteins have already been obtained. Comparing the spectra, we have shown that proteins synthesized with a wheat germ cell-free system have the proper protein folding and enough biological activity. This is the first experimental evidence of the applicability of the wheat germ cell-free protein synthesis system to high-throughput protein structural analysis.     

无细胞蛋白合成体系实现胰岛素原可溶性表达

胰岛素原(Proinsulin,Pins)是胰岛素的合成前体。在大肠杆菌表达系统中,其一般以包涵体的形式存在,需要经过变性复性等后续加工过程才能得到有活性的胰岛素。而无细胞蛋白合成体系(Cell-free protein synthesis,CFPS)作为一种新型体外蛋白合成手段,突破了细胞的生理限制,已成功应用于多种重组蛋白药物的生产。为了探索胰岛素合成的新方法以满足其在新型给药途径研发中的需求,本研究运用CFPS体系进行胰岛素原的可溶性表达。通过将胰岛素原与荧光蛋白进行融合来增加其可溶性,成功在CFPS体系中表达了胰岛素原融合蛋白。最后使用Western blotting对融合红色荧光蛋白的胰岛素原(Pins-mCherry)进行鉴定,利用酶标仪对融合绿色荧光蛋白的胰岛素原(Pins-eGFP)在上清中的表达进行定量分析,结果表明Pins-eGFP部分可溶,其表达量为(12.28±3.45)μg/m L。本研究首次实现了融合胰岛素原在CFPS系统中的可溶性表达,其融合荧光蛋白的策略显著提升了胰岛素原的可溶性,该结果为探究胰岛素合成新方法及开发基于CFPS系统的新型胰岛素给药途径奠定了基础。     

Automated system for high-throughput protein production using the dialysis cell-free method

High-throughput protein production systems have become an important issue, because protein production is one of the bottleneck steps in large-scale structural and functional analyses of proteins. We have developed a dialysis reactor and a fully automated system for protein production using the dialysis cell-free synthesis method, which we previously established to produce protein samples on a milligram scale in a high-throughput manner. The dialysis reactor was designed to be suitable for an automated system and has six dialysis cups attached to a flat dialysis membrane. The automated system is based on a Tecan Freedom EVO 200 workstation in a three-arm configuration, and is equipped with shaking incubators, a vacuum module, a robotic centrifuge, a plate heat sealer, and a custom-made tilting carrier for collection of reaction solutions from the flat-bottom cups with dialysis membranes. The consecutive process, from the dialysis cell-free protein synthesis to the partial purification by immobilized metal affinity chromatography on a 96-well filtration plate, was performed within ca. 14 h, including 8 h of cell-free protein synthesis. The proteins were eluted stepwise in a high concentration using EDTA by centrifugation, while the resin in the filtration plate was washed on the vacuum manifold. The system was validated to be able to simultaneously and automatically produce up to 96 proteins in yields of several milligrams with high well-to-well reliability, sufficient for structural and functional analyses of proteins. The protein samples produced by the automated system have been utilized for NMR screening to judge the protein foldedness and for structure determinations using heteronuclear multi-dimensional NMR spectroscopy. The automated high-throughput protein production system represents an important breakthrough in the structural and functional studies of proteins and has already contributed a massive amount of results in the structural genomics project at the RIKEN Structural Genomics/Proteomics Initiative (RSGI).     

无细胞蛋白表达体系研究进展及在生物制药领域中的应用

作为一种快速高效的体外蛋白合成手段,无细胞蛋白表达体系(Cell-free Protein Synthesis,CFPS)一直以来就被广泛应用于基础生物学领域的研究。与传统的基于细胞的体内表达体系相比,CFPS突破了细胞的生理限制,其可调控性强、对毒性蛋白的耐受力高,使得许多很难在体内合成的复杂蛋白在体外顺利表达。近年来随着研究人员不断对CFPS进行优化,通过简化制备工艺、开发价格低廉的能量再生系统、稳定底物供应、促进蛋白正确折叠等方式,成功研发出生产效率高、成本低廉、反应体积大的表达体系。凭借其高通量和大规模的蛋白表达优势,CFPS为解决生物制药领域中面临的难题提供了新的解决思路,并成功地应用于高通量药物筛选、大规模生产重组蛋白药物、个体化定制肿瘤疫苗等领域,显示出其在生物制药领域的重要应用潜力。     

High-throughput,genome-scale protein production method based on the wheat germ cell-free expression system

Current cell-free protein expression systems are capable of synthesizing proteins with high speed and accuracy; however, the yields are low due to their instability over time. Escherichia coli based systems are not always sufficient for expression of eukaryotic proteins. This report reviews a high-throughput protein production method based on the cell-free system prepared from eukaryote, wheat embryos. We first demonstrate a method for preparation of this extract that exhibited a high degree of stability and activity. To maximize translation yield and throughput, we address and resolve the following issues: (1) optimization of the ORF flanking regions; (2) PCR-based generation of DNA for mRNA production; (3) expression vectors for large-scale protein production; and (4) a translation reaction that does not require a membrane. The combination of these elemental processes with robotic automation resulted in high-throughput protein synthesis.     

Efficient protein selection based on ribosome display system with purified components

Using the PURE (Protein synthesis Using Recombinant Elements) system, we developed an efficient and highly controllable ribosome display method for selection of functional protein. The PURE system is composed of purified factors and enzymes that are responsible for gene expression in Escherichia coli. We performed the detailed analyses and optimization of the ribosome display system and demonstrated the formation of stable mRNA/ribosome/polypeptide ternary complexes. As complex formation is fundamental to successful ribosome display, these improvements resulted in a dramatic increase in the mRNA recovery rate. As a result, a approximately 12,000-fold enrichment of single-chain antibody (scFv) cDNA was achieved in a single round of selection. Specific selection of scFv mRNA from a 1:10(10) dilution in competitor mRNA was achieved with only three rounds of affinity selection. These findings, together with the results in the accompanying paper [T. Matsuura, H. Yanagida, J. Ushioda, I. Urabe, T. Yomo, Nascent chain, RNA, and ribosome complexes generated by pure translation system (see the accompanying paper).], demonstrate that the PURE system can provide a basis for reliable and reproducible ribosome display.     

Nitrophorin synthesis is modulated by protein kinase CK2

Rhodnius prolixus is a blood-sucking bug whose saliva contains a family of nitric oxide-carrying proteins named nitrophorins (NPs). Saliva is injected into the host bloodstream during insect feeding. Nitric oxide is then released from NPs and will act on vascular smooth muscle, promoting vasodilation. Epithelial cells of salivary glands then undergo a massive synthesis of antihemostatics including NPs which produces saliva for the next blood meal. Here, we demonstrate the transient activation of a protein kinase in the salivary glands of R. prolixus after a blood meal. Biochemical, immunological, and pharmacological assays were used to identify this enzyme as protein kinase CK2. CK2 is activated after a blood meal and decreases to basal levels when salivary gland refilling is resumed. Inhibition of CK2 blocked [(35)S]methionine incorporation into newly synthesized salivary gland proteins in cultured tissue. Dissected salivary glands were then incubated with the heme fluorescent analog palladium (II) mesoporphyrin IX (Pd-MP) in the presence of a selective cell-permeable CK2 inhibitor, TBB (4,5,6,7-tetrabromobenzotriazole). NP synthesis was quantified based on fluorescence of the Pd-MP group bound to the NP heme pocket. TBB dramatically blocked NP synthesis. Altogether, these data are the first demonstration to show that antihemostatic synthesis in a blood-sucking arthropods is under protein phosphorylation control.     

Selection of 5'-untranslated sequences that enhance initiation of translation in a cell-free protein synthesis system from wheat embryos

Random libraries of mRNA 5′-leader sequences were screened to obtain some sequences that can stimulate the translation initiation in a cell-free translation system from wheat embryos as efficiently as the Ω sequence from tobacco mosaic virus. Several sequences that are as useful as the Ω sequence and are homologous to no known sequences survived the screening. We expect that these sequences add useful options to the cell-free protein synthesis system that is becoming a powerful tool in the post-genomic researches.     

Prespore-to-stalk conversion involves the production of a pathway-specific glycoprotein, wst25, in the cellular slime mould Dictyostelium discoideum

We have previously identified a stalk-specific wheat germ agglutinin (WGA)-binding protein, wst34, in the cellular slime mould Dictyostelium discoideum [Biochem. Cell Biol. 68 (1990) 699]. Here, we found another stalk-specific WGA-binding protein, wst25, which was detected with two antisera that recognize wst34. Using the two marker proteins, we then analyzed and compared the pathways of prestalk-to-stalk maturation and prespore-to-stalk conversion in vitro and in vivo. Prestalk cells isolated from normally formed slugs can be converted to stalk cells (designated StI) in vitro with 8-bromo-cAMP (Br-cAMP), whereas prespore cells isolated from slugs can be converted to fully vacuolated stalk cells (designated StII) in vitro with Br-cAMP and DIF-1. During the process of prespore-to-stalk conversion, prespore-specific mRNAs, D19 and 2H3, disappeared rapidly, while prestalk-specific mRNAs, ecmA and ecmB, appeared at 2h of incubation and increased thereafter. Most importantly, however, the StII cells thus formed were biochemically different from the StI cells originated from prestalk cells; that is, StI cells expressed wst34 but not wst25, while StII cells expressed wst25 but not wst34. When prespore cells isolated from slugs were allowed to develop on a substratum, they differentiated into spores and stalk cells and formed fruiting bodies, and the stalk cells formed from prespore cells in vivo expressed wst25 but not wst34. The present results indicate that there are two types of stalk cells, StI (prestalk-origin) and StII (prespore-origin), and that wst34 and wst25 are the specific markers for StI and StII, respectively.     

Combinatorial, selective and reversible control of gene expression using oligodeoxynucleotides in a cell-free protein synthesis system

Herein we describe the methods for selective and reversible regulation of gene expression using antisense oligodeoxynucleotides (ODNs) in a cell-free protein synthesis system programmed with multiple DNAs. Either a complete shut down or controlled level of gene expression was attained through the antisense ODN-mediated regulation of mRNA stability in the reaction mixture. In addition to the primary control of gene expression, we also demonstrate that the inhibition of protein synthesis can be reversed by using an anti-antisense ODN sequence that strips the antisense ODN off the target sequence of mRNA. As a result, sequential additions of the antisense and anti-antisense ODNs enabled the stop-and-go expression of protein molecules. Through the on-demand regulation of gene expression, presented results will provide a versatile platform for the analysis and understanding of the complicated networks of biological components.     

Membrane protein synthesis in cell-free systems: From bio-mimetic systems to bio-membranes

When taking up the gauntlet of studying membrane protein functionality, scientists are provided with a plethora of advantages, which can be exploited for the synthesis of these difficult-to-express proteins by utilizing cell-free protein synthesis systems. Due to their hydrophobicity, membrane proteins have exceptional demands regarding their environment to ensure correct functionality. Thus, the challenge is to find the appropriate hydrophobic support that facilitates proper membrane protein folding. So far, various modes of membrane protein synthesis have been presented. Here, we summarize current state-of-the-art methodologies of membrane protein synthesis in biomimetic-supported systems. The correct folding and functionality of membrane proteins depend in many cases on their integration into a lipid bilayer and subsequent posttranslational modification. We highlight cell-free systems utilizing the advantages of biological membranes.