Efficient translation of tobacco mosaic virus RNA and rabbit globin 9S RNA in a cell-free system from commercial wheat germ

Cell-free protein production of a gamma secretase homolog

Cleavage of the transmembrane domain (TMD) of amyloid-β precursor protein (APP) by γ-secretase, an intramembrane aspartyl protease, generates Aβ peptides of various lengths that form plaques in the brains of Alzheimer's disease patients. Although the debate has not been finally resolved whether these plaques trigger the onset of Alzheimer's or are side products, disease-related mutations suggest their implication in the etiology of the dementia. These occur both in presenilin, the catalytic subunit of γ-secretase, and in the TMD of APP. Despite two seminal cryo-electron microscopy structures that show the complex of γ-secretase with its substrates APP and Notch, the mechanism of γ-secretase is not yet fully understood. Especially on which basis it selects its substrates is still an enigma. The presenilin homolog PSH from the archaeon Methanoculleus marisnigri JR1 (MCMJR1) is catalytically active without accessory proteins in contrast to γ-secretase making it an excellent model for studies of the basic cleavage process. We here focused on the cell-free expression of PSH screening a range of conditions. Cleavage assays to verify the activity show that not only the yield, but mainly the activity of the protease depends on the careful selection of expression conditions. Optimal results were found for a cell-free expression at relatively low temperature, 20 °C, employing cell lysates prepared from E. coli Rosetta cells. To speed up protein preparation for immediate functional assays, a crude purification protocol was developed. This allows to produce ready-made PSH in a fast and efficient manner in less than two days.

Cell-free protein synthesis system: A new frontier for sustainable biotechnology-based products

Cell-free protein synthesis (CFPS) system is an innovative technology with a wide range of potential applications that could challenge current thinking and provide solutions to environmental and health issues. CFPS system has been demonstrated to be a successful way of producing biomolecules in a variety of applications, including the biomedical industry. Although there are still obstacles to overcome, its ease of use, versatility, and capacity for integration with other technologies open the door for it to continue serving as a vital instrument in synthetic biology research and industry. In this review, we mainly focus on the cell-free based platform for various product productions. Moreover, the challenges in the bio-therapeutic aspect using cell-free systems and their future prospective for the improvement and sustainability of the cell free systems.

Membrane protein synthesis: no cells required

Despite advances in membrane protein (MP) structural biology and a growing interest in their applications, these proteins remain challenging to study. Progress has been hindered by the complex nature of MPs and innovative methods will be required to circumvent technical hurdles. Cell-free protein synthesis (CFPS) is a burgeoning technique for synthesizing MPs directly into a membrane environment using reconstituted components of the cellular transcription and translation machinery in vitro. We provide an overview of CFPS and how this technique can be applied to the synthesis and study of MPs. We highlight numerous strategies including synthesis methods and folding environments, each with advantages and limitations, to provide a survey of how CFPS techniques can advance the study of MPs.

Advancing synthetic biology through cell-free protein synthesis

The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.

Cell-Free Expression of De Novo Designed Peptides That Form β-Barrel Nanopores

Nanopore sensing has attracted much attention as a rapid, simple, and label-free single-molecule detection technology. To apply nanopore sensing to extensive targets including polypeptides, nanopores are required to have a size and structure suitable for the target. We recently designed a de novo β-barrel peptide nanopore (SVG28) that constructs a stable and monodispersely sized nanopore. To develop the sizes and functionality of peptide nanopores, systematic exploration is required. Here we attempt to use a cell-free synthesis system that can readily express peptides using transcription and translation. Hydrophilic variants of SVG28 were designed and expressed by the PURE system. The peptides form a monodispersely sized nanopore, with a diameter 1.1 or 1.5 nm smaller than that of SVG28. Such cell-free synthesizable peptide nanopores have the potential to enable the systematic custom design of nanopores and comprehensive sequence screening of nanopore-forming peptides.

Adventures in Life and Science, from Light to Rhythms

The author describes her life's pathway from her beginnings at a time when women were not well represented in the sciences. Her grandparents were immigrants to the United States. Although her parents were not able to go to college because of the Great Depression, they supported her education and other adventures. In addition to her interest in science, she describes her interest and involvement in politics. Her education at Oberlin, Stanford, and Harvard prepared her for her independent career at the University of California, Los Angeles, where she was an affirmative action appointment. Her research initially centered on the plant photoreceptor phytochrome, but later in her career she investigated circadian rhythms in plants, discovering and characterizing one of the members of the central oscillator.

Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology

Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.

Expressing Cloned Genes for Protein Production, Purification, and Analysis

Obtaining high quantities of a specific protein directly from native sources is often challenging, particularly when dealing with human proteins. To overcome this obstacle, many researchers take advantage of heterologous expression systems by cloning genes into artificial vectors designed to operate within easily cultured cells, such as Escherichia coli, Pichia pastoris (yeast), and several varieties of insect and mammalian cells. Heterologous expression systems also allow for easy modification of the protein to optimize expression, mutational analysis of specific sites within the protein and facilitate their purification with engineered affinity tags. Some degree of purification of the target protein is usually required for functional analysis. Purification to near homogeneity is essential for characterization of protein structure by X-ray crystallography or nuclear magnetic resonance (NMR) and characterization of the biochemical and biophysical properties of a protein, because contaminating proteins almost always adversely affect the results. Methods for producing and purifying proteins in several different expression platforms and using a variety of vectors are introduced here.

In Vitro Production of Perdeuterated Proteins in H2O for Biomolecular NMR Studies

The cell-free synthesis is an efficient strategy to produce in large scale protein samples for structural investigations. In vitro synthesis allows for significant reduction of production time, simplification of purification steps and enables production of both soluble and membrane proteins. The cell-free reaction is an open system and can be performed in presence of many additives such as cofactors, inhibitors, redox systems, chaperones, detergents, lipids, nanodisks, and surfactants to allow for the expression of toxic membrane proteins or intrinsically disordered proteins. In this chapter we present protocols to prepare E. coli S30 cellular extracts, T7 RNA polymerase, and their use for in vitro protein expression. Optimizations of the protocol are presented for preparation of protein samples enriched in deuterium, a prerequisite for the study of high-molecular-weight proteins by NMR spectroscopy. An efficient production of perdeuterated proteins is achieved together with a full protonation of all the amide NMR probes, without suffering from residual protonation on aliphatic carbons. Application to the production of the 468 kDa TET2 protein assembly for NMR investigations is presented.

Development of a cell-free protein synthesis system for practical use

Conventional cell-free protein synthesis systems had been the major platform to study the mechanism behind translating genetic information into proteins, as proven in the central dogma of molecular biology. Albeit being powerful research tools, most of the in vitro methods at the time failed to produce enough protein for practical use. Tremendous efforts were being made to overcome the limitations of in vitro translation systems, though mostly with limited success. While great knowledge was accumulated on the translation mechanism and ribosome structure, researchers rationalized that it may be impossible to fully reconstitute such a complex molecular process in a test tube. This review will examine how we have solved the difficulties holding back progress. Our newly developed cell-free protein synthesis system is based on wheat embryos and has many excellent characteristics, in addition to its high translation activity and robustness. Combined with other novel elementary technologies, we have established cell-free protein synthesis systems for practical use in research and applied sciences.

Structural investigations of cell-free expressed G protein-coupled receptors

G protein-coupled receptors (GPCRs) are of great pharmaceutical interest and about 35% of the commercial drugs target these proteins. Still there is huge potential left in finding molecules that target new GPCRs or that modulate GPCRs differentially. For a rational drug design, it is important to understand the structure, binding and activation of the protein of interest. Structural investigations of GPCRs remain challenging, although huge progress has been made in the last 20 years, especially in the generation of crystal structures of GPCRs. This is mostly caused by issues with the expression yield, purity or labeling. Cell-free protein synthesis (CFPS) is an efficient alternative for recombinant expression systems that can potentially address many of these problems. In this article the use of CFPS for structural investigations of GPCRs is reviewed. We compare different CFPS systems, including the cellular basis and reaction configurations, and strategies for an efficient solubilization. Next, we highlight recent advances in the structural investigation of cell-free expressed GPCRs, with special emphasis on the role of photo-crosslinking approaches to investigate ligand binding sites on GPCRs.

Proton-Detected Solid-State NMR of the Cell-Free Synthesized α-Helical Transmembrane Protein NS4B from Hepatitis C Virus

Proton-detected 100 kHz magic-angle-spinning (MAS) solid-state NMR is an emerging analysis method for proteins with only hundreds of microgram quantities, and thus allows structural investigation of eukaryotic membrane proteins. This is the case for the cell-free synthesized hepatitis C virus (HCV) nonstructural membrane protein 4B (NS4B). We demonstrate NS4B sample optimization using fast reconstitution schemes that enable lipid-environment screening directly by NMR. 2D spectra and relaxation properties guide the choice of the best sample preparation to record 2D 1 H-detected 1 H,15 N and 3D 1 H,13 C,15 N correlation experiments with linewidths and sensitivity suitable to initiate sequential assignments. Amino-acid-selectively labeled NS4B can be readily obtained using cell-free synthesis, opening the door to combinatorial labeling approaches which should enable structural studies.

Automated Cell-Free Multiprotein Synthesis Facilitates the Identification of a Secretory, Oligopeptide Elicitor-Like, Immunoreactive Protein of the Oomycete Pythium insidiosum

Technical limitations of conventional biotechnological methods (i.e., genetic engineering and protein synthesis) prevent extensive functional studies of the massive amounts of genetic information available today. We employed a cell-free protein synthesis system to rapidly and simultaneously generate multiple proteins from genetic codes of the oomycete Pythium insidiosum, which causes the life-threatening disease called pythiosis, in humans and animals worldwide. We aimed to screen for potential diagnostic and therapeutic protein targets of this pathogen. Eighteen proteins were synthesized. Of the 18 proteins, one was a secreted immunoreactive protein, called I06, that triggered host immunity and was recognized explicitly by all tested sera from pythiosis patients. It is one of the OPEL proteins; these proteins are present only in the unique group of microorganisms called oomycetes. Here, we demonstrated that cell-free protein synthesis was useful for the production of multiple proteins to facilitate functional studies and identify a potential target for diagnosis and treatment of pythiosis.

Protein production relies on time-consuming genetic engineering and in vivo expression, which is a bottleneck for functional studies in the postgenomic era. Cell-free protein synthesis (CFPS) overcomes the limitation of in vivo protein biosynthesis by processing in vitro transcription and translation of multiple genes to proteins within hours. We employed an automated CFPS to simultaneously synthesize proteins from 24 genes of the oomycete Pythium insidiosum (which causes the life-threatening disease pythiosis) and screen for a diagnostic and therapeutic target. CFPS successfully synthesized 18 proteins (∼75% success rate). One protein, namely, I06, was explicitly recognized by all pythiosis sera, but not control sera, tested. Py. insidiosum secreted a significant amount of I06. The protein architecture of I06 is compatible with the oligopeptide elicitor (OPEL) of the phylogenetically related plant-pathogenic oomycete Phytophthora parasitica. The OPEL-like I06 protein of Py. insidiosum can stimulate host antibody responses, similar to the P. parasitica OPEL that triggers plant defense mechanisms. OPEL-like I06 homologs are present only in the oomycetes. Py. insidiosum contains two OPEL-like I06 homologs, but only one of the two homologs was expressed during hyphal growth. Twenty-nine homologs derived from 15 oomycetes can be phylogenetically divided into two groups. The OPEL-like genes might occur in the common ancestor, before independently undergoing gene gain and loss during the oomycete speciation. In conclusion, CFPS offers a fast in vitro protein synthesis. CFPS simultaneously generated multiple proteins of Py. insidiosum and facilitated the identification of the secretory OPEL-like I06 protein, a potential target for the development of a control measure against the pathogen.

IMPORTANCE Technical limitations of conventional biotechnological methods (i.e., genetic engineering and protein synthesis) prevent extensive functional studies of the massive amounts of genetic information available today. We employed a cell-free protein synthesis system to rapidly and simultaneously generate multiple proteins from genetic codes of the oomycete Pythium insidiosum, which causes the life-threatening disease called pythiosis, in humans and animals worldwide. We aimed to screen for potential diagnostic and therapeutic protein targets of this pathogen. Eighteen proteins were synthesized. Of the 18 proteins, one was a secreted immunoreactive protein, called I06, that triggered host immunity and was recognized explicitly by all tested sera from pythiosis patients. It is one of the OPEL proteins; these proteins are present only in the unique group of microorganisms called oomycetes. Here, we demonstrated that cell-free protein synthesis was useful for the production of multiple proteins to facilitate functional studies and identify a potential target for diagnosis and treatment of pythiosis.

RNAi-Based Biocontrol of Wheat Nematodes Using Natural Poly-Component Biostimulants

With the growing global demands on sustainable food production, one of the biggest challenges to agriculture is associated with crop losses due to parasitic nematodes. While chemical pesticides have been quite successful in crop protection and mitigation of damage from parasites, their potential harm to humans and environment, as well as the emergence of nematode resistance, have necessitated the development of viable alternatives to chemical pesticides. One of the most promising and targeted approaches to biocontrol of parasitic nematodes in crops is that of RNA interference (RNAi). In this study we explore the possibility of using biostimulants obtained from metabolites of soil streptomycetes to protect wheat (Triticum aestivum L.) against the cereal cyst nematode Heterodera avenae by means of inducing RNAi in wheat plants. Theoretical models of uptake of organic compounds by plants, and within-plant RNAi dynamics, have provided us with useful insights regarding the choice of routes for delivery of RNAi-inducing biostimulants into plants. We then conducted in planta experiments with several streptomycete-derived biostimulants, which have demonstrated the efficiency of these biostimulants at improving plant growth and development, as well as in providing resistance against the cereal cyst nematode. Using dot blot hybridization we demonstrate that biostimulants trigger a significant increase of the production in plant cells of si/miRNA complementary with plant and nematode mRNA. Wheat germ cell-free experiments show that these si/miRNAs are indeed very effective at silencing the translation of nematode mRNA having complementary sequences, thus reducing the level of nematode infestation and improving plant resistance to nematodes. Thus, we conclude that natural biostimulants produced from metabolites of soil streptomycetes provide an effective tool for biocontrol of wheat nematode.

Protein sample preparation for solid-state NMR investigations

Preparation of a protein sample for solid-state NMR is in many aspects similar to solution-state NMR approaches, mainly with respect to the need for stable isotope labeling. But the possibility of using solid-state NMR to investigate membrane proteins in (native) lipids adds the important requirement of adapted membrane-reconstitution schemes. Also, dynamic nuclear polarization and paramagnetic NMR in solids need specific schemes using metal ions and radicals. Sample sedimentation has enabled structural investigations of objects inaccessible to other structural techniques, but rotor filling using sedimentation has become increasingly complex with smaller and smaller rotors, as needed for higher and higher magic-angle spinning (MAS) frequencies. Furthermore, solid-state NMR can investigate very large proteins and their complexes without the concomitant increase in line widths, motivating the use of selective labeling and unlabeling strategies, as well as segmental labeling, to decongest spectra. The possibility of investigating sub-milligram amounts of protein today using advanced fast MAS techniques enables alternative protein synthesis schemes such as cell-free expression. Here we review these specific aspects of solid-state NMR sample preparation.

Wheat Germ Cell-Free Overexpression for the Production of Membrane Proteins

Due to their hydrophobic nature, membrane proteins are notoriously difficult to express in classical cell-based protein expression systems. Often toxic, they also undergo degradation in cells or aggregate in inclusion bodies, making delicate issues further solubilization and renaturation. These are major bottlenecks in their structural and functional analysis. The wheat germ cell-free (WGE-CF) system offers an effective alternative not only to classical cell-based protein expression systems but also to other cell-free systems for the expression of membrane proteins. The WGE-CF indeed allows the production of milligram amounts of membrane proteins in a detergent-solubilized, homogenous, and active form. Here, we describe the method to produce a viral integral membrane protein, which is the non-structural protein 2 (NS2) of hepatitis C virus, in view of structural studies by solid-state NMR in a native-like lipid environment.

Synthetic biology platform technologies for antimicrobial applications

The growing prevalence of antibiotic resistance calls for new approaches in the development of antimicrobial therapeutics. Likewise, improved diagnostic measures are essential in guiding the application of targeted therapies and preventing the evolution of therapeutic resistance. Discovery platforms are also needed to form new treatment strategies and identify novel antimicrobial agents. By applying engineering principles to molecular biology, synthetic biologists have developed platforms that improve upon, supplement, and will perhaps supplant traditional broad-spectrum antibiotics. Efforts in engineering bacteriophages and synthetic probiotics demonstrate targeted antimicrobial approaches that can be fine-tuned using synthetic biology-derived principles. Further, the development of paper-based, cell-free expression systems holds promise in promoting the clinical translation of molecular biology tools for diagnostic purposes. In this review, we highlight emerging synthetic biology platform technologies that are geared toward the generation of new antimicrobial therapies, diagnostics, and discovery channels.

My Path from Chemistry to Phytochrome and Circadian Rhythms

I summarize my scientific journey from my first interest in science to my career investigating how plants use the phytochrome photoreceptor to regulate what genes they express. I then describe how this work led to an understanding of how circadian rhythms function in plants and to the discovery of CCA1, a component of the plant central oscillator.

Cell-Free Protein Synthesis: Pros and Cons of Prokaryotic and Eukaryotic Systems

From its start as a small-scale in vitro system to study fundamental translation processes, cell-free protein synthesis quickly rose to become a potent platform for the high-yield production of proteins. In contrast to classical in vivo protein expression, cell-free systems do not need time-consuming cloning steps, and the open nature provides easy manipulation of reaction conditions as well as high-throughput potential. Especially for the synthesis of difficult to express proteins, such as toxic and transmembrane proteins, cell-free systems are of enormous interest. The modification of the genetic code to incorporate non-canonical amino acids into the target protein in particular provides enormous potential in biotechnology and pharmaceutical research and is in the focus of many cell-free projects. Many sophisticated cell-free systems for manifold applications have been established. This review describes the recent advances in cell-free protein synthesis and details the expanding applications in this field.

Overview of cell-free protein synthesis: historic landmarks, commercial systems, and expanding applications

During the early days of molecular biology, cell-free protein synthesis played an essential role in deciphering the genetic code and contributed to our understanding of translation of protein from messenger RNA. Owing to several decades of major and incremental improvements, modern cell-free systems have achieved higher protein synthesis yields at lower production costs. Commercial cell-free systems are now available from a variety of material sources, ranging from "traditional" E. coli, rabbit reticulocyte lysate, and wheat germ extracts, to recent insect and human cell extracts, to defined systems reconstituted from purified recombinant components. Although each cell-free system has certain advantages and disadvantages, the diversity of the cell-free systems allows in vitro synthesis of a wide range of proteins for a variety of downstream applications. In the post-genomic era, cell-free protein synthesis has rapidly become the preferred approach for high-throughput functional and structural studies of proteins and a versatile tool for in vitro protein evolution and synthetic biology. This unit provides a brief history of cell-free protein synthesis and describes key advances in modern cell-free systems, practical differences between widely used commercial cell-free systems, and applications of this important technology.

Improved cell-free RNA and protein synthesis system

Cell-free RNA and protein synthesis (CFPS) is becoming increasingly used for protein production as yields increase and costs decrease. Advances in reconstituted CFPS systems such as the Protein synthesis Using Recombinant Elements (PURE) system offer new opportunities to tailor the reactions for specialized applications including in vitro protein evolution, protein microarrays, isotopic labeling, and incorporating unnatural amino acids. In this study, using firefly luciferase synthesis as a reporter system, we improved PURE system productivity up to 5 fold by adding or adjusting a variety of factors that affect transcription and translation, including Elongation factors (EF-Ts, EF-Tu, EF-G, and EF4), ribosome recycling factor (RRF), release factors (RF1, RF2, RF3), chaperones (GroEL/ES), BSA and tRNAs. The work provides a more efficient defined in vitro transcription and translation system and a deeper understanding of the factors that limit the whole system efficiency.

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.

Synthesis and site-directed fluorescence labeling of azido proteins using eukaryotic cell-free orthogonal translation systems

Eukaryotic cell-free systems based on wheat germ and Spodoptera frugiperda insect cells were equipped with an orthogonal amber suppressor tRNA-synthetase pair to synthesize proteins with a site-specifically incorporated p-azido-l-phenylalanine residue in order to provide their chemoselective fluorescence labeling with azide-reactive dyes by Staudinger ligation. The specificity of incorporation and bioorthogonality of labeling within complex reaction mixtures was shown by means of translation and fluorescence detection of two model proteins: β-glucuronidase and erythropoietin. The latter contained the azido amino acid in proximity to a signal peptide for membrane translocation into endogenous microsomal vesicles of the insect cell-based system. The results indicate a stoichiometric incorporation of the azido amino acid at the desired position within the proteins. Moreover, the compatibility of cotranslational protein translocation, including glycosylation and amber suppression-based incorporation of p-azido-l-phenylalanine within a cell-free system, is demonstrated. The presented approach should be particularly useful for providing eukaryotic and membrane-associated proteins for investigation by fluorescence-based techniques.

The absence of A-to-I editing in the anticodon of plant cytoplasmic tRNA (Arg) ACG demands a relaxation of the wobble decoding rules

It is a prevalent concept that, in line with the Wobble Hypothesis, those tRNAs having an adenosine in the first position of the anticodon become modified to an inosine at this position. Sequencing the cDNA derived from the gene coding for cytoplasmic tRNA (Arg) ACG from several higher plants as well as mass spectrometric analysis of the isoacceptor has revealed that for this kingdom an unmodified A in the wobble position of the anticodon is the rule rather than the exception. In vitro translation shows that in the plant system the absence of inosine in the wobble position of tRNA (Arg) does not prevent decoding. This isoacceptor belongs to the class of tRNA that is imported from the cytoplasm into the mitochondria of higher plants. Previous studies on the mitochondrial tRNA pool have demonstrated the existence of tRNA (Arg) ICG in this organelle. In moss the mitochondrial encoded distinct tRNA (Arg) ACG isoacceptor possesses the I34 modification. The implication is that for mitochondrial protein biosynthesis A-to-I editing is necessary and occurs by a mitochondrion-specific deaminase after import of the unmodified nuclear encoded tRNA (Arg) ACG.

Chapter 2. Development of key technologies for high-throughput cell-free protein production with the extract from wheat embryos

The cell-free translation system from wheat embryos had been considered to be inefficient as compared with the E. coli cell-based and cell-free protein production methods. However, it was revealed that the extract from extensively washed wheat embryo particles can provide a very productive cell-free protein synthesis system. Since then, the method has been improved, so that it fits the postgenomic researches. New mRNA configurations enabled us to synthesize many different proteins in parallel and to prepare large amounts of proteins, which fits the need for screening of suitable proteins for structural and functional analyses before large-scale production. The new reaction formats promoted the developments of new machines that perform highly parallel and highly productive protein synthesis reactions automatically. It was revealed that, by parallel synthesis of many proteins, much more multidomain proteins are produced in soluble forms in the wheat system than in the prokaryotic systems. The wheat system provides a rapid and cost-effective method for stable isotope labeling of proteins for NMR analyses. Selenomethionine substitution of proteins for X-ray crystallography through the cell-free synthesis was also achieved. Synthesis of some families of proteins that were difficult to be produced by conventional methods has been tested. At least, cytotoxic restriction enzymes were readily produced in a large amount. Some multisubunit proteins and cofactor-binding proteins could be synthesized by the method and were characterized successfully. Membrane proteins have also been tested, and a transporter was synthesized in an active form. Although some issues remains to be solved, we expect that the wheat cell-free protein synthesis system can contribute to the structural and functional genomics and to the future understanding of life.

Structural diversity and differential light control of mRNAs coding for angiosperm glyceraldehyde-3-phosphate dehydrogenases

Subunits A and B of chloroplast glyceraldehyde-3-phosphate dehydrogenase are synthesized as higher molecular weight precursors when polyadenylylated mRNA from angiosperm seedlings is translated in vitro by wheat germ ribosomes. The in vivo levels of mRNA coding for these precursors are strongly light dependent, and the increase in translational activity stimulated by continuous white light, relative to dark-grown seedlings, is at least 5- to 10-fold for the seven plant species investigated. As opposed to this, light does not seem to change mRNA levels coding for cytosolic glyceraldehyde-3-phosphate dehydrogenase, and the polypeptides synthesized in vitro have the same size as the authentic subunits. In addition, precursors of the chloroplast enzyme were identified for 12 different angiosperm species and compared with their respective subunits synthesized in vivo. The patterns of the in vitro and in vivo products correlate in several major characteristics. They both display a remarkable interspecific heterogeneity with respect to size and number of polypeptides. The peptide extensions of the enzyme precursors calculated from these data vary between 4,000 and 12,000 daltons and seem to fall into three major size classes. The present data demonstrate that chloroplast glyceraldehyde-3-phosphate dehydrogenase, like its cytosolic counterpart, is encoded in the nucleus. Yet, the two dehydrogenases are controlled differently at both the ontogenetic and phylogenetic levels. They follow separate biosynthetic pathways with respect to light regulation, post-translational processing, and transport and also exhibit different evolutionary rates. The fast evolutionary change observed for the chloroplast enzyme contrasts sharply with the conservative structure and sequence of the cytosolic enzyme.

Intercellular communication in plants: Evidence for a rapidly generated, bidirectionally transmitted wound signal

Wounding (whether by excision, abrasion, or puncture) elicited rapid, massive, and enduring formation of polysomes in aged pea stems and other mature tissues. The response depended on temperature and severity of wounding but not on water uptake, and it occurred in tissues adjacent to, distant from, above, and below the site of injury. The kinetics of polysome formation were similar in tissues adjacent to or up to 150 mm distant from the point of injury. The wound-induced increases in protein-synthesizing capacity of the polysomes both in vivo and in vitro were much greater than the increases in rRNA and poly(A)(+)RNA. The results indicate that wounding evokes the almost immediate production of a wound signal that travels rapidly both acropetally and basipetally to stimulate the recruitment of preexisting ribosomes onto primarily preexisting mRNA, thence forming polysomes with greatly enhanced protein-synthesizing capacity.

Maturation of catalase precursor proceeds to a different extent in glyoxysomes and leaf peroxisomes of pumpkin cotyledons

As an approach to study the mechanism of the microbody transition (glyoxysomes to leaf peroxisomes) in greening pumpkin cotyledons, catalase molecules were purified from the two different types of microbody and their structural properties were compared. The purified glyoxysomal catalase was found to consist of four identical subunits (55 kDa), whereas the leaf peroxisomal catalase contains two different forms of monomeric subunit (55 and 59 kDa). These different catalase species cross-reacted with the rabbit antibody raised against the glyoxysomal enzyme. During gel filtration on an Ultrogel AcA 34 column, the leaf peroxisomal 55-kDa polypeptide eluted slightly faster than the leaf peroxisomal 59-kDa polypeptide. The profile of catalase activities exactly paralleled the elution pattern of the 55-kDa molecules, which indicated that the 59-kDa polypeptide was enzymically inactive. Peptide mapping analysis using Staphylococcus aureus protease V8 showed that the glyoxysomal 55-kDa polypeptide was identical to the leaf peroxisomal 55-kDa species, whereas the leaf peroxisomal 59-kDa polypeptide had a different primary structure from the 55-kDa polypeptide. In an in vitro translation system directed by mRNA isolated from etiolated and green cotyledons, glyoxysomal and leaf peroxisomal catalases were synthesized as the identical 59-kDa polypeptide. From peptide mapping analysis, the in vitro-translated 59-kDa polypeptide was found to have a nearly identical primary structure to that of the leaf peroxisomal 59-kDa species. In vivo pulse-chase labeling experiments using etiolated cotyledons showed the conversion of the 59-kDa polypeptide to the 55-kDa molecular species. The overall results strongly indicate that the 59-kDa polypeptide is a precursor form of catalase in pumpkin cotyledons.

Proteins encoded by Agrobacterium tumefaciens Ti plasmid DNA (T-DNA) in crown gall tumors

In order to detect proteins that may be produced in crown gall tumors as a result of expression of incorporated Agrobacterium tumefaciens Ti plasmid DNA (T-DNA), we have isolated mRNA complementary to T-DNA and translated this in a protein-synthesizing system derived from wheat germ. mRNA prepared from cultured E1 tumor from Nicotiana tabacum hybridized with HindIII fragment 1 sequences of T-DNA immobilized on cellulose nitrate filters. Two proteins of 30,000 and 16,500 M(r) were produced when this selected RNA was released and translated. Other tumor lines from N. tabacum were investigated, and a protein of slightly less than 30,000 M(r) was encoded by HindIII fragment 1 sequences of 15955/01 tumor. No products were observed for 15955/1 tumor line, which differs from E1/B6-806 and 15955/01 in that it does not produce octopine. mRNA species of each of the tumor lines hybridized to Bst I fragment 8 sequences of T-DNA and produced a common protein of 15,000 M(r). Because this protein is derived from the region of the T-DNA that is conserved in octopine- and nopaline-type crown gall tumors, it may play a role in oncogenicity.

Isolation and characterization of cDNA clones for carrot extensin and a proline-rich 33-kDa protein

Extensins are hydroxyproline-rich glycoproteins associated with most dicotyledonous plant cell walls. To isolate cDNA clones encoding extensin, we started by isolating poly(A)(+) RNA from carrot root tissue, and then translating the RNA in vitro, in the presence of tritiated leucine or proline. A 33-kDa peptide was identified in the translation products as a putative extensin precursor because: (i) it is rich in proline and poor in leucine, and (ii) the message appears to be more abundant when carrot tissue is wounded. From a cDNA library constructed with poly(A)(+) RNA from wounded carrots, one cDNA clone (pDC5) was identified that specifically hybridized to poly(A)(+) RNA encoding this 33-kDa peptide. We isolated three cDNA clones (pDC11, pDC12, and pDC16) from another cDNA library using pDC5 as a probe. DNA sequence data, RNA hybridization analysis, and hybrid released in vitro translation indicate that the cDNA clone pDC11 encodes extensin and that cDNA clones pDC12 and pDC16 encode the 33-kDa peptide, which as yet has an unknown identity and function. The assumption that the 33-kDa peptide was an extensin precursor was invalid. RNA hybridization and DNA sequence analysis indicate that pDC5 is a hybrid clone corresponding to two RNA species. RNA hybridization analysis showed that RNA encoded by both clone types is accumulated upon wounding.

Heat shock proteins of higher plants

The pattern of protein synthesis changes rapidly and dramatically when the growth temperature of soybean seedling tissue is increased from 28 degrees C (normal) to about 40 degrees C (heat shock). The synthesis of normal proteins is greatly decreased and a new set of proteins, "heat shock proteins," is induced. The heat shock proteins of soybean consist of 10 new bands on one-dimensional NaDodSO(4) gels; a more complex pattern is observed on two-dimensional gels. When the tissue is returned to 28 degrees C after 4 hr at 40 degrees C, there is progressive decline in the synthesis of heat shock proteins and reappearance of a normal pattern of synthesis by 3 or 4 hr. In vitro translation of poly(A)(+)RNAs isolated from tissues grown at 28 and 40 degrees C shows that the heat shock proteins are translated from a new set of mRNAs induced at 40 degrees C; furthermore, the abundant class mRNAs for many of the normal proteins persist even though they are translated weakly (or not at all) in vivo at 40 or 42.5 degrees C. The heat shock response in soybean appears similar to the much-studied heat shock phenomenon in Drosophila.

Synthesis of pathogenesis-related proteins in tobacco is regulated at the level of mRNA accumulation and occurs on membrane-bound polysomes

The pathogenesis-related (PR) proteins of tobacco plants are induced in response to a variety of pathogenic and chemical agents. Although the function of these proteins is unknown, they are associated with resistance to multiplication and/or spread of tobacco mosaic virus. We report that functional mRNAs encoding PR proteins are present only when synthesis of these proteins has been induced, suggesting that their synthesis is controlled in part at the level of mRNA accumulation. In addition PR proteins appear to be synthesized and processed in a manner analogous to proteins destined for the endoplasmic reticulum since (i) the in vitro translation products synthesized in the wheat-germ cell-free system are slightly larger than the in vivo products, (ii) translation of PR mRNAs in the rabbit reticulocyte lysate system is blocked unless that system is supplemented with dog pancreas microsomes, and (iii) mRNAs for PR proteins are associated predominantly with membrane-bound polysomes in vivo. This pathway of synthesis and posttranslational modification suggests possible sites of action of these proteins.

Specific heat shock proteins are transported into chloroplasts

We demonstrate that in three plant species-soybean, pea, and corn-certain nuclear-encoded heat shock proteins are transported into chloroplasts. In vitro translation products of poly(A)-RNA from control or heat-shocked plants were incubated with isolated intact pea chloroplasts and differences in the profile of imported proteins were analyzed. In all three species, abundant polypeptides between 21 and 27 kDa are present in the heat shock sample and absent in the controls. These polypeptides are protected from trypsin and chymotrypsin digestion after their import into chloroplasts and are recovered primarily with the soluble chloroplast protein fraction. Chloroplasts isolated from pea or corn leaves labeled in vivo at heat shock temperatures, but not at normal growth temperatures, contain the same polypeptides observed in vitro. Synthesis of the heat shock polypeptides can be inhibited in vivo by cycloheximide but not by chloramphenicol, further indicating they are products of cytoplasmic protein synthesis. The in vitro transport experiments demonstrate that synthesis of the chloroplast-localized heat shock proteins results from heat-induced accumulation of the corresponding poly(A)-RNAs. The same mRNAs are also produced in response to heat shock by a nonphotosynthetic tissue, the etiolated soybean hypocotyl.

Hormone-induced increase in levels of functional mRNA and alpha-amylase mRNA in barley aleurones

Incubation of barley aleurone cells with gibberellic acid produces a progressive increase in the RNA content of the cells. The activity of poly(A)-containing RNA, measured in an in vitro wheat germ protein-synthesizing system, reaches a maximum approximately 12 hr after hormone addition and declines thereafter. The structurally intact functional mRNA content in these cells, measured as poly(A)-RNA with 5' "caps," also shows a maximum at 12 hr and correlates with the translational capacity of poly(A)-RNA. Activation of mRNA by guanylylation or methylation after addition of gibberellic acid is ruled out. Available evidence indicates that gibberellic acid stimulates protein synthesis by increasing the synthesis of mRNA. Studies with cycloheximide suggest that the induction of synthesis of alpha-amylase mRNA by gibberellic acid requires protein synthesis after hormone addition.

Expression of wound tumor virus gene products in vivo and in vitro

Infection of Agallia constricta vector cell monolayers with wound tumor virus results in the synthesis of 12 virus-specific polypeptides. Confirmation that these polypeptides are virus encoded rather than virus induced was obtained by cell-free translation of in vitro synthesized viral mRNA. In addition, transcription by purified wound tumor virus particles was coupled with translation of the resulting transcripts in a wheat embryo cell-free extract. Six previously described structural polypeptides, one presumptive structural polypeptide, and five previously unidentified nonstructural polypeptides were synthesized in infected vector cell monolayers, in cell-free extracts directed by in vitro synthesized viral mRNA, and in the homologous plant cell-free system, in which viral transcription was coupled with translation. Pulse-chase experiments revealed no evidence of precursor-product relationships for the wound tumor virus-specific polypeptides.

Light regulation of specific mRNA species in Lemna gibba L. G-3

Polyadenylated RNA was isolated from Lemna gibba L. G-3 and translated in a cell-free system from wheat germ. When plants were placed into complete darkness for 4 days, then returned to light for 18 hr, increased amounts of polyadenylated mRNA for at least two polypeptides were detected by in vitro translation over those amounts present in the dark. These two polypeptides have molecular weights of 32,000 and 20,000. The 20,000 dalton polypeptide was identified by immunoprecipitation as the precursor to the small subunit of the photosynthetic enzyme ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39]. The polyadenylated mRNA that codes for the small subunit is not detectable by immunoprecipitation of translation products in the dark-treated tissue. Plants growing in the light actively synthesize both subunits of ribulose-1,5-bisphosphate carboxylase, but synthesis of these proteins was found to be greatly diminished in plants placed in darkness for 4 days. These results indicate that white light can dramatically affect the steady-state levels of specific polyadenylated mRNAs.

Purification and translation of zein messenger RNA from maize endosperm protein bodies

The messenger RNAs coding for the zein storage protein have been purified from other contaminating RNAs. The average molecular lengths are 1.1-1.2 kilobases, as determined by polyacrylamide gel electrophoresis and by electron microscopy. Products of messenger-dependent protein synthesis in vitro appear to be 1100 and 2000 daltons heavier than the native polypeptides. Zein is like secretory proteins in having a precursor with an additional amino-terminal sequence. Although only one mRNA is seen in polyacrylamide gel electrophoresis, the combined size of the polypeptide products formed exceeds the coding capacity for one message of the size determined in this study. This suggests that there are at least two mRNAs of similar sizes for the zein polypeptides rather than one dicistronic message.

The cell-free protein synthesis system from wheat germ

The wheat-germ cell-free protein synthesis system had been one of the most efficient eukaryotic cell-free systems since it was first developed in 1964. However, radio-labeled amino acids had long been essential for detection of the products. Since the discovery of a method for prevention of the contamination by a protein synthesis inhibitor originated from endosperm, the wheat cell-free system has found a wide variety of applications in postgenomic high-throughput screening, structural biology, medicine, and so on. In this chapter, we describe a method for preparation of the cell-free extract and a standard protein synthesis method, as the methods for the applications are found in later chapters.

In vitro translation of plant viral RNA

This unit describes the preparation of a wheat germ extract that provides all the soluble components of the plant translational machinery. Many RNA plant viruses have positive-strand genomes and the viral RNA serves as messenger RNA (mRNA). The preparation of mRNA by in vitro transcription is also described. The translation assay requires optimization of the amount of wheat germ extract, level of mRNA, and the concentration of Mg(2+) and K(+) for each mRNA. The translational efficiency of RNAs or mutants may be compared (e.g., capped versus uncapped RNAs to measure cap-independent translation) or the amount/size of the protein product may be determined.

Wheat germ cell-free translation, purification, and assembly of a functional human stearoyl-CoA desaturase complex

A wheat germ cell-free extract was used to perform in vitro translation of human stearoyl-CoA desaturase in the presence of unilamelar liposomes, and near complete transfer of the expressed integral membrane protein into the liposome was observed. Moreover, co-translation of the desaturase along with human cytochrome b(5) led to transfer of both membrane proteins into the liposomes. A simple, single step purification via centrifugation in a density gradient yielded proteoliposomes with the desaturase in high purity as judged by capillary electrophoresis. After in vitro reconstitution of the non-heme iron and heme active sites, the function of the reconstituted enzyme complex was demonstrated by conversion of stearoyl-CoA to oleoyl-CoA. This simple translation approach obviates the use of detergents or other lipids to stabilize and isolate a catalytically active integral membrane enzyme. The applicability of cell-free translation to the assembly and purification of other integral membrane protein complexes is discussed.

Isolation of a biologically active messenger RNA: preparation from fish pancreatic islets by oligo(2'-deoxythymidylic acid) affinity chromatography

RNA was extracted from the pancreatic islets of channel catfish in the presence of the ribonuclease inhibitor, diethyl pyrocarbonate (oxydiformate). High molecular weight RNA was observed on sucrose gradient analysis. enrichment of mRNA was achieved by oligo(2'-deoxythymidylic acid)-cellulose affinity chromatography. The mRNA fraction stimulated incorporation of [35S]methionine into protein up to 30-times the background in the wheat-germ cell-free system. Analysis by sodium dodecyl sulphate-polyacrylamide gel electrophoresis revealed two major proteins corresponding to molecular weights of 27 000 and 11 000. These proteins were not observed in the absence of mRNA or in the presence of mRNAs from other tissues. They were also synthesized in the ascites tumour cell-free system. No protein co-migrating with proinsulin or insulin was detected in either the ascites or wheat-germ cell-free systems. Pancreatic islet slices also synthesized the proteins of 27 000 and 11 000 molecular weight and smaller ones as well.

Overview of eukaryotic in vitro translation and expression systems

The ability to investigate cellular processes in vitro permits detailed analysis of the process and its molecular components. Eukaryotic translation and expression is one system that has been well studied. This overview describes the development of in vitro systems, including such approaches as continuous-flow systems, coupled transcription/translation, and the incorporation of non-natural amino acids. It also discusses molecular and genetic studies to probe translation, including post-translational fate of the synthesized proteins.

Expression and purification of recombinant wheat translation initiation factors eIF1, eIF1A, eIF4A, eIF4B, eIF4F, eIF(iso)4F, and eIF5

Protein synthesis initiation factors from wheat germ were cloned into E. coli expression vectors for expression and purification. The ability to obtain large amounts of functional initiation factors and mutants of the factors will facilitate the biophysical and biochemical analysis of the process of initiation in plants. The initiation factors, eIF1, eIF1A, eIF4A, eIF4B, eIF4F, eIF(iso)4F, and eIF5, were successfully expressed and purified from E. coli. In most cases, the use of 6X-histidine tags was avoided to prevent any possible artifacts of folding or activity because of the presence of the tag. The amounts of highly purified wheat initiation factors obtained ranged from 0.5 to 24mg of protein per liter of culture, depending on the particular initiation factor. The initiation factors were of very high purity, and the activities of the wheat recombinant factors purified from E. coli were found to be comparable to or better than those purified from wheat germ.