Eukaryotic Cell-free Systems Research Articles

Fluorescent labeling of cell-free synthesized proteins by incorporation of fluorophore-conjugated nonnatural amino acids

Although fluorescent dyes, such as fluorescein derivatives, have bulky and complex structures, nonnatural amino acids carrying these fluorescein derivatives are acceptable by the Escherichia coli ribosome and are useful for the cotranslational fluorescent labeling of cell-free synthesized proteins. Surprisingly, the incorporation efficiency of nonnatural amino acids carrying fluorescein derivatives into translated proteins depends on the source of the translational machinery used in cell-free protein synthesis. That is, whereas the E. coli ribosome efficiently supported the incorporation of nonnatural amino acids carrying fluorescein derivatives into a protein structure, no detectable fluorescent signal was observed from the protein expressed in the eukaryotic cell-free protein synthesis system performed in the presence of fluorescein-conjugated aminoacylated transfer RNA (tRNA).

Inhibition by suramin of protein synthesis in vitro. Ribosomes as the target of the drug

Suramin, a drug widely used both as a therapeutic agent and in research, inhibits translation in eukaryotic cell-free systems from rabbit reticulocyte lysate (IC 50 = 142–241 μM). Suramin affects both initiation (block of 43S pre-initiation complex formation) and elongation (impairment of poly(U) translation). The drug induces an increase in the pools of ribosomal subunits and the formation of high molecular weight ribosomal complexes, thus causing the disappearance of polysomes. Ribosomes isolated from suramin-treated translating mixtures are inactivated. [ 3H]Suramin binds to ribosomes and to isolated 60S and 40S ribosomal subunits (116, 106 and 3 binding sites, respectively) showing higher affinity for the small subunit ( K d = 2 μM).

5′‐poly(A) sequence as an effective leader for translation in eukaryotic cell‐free systems

Poly(A) sequence of 25 adenylic residues placed immediately before the start codons of the green fluorescent protein (GFP) and firefly luciferase (Luc) mRNAs is shown to provide a high rate of translation of the heterologous messages in eukaryotic cell-free translation systems. Also the poly(A) leader is found to provide the abolition of the inhibition of translation at excess mRNA concentrations. The possibility of the practical use of the constructs with the poly(A) leader for preparative protein production is demonstrated in the wheat germ continuous-exchange cell-free (CECF) translation system.

Four-base codon-mediated incorporation of nonnatural amino acids into proteins in a eukaryotic cell-free translation system

Various four-base codons have been shown to work for the introduction of non-natural amino acids into proteins in an Escherichia coli cell-free translation system. Here, a four-base codon-mediated non-natural mutagenesis was applied to a eukaryotic rabbit reticulocyte cell-free translation system. Mutated streptavidin mRNAs containing four-base codons were prepared and added to a rabbit reticulocyte lysate in the presence of tRNAs that were aminoacylated with a non-natural amino acid and had the corresponding four-base anticodons. A Western blot analysis of translation products indicated that the four-base codons CGGU, CGCU, CCCU, CUCU, CUAU, and GGGU were efficiently decoded by the aminoacyl-tRNAs having the corresponding four-base anticodons. In contrast, the four-base codons AGGU, AGAU, CGAU, UUGU, UCGU, and ACGU were not decoded. The stop codon-derived four-base codons UAGU, UAAU, and UGAU were found to be inefficient, whereas the amber codon UAG and opal codon UGA were efficient for the incorporation of non-natural amino acids. The application of the expanded genetic code in a eukaryotic cell-free system opens the possibility of a four-base codon-mediated incorporation of non-natural amino acids into proteins in living eukaryotic cells.

Effective non‐viral leader for cap‐independent translation in a eukaryotic cell‐free system

The 61 nt 5'-untranslated region (5'-UTR) of mRNA encoding for a light-emitting protein of hydroid polyp Obelia longissima, obelin, is shown to provide a high level of cap-independent translation of heterologous mRNAs in cell-free translation systems based on wheat germ extracts. The inhibition of translation typically observed when excess mRNA is present or produced in a eukaryotic system (the so-called self-inhibition phenomenon) is found abated with mRNA constructs carrying the obelin mRNA leader. The role of the sequestration of a limiting initiation factor, probably eIF4F, in the self-inhibition phenomenon and the possible independence of the obelin mRNA leader from eIF4F are discussed. We propose the obelin mRNA leader be used for effective cap-independent translation in eukaryotic cell-free systems, including combined transcription-translation systems with uncontrolled phage polymerase-catalyzed accumulation of mRNA.

Cell-free protein synthesis systems: increasing their performance and applications.

The Escherichia coli cell-free protein synthesis system can now be used for various proteins that need special requirements, such as disulfide bond formation between intra- and inter-molecules, hetero-dimerization, and specific chaperons. In addition, a novel protein library construction method termed "SIMPLEX" has been developed. Some applications with SIMPLEX are described. A highly efficient eukaryotic cell-free translation system using wheat germ extract has also been developed. An advanced framework for a rapid eukaryotic gene expression and analysis is shown.

MazF Cleaves Cellular mRNAs Specifically at ACA to Block Protein Synthesis in Escherichia coli

Escherichia coli contains operons called “addiction modules,” encoding toxin and antitoxin, which are responsible for growth arrest and cell death. Here, we demonstrate that MazF toxin encoded by “mazEF addiction module” is a sequence-specific (ACA) endoribonuclease functional only for single-stranded RNA. MazF works as a ribonuclease independent of ribosomes, and is, therefore, functionally distinct from RelE, another E. coli toxin, which assists mRNA cleavage at the A site on ribosomes. Upon induction, MazF cleaves whole cellular mRNAs to efficiently block protein synthesis. Purified MazF inhibited protein synthesis in both prokaryotic and eukaryotic cell-free systems. This inhibition was released by MazE, the labile antitoxin against MazF. Thus, MazF functions as a toxic endoribonuclease to interfere with the function of cellular mRNAs by cleaving them at specific sequences leading to rapid cell growth arrest and cell death. The role of such endoribonucleases may have broad implication in cell physiology under various growth conditions.

Genetically engineered active Qβ replicase in rabbit reticulocyte cell-free system: a fusion protein of EF-Tu and EF-Ts is functional as the subunit of Qβ replicase

Qβ replicase functioning in Escherichia coli is an RNA-dependent RNA polymerase composed of one phage-coded subunit and three host-coded proteins: ribosomal protein S1, and protein elongation factors EF-Tu and EF-Ts. Qβ replicase lacking ribosomal protein S1 (α-less replicase) is capable of replicating some small RNAs. We attempted to create functional α-less replicase by co-expression of the mRNAs that code for the subunits of α-less replicase in a rabbit reticulocyte cell-free translation system. Replicase activity, however, could not be detected when both EF-Tu and EF-Ts were co-expressed with the phage-coded subunit. On the other hand, active α-less replicase was obtained when an EF-Ts-EF-Tu fusion protein was co-expressed with the phage-coded subunit. Consequently, we succeeded in generating genetically engineered active α-less Qβ replicase which functions in a eukaryotic cell-free system.

Cell-free expression and functional reconstitution of CALM in clathrin assembly.

Clathrin-mediated vesicle formation is an essential step in the intracellular trafficking of the protein and lipid. Binding of clathrin assembly protein to clathrin triskelia induces their assembly into clathrin-coated vesicles (CCVs). In order to better understand a possible role of post-translational modification of CALM (clathrin assembly protein lymphoid myeloid), the homologue of AP180, in the assembly of CCVs, CALM was expressed in the cell-free reticulocyte translation system that is capable of carrying out post-translational modification. The apparent molecular weight of the expressed recombinant CALM was estimated as 105 kD. Alkaline phosphatase treatment of CALM resulted in a mobility shift on SDS-PAGE. We found that CALM was associated with the proteins harboring SH3 domain, promote assembly of clathrin triskelia into clathrin cage and bound to the preformed clathrin cage. CALM was also proteolyzed by caspase 3 and calpain but not by caspase 8. These results indicated that the post-translationally modified CALM, expressed in the eukaryotic cell-free reticulocyte translation system was able to mediate the assembly of clathrin and the coated-vesicle formation.

Ribosomal RNA supplementation highly reinforced cell-free translation activity of wheat germ

We have constructed an inexpensive, highly efficient eukaryotic cell-free translation system. Wheat germ rRNA (WG rRNA) was prepared by phenol/chloroform (P/C) extraction, a simple and quick method, from wheat germ, an inexpensive and commercially available by-product of flour production. Addition of a small amount of WG rRNA into a wheat germ cell-free translation system increased the protein productivity of the system 6- to 8-fold. Isolated 18S or 28S rRNA alone enhanced the protein production only 2-fold or 3.9-fold, respectively, at maximum. On the other hand, their equimolar mixture enhanced the production as much as the whole WG rRNA, indicating 18S and 28S rRNA synergistically functioned to enhance protein synthesis. Addition of WG rRNA slightly improved the stability of mRNA in the cell-free translation system, which explained only partly the enhancement of protein production. Addition of WGE or ribosome containing approximately the same amount of rRNA in the form of protein-rRNA complex as WG rRNA added to the system did not increase the protein production in the translation system. When ribosome in the cell-free translation system was replaced with WG rRNA, the system did not exhibit any detectable translation activity, indicating that the translation activity of WG rRNA is negligible in comparison with that of ribosome. These results indicated that WG rRNA affected some mechanisms regulating the translation rate in wheat germ cell-free system, resulting in increased protein production.

Modulation of HPV16 E7 translation by tRNAs in eukaryotic cell-free translation systems.

Translational regulation of HPV16 E7 mRNA is of particular interest since the viral E7 protein has oncogenic activity. Here we report that additional supplementation of cell-free reticulocyte/wheat-germ translation systems with rat liver tRNA pool favors the expression of the viral oncoprotein E7 which otherwise is scarcely translatable. The translational activation is explained by the positive correlation between the frequency of the glutamic and aspartic codons in E7 mRNA, and the increased concentration of the corresponding tRNAs following tRNA supplementation. The present in vitro data suggest a link between E7 expression and cell conditions conductive to tRNA changes such as development, cell proliferation and aging.

Expression and activity of a recombinant chimeric protein composed of pokeweed antiviral protein and of human interleukin-2

The pokeweed antiviral protein (PAP) has already been used to chemically construct immunotoxins. Here we tested the recombinant approach for the production of PAP-containing cytotoxic fusion-proteins. A cDNA encoding a mutated PAP (PAP9), which is expressed at high levels in bacteria, was fused to human interleukin-2 (IL-2) cDNA. The resulting PAP9–IL-2 protein was as active as the free PAP9 in inhibiting an eukaryotic cell-free translation system. Only the chimeric protein desaminated the 28S rRNA and inhibited translation of the CTLL-2 cell line which expresses the IL-2 receptor. These results show that PAP is a suitable toxin for the production of recombinant immunotoxins.

Primary Structure of ω‐Hordothionin, a Member of a Novel Family of Thionins from Barley Endosperm, and Its Inhibition of Protein Synthesis in Eukaryotic and Prokaryotic Cell‐Free Systems

A new sulfur-rich basic polypeptide, so called omega-hordothionin, has been isolated from barley endosperm by extractions with NaCl and ammonium bicarbonate followed by reverse-phase high performance liquid chromatography. Purified omega-hordothionin was found to be homogeneous by SDS/polyacrylamide gel electrophoresis, N-terminal amino-acid sequencing and electrospray-ionization mass spectrometric analysis. The complete primary structure of omega-hordothionin was determined by automatic degradation of the intact molecule and peptides obtained by proteolytic cleavage. Omega-hordothionin consists of a single polypeptide chain of 48 amino acids with a molecular mass of 5508 Da deduced from its amino acid sequence, which fully coincides with the 5508.2 Da determined by electrospray-ionization mass spectrometry. The isolated polypeptide showed a characteristic composition with a high content of basic amino acids (five arginine residues, two lysine residues and six histidine residues) and eight cysteine residues, and has strong sequence identity (66%) with the sorghum SI alpha 1 alpha-amylase inhibitor. Omega-hordothionin, like gamma-hordothionin, exhibited translation inhibitory activity on both eukaryotic cell-free systems from mammalian (rat liver and rabbit reticulocyte lysates) and prokaryotic cell-free systems (Escherichia coli). However, in contrast to gamma-hordothionin, omega-hordothionin did not inhibit plant systems such as Triticum aestivum, Cucumis sativus, Vicia sativa and Hordeum vulgare. Gamma-hordothionin also inhibited the alpha-amylase activity from human saliva, while omega-hordothionin and the other different genetic variants of thionins, alpha-hordothionin and beta-hordothionin, failed to show any inhibitory effect.

Isolation and characterization of two new N-glycosidase type-1 ribosome-inactivating proteins, unrelated in amino-acid sequence, from Petrocoptis species.

Two new N-glycosidase type-1 ribosome-inactivating proteins (RIPs), denoted petroglaucin 1 and petrograndin, respectively, were isolated from the plants Petrocoptis glaucifolia (Lag.) Boiss sp. viscosa (Rothm.) Lainz and Petrocoptis grandiflora Rothm. These new RIPs do not share H2N-terminal amino-acid sequence homology with petroglaucin (now denoted as petroglaucin 2), the only other type-1 RIP to be isolated from P. glaucifolia (Arias et al. (1992) Planta 186, 532-540). Petroglaucin 1 shares amino-acid sequence homology with RIPs from Cucurbitaceae while petroglaucin 2 and petrograndin do so with saporins and dianthin 30 (Caryophyllaceae). The new RIPs strongly inhibited protein synthesis at subnanomolar concentrations in rabbit reticulocyte lysates and other eukaryotic cell-free systems, but they were inactive on bacterial ribosomes.

Analysis of promoter-specific repression by triple-helical DNA complexes in a eukaryotic cell-free transcription system

A site-specific triple-helical DNA complex has previously been shown to inhibit DNA binding by eukaryotic transcription factor Sp1. To examine the functional consequences of such inhibition, homopurine target sequences for oligonucleotide-directed triple-helix formation were inserted in various configurations relative to Sp1 transcription activator binding sites, upstream of the TATA element of recombinant eukaryotic promoters. The resulting promoters were tested for activity in the presence or absence of recombinant human Sp1 in a Drosophila in vitro transcription system lacking endogenous Sp1. When triple-helical complexes were assembled on the promoters by incubation with specific oligodeoxyribonucleotides, promoter-specific repression of basal transcription was observed in the absence of Sp1. Transcriptional repression required the preassembly of triple-helical complexes before addition of nuclear extract. The degree of basal repression was a function of the number and proximity of triple-helical complexes relative to the basal promoter complex. Repression did not result from triple-helix-induced template degradation. Addition of recombinant Sp1 did not cause derepression. These results suggest that triple-helical complexes can repress transcription primarily by blocking promoter DNA assembly into initiation complexes rather than by occluding Sp1 binding. One of several plausible mechanisms for triple-helix-induced repression involves changes in DNA flexibility. Evidence in favor of this model is provided by a permutation-dependent gel mobility assay in which formation of site-specific triple-helical complexes is shown to stiffen double-helical DNA.

Primary structure and inhibition of protein synthesis in eukaryotic cell‐free system of a novel thionin, γ‐hordothionin, from barley endosperm

A new sulfur-rich and basic polypeptide, designated as gamma-hordothionin, has been isolated from barley endosperm by a semi-preparative purification consisting of extraction with a volatile salt solution followed by high-performance liquid chromatography using a reversed-phase C4 column. The isolated polypeptide was found to be homogeneous by micro-two-dimensional gel electrophoresis in the presence of sodium dodecyl sulfate. The complete primary structure of gamma-hordothionin was determined by automatic degradation of the intact, S-carboxymethylated and S-pyridylethylated gamma-hordothionin and fragments obtained by proteolytic cleavage. gamma-Hordothionin consists of a single polypeptide chain of 47 amino acids with a calculated molecular mass of 5250 Da and contains four disulfide bridges. gamma-Hordothionin inhibits translation in cell-free systems derived from mammalian (rabbit reticulocyte, mouse liver) as well as non-mammalian (Artemia embryo) cells, at several levels. At low concentrations (1-10 microM) the protein seems to affect mainly the polypeptide-chain-initiation process, although it might also act at the elongation level. At higher concentrations (20-80 microM) this inhibitor induces activation of an eukaryotic polypeptide-chain initiation factor 2 alpha-subunit (eIF-2 alpha) kinase in hemin-supplemented reticulocyte lysates, as does hemin deficiency. The presence of the disulfide bridges in gamma-hordothionin appears to be essential for the eIF-2 alpha kinase activation. Based on its similarity at both the structural and functional level with the different genetic variants of thionins (alpha and beta-thionins, from wheat and barley), gamma-hordothionin is a putative member of the thionin family.

Effect of the antibiotic purpuromycin on cell-free protein-synthesizing systems.

Purpuromycin, an antibiotic isolated from the culture broth of Actinoplanes ianthinogenes, which is very active against Gram-positive bacteria and fungi, inhibits protein synthesis in both prokaryotic and eukaryotic cell-free systems. The ID50 was 9 microM with the endogenous mRNA-directed rabbit reticulocyte lysate, 17 microM with a poly(U)-directed system from Escherichia coli and 69 microM with a poly(U)-directed system from Artemia salina cysts. Of the three steps of elongation, purpuromycin does not affect the peptidyl-transferase reaction, inhibits the elongation factor 1 (EF-1) dependent binding of phenylalanyl-tRNA and stimulates the GTP-dependent binding of EF-2. When protein synthesis is stopped by the addition of purpuromycin, the nascent peptide chains are found in the puromycin-reactive P site. The results suggest that the mechanism of action of purpuromycin is similar to that of fusidic acid. Both antibiotics would seem to produce a stable guanine nucleotide-ribosome-EF-2 complex which allows one round of translocation but prevents, because of a common or overlapping ribosomal binding site for the two elongation factors, the subsequent EF-1-dependent binding of aminoacyl-tRNA.

Base-pair formation between noncapped influenza virus in vitro transcripts and 18S rRNA in rabbit reticulocyte 80S ribosome-mRNA complexes detected by psoralen photoreaction.

RNA-RNA interactions between 18S ribosomal RNA and noncapped influenza cRNA were detected by psoralen photochemical cross-linking in reticulocyte 80S ribosome-cRNA complexes. In vitro transcripts of type A influenza virus synthesized by endogenous RNA polymerase with adenylyl-(3'----5')-guanosine primer formed 80S complexes with rabbit reticulocyte ribosomes. The extent of the complex formation by these noncapped cRNAs was less than that by the m7G-capped reovirus in vitro transcripts, but the former RNAs in the 80S complexes were cross-linked to 18S rRNA as efficiently as the latter RNAs by photoreaction with an RNA cross-linking agent, 4'-aminomethyl-4,5',8-trimethylpsoralen. These results suggested that mRNA with or without the cap structure on the 5'-terminal can form complexes with the ribosomes in a eukaryotic cell-free translation system by base-pair formation with 18S rRNA. Correspondingly, sequences capable of forming extensive base-pairs including four- to five-base complementarities were found between the 3'-terminal of rabbit reticulocyte 18S ribosomal RNA and the 5'-noncoding regions of either influenza virus transcripts or reovirus mRNA.

Inhibition of translation by the fungal toxin cyclopiazonic acid

Cyclopiazonic acid is a toxic metabolite of fungal origin that inhibits protein synthesis in intact HeLa cells and eukaryotic cell-free systems. It has been shown that cyclopiazonic acid blocks the GTP- and EF-1-dependent binding of (3H)Phe-tRNA to 80S ribosomes. Moreover the translocation of N-Ac-(3H)Phe-tRNA by 80S ribosomes that takes place in the presence of EF-2 and GTP is also halted by cyclopiazonic acid. It is concluded that this drug affects a ribosomal site involved in the alternative interaction of elongation factors EF-1 and EF-2.

The mode of action of the antitumor drug bouvardin, an inhibitor of protein synthesis in eukaryotic cells

Bouvardain is an antitumor drug that inhibits protein synthesis in intact eukaryotic cells and cell-free systems. Our present studies have shown that bouvardin acts at the level of the 80 S ribosome in a site somehow involved with the interaction of EF1 and EF2. Indeed bouvardin inhibits EF1-dependent binding of aminoacyl-tRNA and EF2-dependent translocation of peptidyl-tRNA but does not affect the non-enzymic translocation since this relation does not require EF2. The site of the 80 S ribosome involved in the interaction with bouvardin appears to be independent from the cycloheximide and the cryptopleurine binding sites since yeast mutants resistant to cycloheximide or cryptopleurine are sensitive to bouvardin.