T4 RNA ligase mediated preparation of novel "chemically misacylated" tRNAPheS

Prolegomena to Future Experimental Efforts on Genetic Code Engineering by Expanding Its Amino Acid Repertoire

Protein synthesis and its relation to the genetic code was for a long time a central issue in biology. Rapid experimental progress throughout the past decade, crowned with the recently elucidated ribosomal structures, provided an almost complete description of this process. In addition important experiments provided solid evidence that the natural protein translation machinery can be reprogrammed to encode genetically a vast number of non-coded (i.e. noncanonical) amino acids. Indeed, in the set of 20 canonical amino acids as prescribed by the universal genetic code, many desirable functionalities, such as halogeno, keto, cyano, azido, nitroso, nitro, and silyl groups, as well as C=C or C[triple bond]C bonds, are absent. The ability to encode genetically such chemical diversity will enable us to reprogram living cells, such as bacteria, to express tailor-made proteins exhibiting functional diversity. Accordingly, genetic code engineering has developed into an exciting emerging research field at the interface of biology, chemistry, and physics.

Site- and subunit-specific incorporation of unnatural amino acids into HIV-1 reverse transcriptase

A highly efficient cell-free translation system has been combined with suppressor tRNA technology to substitute nor-Tyr and 3-fluoro-Tyr in place of Tyr183 at the DNA polymerase active site of p66 of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). Supplementing the wild-type HIV-1 p51 RT subunit into this translation system permitted reconstitution of the biologically relevant p66/p51 heterodimer harboring Tyr analogs exclusively on the catalytically competent p66 subunit. Addition of an affinity tag at the p66 C-terminus allowed rapid, one-step purification of reconstituted and selectively mutated heterodimer HIV-1 RT via strep-Tactin-agarose affinity chromatography. The purified enzyme was demonstrated to be free of contaminating nucleases, allowing characterization of the DNA polymerase and ribonuclease H activities associated with HIV-1 RT. Preliminary characterization of HIV-1 RT(nor-Tyr) and HIV-1 RT(m-fluoro-Tyr) is presented. The success of this strategy will facilitate detailed molecular analysis of structurally and catalytically critical amino acids via their replacement with closely related, unnatural analogs.

Amino Acid Backbone Specificity of the Escherichia coli Translation Machinery

Using a pure Escherichia coli translation system, we tested the intrinsic specificity of the protein biosynthetic machinery by determining the relative yields of peptide synthesis for incorporation of a series of acyl-%@mt;sys@%tRNA%@sx@%GAC%@be@%AsnB%@sxx@%%@mx@% 's with varied backbone structures at the sense codon GUU (Val). The results showed that different amino acids on the same tRNA adaptor give significantly different peptide yields and the potential for cross-talk between the amino acid and tRNA body/anticodon in aa-tRNA decoding by the ribosome. They further support the substrate plasticity of the ribosomal biosynthetic machinery and provide immediate candidates for ribosomally encoded polymer synthesis.

A possible approach to site-specific insertion of two different unnatural amino acids into proteins in mammalian cells via nonsense suppression

The site-specific insertion of an unnatural amino acid into proteins in vivo via nonsense suppression has resulted in major advances in recent years. The ability to incorporate two different unnatural amino acids in vivo would greatly increase the scope and impact of unnatural amino acid mutagenesis. Here, we show the concomitant suppression of an amber and an ochre codon in a single mRNA in mammalian cells by importing a mixture of aminoacylated amber and ochre suppressor tRNAs. This result provides a possible approach to site-specific insertion of two different unnatural amino acids into any protein of interest in mammalian cells. To our knowledge, this result also represents the only demonstration of concomitant suppression of two different termination codons in a single gene in vivo.

Using a solid-phase ribozyme aminoacylation system to reprogram the genetic code

Here, we report a simple and economical tRNA aminoacylation system based upon a resin-immobilized ribozyme, referred to as Flexiresin. This catalytic system features a broad spectrum of activities toward various phenylalanine (Phe) analogs and suppressor tRNAs. Most importantly, it allows users to perform the tRNA aminoacylation reaction and isolate the aminoacylated tRNAs in a few hours. We coupled the Flexiresin system with a high-performance cell-free translation system and demonstrated protein mutagenesis with seven different Phe analogs in parallel. Thus, the technology developed herein provides a new tool that significantly simplifies the procedures for the synthesis of aminoacyl-tRNAs charged with nonnatural amino acids, which makes the nonnatural amino acid mutagenesis of proteins more user accessible.

Designer Ribozymes: Programming the tRNA Specificity into Flexizyme

Fx3 is an artificial ribozyme with the ability to aminoacylate various tRNAs with phenylalanine and its nonnatural derivatives. Herein we report a simple strategy to build tRNA specificity into the generic Fx3, by appending to its 3'-end a tRNA-specific sequence (TSS), which is complementary to the acceptor stem of the cognate tRNA. This new designer ribozyme, referred to as Fx10, is able to recognize its cognate tRNA via a 10-base-pair interaction that is formed after the invasion of the tRNA acceptor stem by the TSS. We have demonstrated that Fx10 can aminoacylate its cognate tRNA with a high degree of specificity and also discriminate against the noncognate tRNAs. Because the tRNA specificity can be easily programmed into Fx10, it is a custom-made catalyst to generate nonnatural aminoacyl-tRNAs.

The affinity of elongation factor Tu for an aminoacyl-tRNA is modulated by the esterified amino acid

When different mutations were introduced into the anticodon loop and at position 73 of YFA2, a derivative of yeast tRNA(Phe), a single tRNA body was misacylated with 13 different amino acids. The affinities of these misacylated tRNAs for Thermus thermophilus elongation factor Tu (EF-Tu).GTP were determined using a ribonuclease protection assay. A range of 2.5 kcal/mol in the binding energies was observed, clearly demonstrating that EF-Tu specifically recognizes the side chain of the esterified amino acid. Furthermore, this specificity can be altered by introducing a mutation in the amino acid binding pocket on the surface of EF-Tu. Also, when discussed in conjunction with the previously determined specificity of EF-Tu for the tRNA body, these experiments further demonstrate that EF-Tu uses thermodynamic compensation to bind cognate aminoacyl-tRNAs similarly.

Incorporation of Nonnatural Amino Acids Into Proteins

The genetic code is established by the aminoacylation of transfer RNA, reactions in which each amino acid is linked to its cognate tRNA that, in turn, harbors the nucleotide triplet (anticodon) specific to the amino acid. The accuracy of aminoacylation is essential for building and maintaining the universal tree of life. The ability to manipulate and expand the code holds promise for the development of new methods to create novel proteins and to understand the origins of life. Recent efforts to manipulate the genetic code have fulfilled much of this potential. These efforts have led to incorporation of nonnatural amino acids into proteins for a variety of applications and have demonstrated the plausibility of specific proposals for early evolution of the code.

Efficient synthesis of nonnatural mutants in Escherichia coli S30 in vitro protein synthesizing system

Factors that affect the efficiency of in vitro synthesis of mutant proteins that contain nonnatural amino acids were investigated. The process of the nonnatural mutagenesis consists of chemical aminoacylation of a tRNA that contains a 4-base anticodon, followed by in vitro synthesis in the presence of an mRNA that contains the corresponding 4-base codon. Detailed studies on the time courses of the synthesis revealed two major factors that suppress the yield of nonnatural mutants compared with the wild-type protein. First, a cyclic tRNA that exists as a by-product of the chemical aminoacylation inhibits the protein synthesis. Second, the very short lifetime of a tRNA aminoacylated with a nonnatural amino acid limits the protein yield. As a simple and practical way of surmounting these factors, aminoacyl tRNA was added into the in vitro system at 5 min after the start of the synthesis. The addition increased the protein yield up to the level of conventional proteins in the in vitro system.

A versatile tRNA aminoacylation catalyst based on RNA

Aminoacyl-tRNA synthetase (ARS) ribozymes have potential to develop a novel genetic coding system. Although we have previously isolated such a ribozyme that recognizes aromatic amino acids, it could not be used as a versatile catalyst due to its limited ability of aminoacylation to a particular tRNA used for the selection. To overcome this limitation, we used a combination of evolutionary and engineering approaches to generate an optimized ribozyme. The ribozyme, consisting of 45 nucleotides, displays a broad spectrum of activity toward various tRNAs. Most significantly, this ribozyme is able to exhibit multiple turnover activity and charge parasubstituted Phe analogs onto an engineered suppressor tRNA (tRNA(Asn)(CCCG)). Thus, it provides a useful and flexible tool for the custom synthesis of mischarged tRNAs with natural and nonnatural amino acids.

In vitro selection for sense codon suppression

The universal genetic code links the 20 naturally occurring amino acids to the 61 sense codons. Previously, the UAG amber stop codon (a nonsense codon) has been used as a blank in the code to insert natural and unnatural amino acids via nonsense suppression. We have developed a selection methodology to investigate whether the unnatural amino acid biocytin could be incorporated into an mRNA display library at sense codons. In these experiments we probed a single randomized NNN codon with a library of 16 orthogonal, biocytin-acylated tRNAs. In vitro selection for efficient incorporation of the unnatural amino acid resulted in templates containing the GUA codon at the randomized position. This sense suppression occurs via Watson-Crick pairing with similar efficiency to UAG-mediated nonsense suppression. These experiments suggest that sense codon suppression is a viable means to expand the chemical and functional diversity of the genetic code.

Incorporation of non-natural amino acids into proteins

Chemical and biological diversity of protein structures and functions can be widely expanded by position-specific incorporation of non-natural amino acids carrying a variety of specialty side groups. After the pioneering works of Schultz's group and Chamberlin's group in 1989, noticeable progress has been made in expanding types of amino acids, in finding novel methods of tRNA aminoacylation and in extending genetic codes for directing the positions. Aminoacylation of tRNA with non-natural amino acids has been achieved by directed evolution of aminoacyl-tRNA synthetases or some ribozymes. Codons have been extended to include four-base codons or non-natural base pairs. Multiple incorporation of different non-natural amino acids has been achieved by the use of a different four-base codon for each tRNA. The combination of these novel techniques has opened the possibility of synthesising non-natural mutant proteins in living cells.

A tRNA aminoacylation system for non-natural amino acids based on a programmable ribozyme

The ability to recognize tRNA identities is essential to the function of the genetic coding system. In translation aminoacyl-tRNA synthetases (ARSs) recognize the identities of tRNAs and charge them with their cognate amino acids. We show that an in vitro evolved ribozyme can also discriminate between specific tRNAs, and can transfer amino acids to the 3' ends of cognate tRNAs. The ribozyme interacts with both the CCA-3' terminus and the anticodon loop of tRNA(fMet), and its tRNA specificity is controlled by these interactions. This feature allows us to program the selectivity of the ribozyme toward specific tRNAs, and therefore to tailor effective aminoacyl-transfer catalysts. This method potentially provides a means of generating aminoacyl tRNAs that are charged with non-natural amino acids, which could be incorporated into proteins through cell-free translation.

Rational design to block amino acid editing of a tRNA synthetase

Investigations in chemical biology have focused on the synthesis of custom-designed proteins with site-specific incorporation of novel amino acids. Their success requires stable production of misacylated tRNAs. Utilization of aminoacyl-tRNA synthetases has been hindered because of enzyme molecular recognition mechanisms that ensure high fidelity of protein synthesis. Leucyl-tRNA synthetase naturally misaminoacylates chemically diverse standard and nonstandard amino acids, but contains a separate amino acid editing active site to hydrolyze incorrectly mischarged tRNAs. In this work, a rational mutagenesis design to block enzyme editing is described and involves substitution of bulky amino acids into the amino acid binding pocket of the hydrolytic active site. These engineered enzymes stably misacylated isoleucine to tRNALeu. The use of these mutant leucyl-tRNA synthetases has the potential to produce pools of mischarged tRNAs that are linked to nonstandard amino acids for in vitro translation. In addition, since many of the leucyl-tRNA synthetases do not interact with or rely upon the tRNA anticodon for identity, these enzymes may offer an excellent scaffold for the development of orthogonal tRNA synthetase/tRNA pairs that can potentially be used to customize protein synthesis.

Aminoacyl-tRNA synthesis by a resin-immobilized ribozyme

We report herein a new method for the aminoacylation of tRNA, using a resin-immobilized ribozyme and the cyanomethyl ester (CME) of an amino acid substrate. The oxidized form of the ribozyme was immobilized on a hydrazine resin via covalent linkage. We performed aminoacylation of tRNAs using this ribozyme-resin to isolate aminoacyl-tRNAs. The column was recycled up to 5 times without significant activity loss. Thus, our ribozyme-based aminoacylation system has significant potential to be a powerful and practical technique for supplying various nonnatural aminoacyl-tRNAs for a highly efficient in vitro translation system.

A bifunctional tRNA for in vitro selection

In vitro selection is a powerful approach for generating novel aptamers and catalysts. Currently, several methods are being developed to extend this technique to proteins. In principle, selection methods could be applied to any library whose members can be replicated. Here, we describe a bifunctional tRNA that fuses translation products to their mRNAs. The utility of peptide-tRNA-mRNA fusions for in vitro selection was illustrated by the selective enrichment of tagged peptides-together with their mRNAs-by affinity chromatography. Our system can generate libraries larger than 10(11). Because library members can be copied and amplified, they provide a means for applying in vitro selection procedures to peptides and proteins. Furthermore, because the system is amenable to translation with misacylated tRNAs, a wide range of unusual monomers could be used to make libraries of nonstandard polymers for selection experiments.

Preparation of glycosylated amino acid derivatives for glycoprotein synthesis by in vitro translation system

General preparation of glycosylated amino acylated nucleotide for in vitro peptide synthesis was described. Both O-glycosylated amino acyl nucleotides and C-glycosylated amino acyl nucleotide were synthesized by choosing the appropriate protecting group.

An improved synthesis of the dinucleotides pdCpA and pdCpdA

An improved route was developed for the preparation of the dinucleotide hybrid 5'-O-phosphoryl-2'-deoxycytidylyl-(3'--> 5')adenosine (pdCpA) 7. This simple and concise synthesis involves the successive coupling of 2-cyanoethyl N, N, N', N'-tetra- isopropylphosphorodiamidite with 4-N-benzoyl-5'-O-(4, 4'-dimethoxytrityl)-2'-deoxy-cytidine 1 and 6-N,6-N,2'-O,3'-O-tetrabenzoyladenosine 2 as the key step. Some dinucleotide derivatives bearing different protecting groups were also synthesized and the selective deprotection conditions were studied in detail. The utility and efficiency of this approach has been further demonstrated by its application to the synthesis of total DNA dinucleotide pdCpdA 17 and total RNA dinucleotide 21.

Studies toward the site specific incorporation of sugars into proteins: synthesis of glycosylated aminoacyl-tRNAs

A series of glycosylated serine derivatives was synthesized from peracetylated sugars and Fmoc-protected serine; these were chemically esterified with the tris-(tetrabutylammonium) salt of pdCpA. The fully protected and deprotected glycosylated aminoacyl pdCpAs were ligated enzymatically to an abbreviated tRNA (tRNA-C(OH)) to provide the title compounds that are key intermediates in the elaboration of glycoproteins using readthrough of a nonsense codon.

Synthesis of N-labeled peptidyl AMP

This paper deals with the synthesis of a new type of N-labeled peptidyl AMP, which would be used as a good substrate for analysis of the peptidyl transfer reaction on ribosome and for co-crystallization with ribosome. 4-(Dimethylamino)azobenzene-4'-sulfonyl (Dabsyl) was selected as the labeling group. (N-Dabsylglycyl)-L-leucyl AMP was synthesized from glycyl-L-leucine via a three-step procedure.

Sense codon-dependent introduction of unnatural amino acids into multiple sites of a protein

Cell-free protein synthesis, driven by a crude S30 extract from Escherichia coli, has been applied to the preparation of proteins containing unnatural amino acids at specific positions. We have developed methods for inactivating tRNA(Asp) and tRNA(Phe) within a crude E. coli tRNA by an antisense treatment and for digesting most of the tRNA within the S30 extract without essential damage to the ribosomal activity. In the present study, we applied these methods to the substitution of Asp and Phe residues of the HIV-1 protease with unnatural amino acids. With 10 mM Mg(2+), the translation efficiency was higher than that with the other tested concentration, and the misreading efficiency was low. The protease mRNA was translated in the presence of an antisense DNA-treated tRNA mixture and 2-naphthylalanyl- and/or p-phenylazophenylalanyl-tRNA. The results suggest that a good portion of the translation products are substituted at all of the seven positions originally occupied by Asp or Phe.

Facile characterization of translation initiation via nonsense codon suppression

A new strategy for studying the mechanism of translation initiation in eukaryotes has been developed. The strategy involves the use of an in vitro translation system to incorporate a non-natural fluorescent amino acid into a protein from a suppressor tRNAPheCUA misacylated with that amino acid. It is thereby possible to monitor translation initiation efficiency at an AUG codon in different contexts; this is illustrated for three constructs encoding Escherichia coli dihydrofolate reductase mRNA with different translation initiation regions. Fluorescence measurements after in vitro translation of the mRNAs in rabbit reticulocyte lysate reflected differences in the position and efficiency of translation initiation and, therefore, can be used for characterization of the translation initiation process.

Misacylated Transfer RNAs Having a Chemically Removable Protecting Group

The 4-pentenoyl group and a number of derivatives have been studied as protecting groups for N(alpha) of the aminoacyl moiety in misacylated tRNAs. The unsubstituted 4-pentenoyl group itself was found to function as efficiently as any of the derivatives studied. Four different N-(4-pentenoyl)aminoacyl-tRNA(CUA)s were prepared and shown to undergo deprotection readily upon admixture of aqueous iodine; the derived misacylated tRNAs all functioned well as suppressors of a nonsense codon in an in vitro protein biosynthesizing system. Also prepared were four N(alpha)-(4-pentenoyl)aspartyl-tRNA(CUA)s that were protected on the side chain carboxylate as the nitroveratryl ester. Following treatment with aqueous iodine, the misacylated suppressor tRNAs incorporated the aspartate derivatives into position 27 of dihydrofolate reductase by suppression of a UAG codon in the mRNA. The suppression yields were significantly better than those obtained when side chain protection was absent. The resulting "caged proteins" were inactive, but full catalytic potential was restored by irradiation under conditions sufficient to effect deprotection of the side chain carboxylate moiety.

In vitro suppression as a tool for the investigation of translation initiation

An in vitro protein synthesizing system that employs rabbit reticulocyte lysates has been employed for protein production from mRNAs containing nonsense (UAG) codons in the presence of misacylated suppressor tRNAs.The system includes a misacylated Escherichia coli tRNAAlaCUA that functions at least as efficiently as any suppressor tRNA transcript reported to date and which has been shown not to be a substrate for (re)activation by alanyl-tRNA synthetase. Application of the optimized system for preparation of dihydrofolate analogs has also permitted analysis of competing mechanisms that control the sites(s) of translation initiation.

Adaptability of nonnatural aromatic amino acids to the active center of the E. coli ribosomal A site

3'-N-Aminoacyl analogs of puromycin with nonnatural aromatic amino acids were synthesized and their inhibitory activity in E. coli in vitro protein synthesizing system was evaluated. The analogs with L-2-naphthylalanine, L-p-biphenylalanine, L-2-anthrylalanine and trans-L-p-phenylazophenylalanine were found to inhibit the protein synthesis with high efficiency. The inhibition suggests that these nonnatural amino acids are accepted by the active center of the E. coli ribosomal A site. A model for the adaptability of nonnatural aromatic amino acids to the active center is proposed.

Amplification of protein expression in a cell free system

Large quantities of a catalytically active protein have been produced in a cell free system. More than 10(9) copies of protein were produced from each DNA plasmid containing DNAfol, the bacterial gene encoding dihydrofolate reductase (DHFR). The strategy employed, denoted gene amplification with transcription/translation (GATT), involves sequential coupling of (i) DNA amplification by the polymerase chain reaction (PCR) and (ii) in vitro RNA transcription by T7 RNA polymerase, followed by (iii) translation of the run-off transcripts in a rabbit reticulocyte system. The protein product had the expected size (18 kDa) and catalyzed the NADPH-dependent reduction of 7,8-dihydrofolic acid to 5,6,7,8-tetrahydrofolic acid as efficiently as authentic DHFR. Potential applications of the strategy include large scale production of enzymes containing synthetic amino acids and facilitation of the characterization of the function of genes encountered in genomic mapping studies.

Site-specific mutagenesis with unnatural amino acids

The incorporation of unnatural amino acids into proteins by site-specific mutagenesis provides a valuable new methodology for the generation of novel proteins that possess unique structural and functional features.

A general method for site-specific incorporation of unnatural amino acids into proteins

A new method has been developed that makes it possible to site-specifically incorporate unnatural amino acids into proteins. Synthetic amino acids were incorporated into the enzyme beta-lactamase by the use of a chemically acylated suppressor transfer RNA that inserted the amino acid in response to a stop codon substituted for the codon encoding residue of interest. Peptide mapping localized the inserted amino acid to a single peptide, and enough enzyme could be generated for purification to homogeneity. The catalytic properties of several mutants at the conserved Phe66 were characterized. The ability to selectively replace amino acids in a protein with a wide variety of structural and electronic variants should provide a more detailed understanding of protein structure and function.

Ribosomal binding and dipeptide formation by misacylated tRNA(Phe),S

Eight structurally modified peptidyl-tRNA(Phe),s were employed to study P-site binding and peptide bond formation in a cell-free system involving Escherichia coli ribosomes programmed with poly(uridylic acid). It was found that the two analogues (N-acetyl-D-phenylalanyl-tRNA(Phe) and N-acetyl-D-tyrosyl-tRNA(Phe] containing D-amino acids functioned poorly as donors in the peptidyltransferase reaction and that two N-acetyl-L-phenylalanyl-tRNA(Phe)'s differing from the prototype substrate in that they contained 2'- or 3'-deoxyadenosine at the 3'-terminus failed to form dipeptide at all when L-phenylalanyl-tRNA(Phe) was the acceptor tRNA. Interestingly, all four of these peptidyl-tRNA's bound to ribosomes to about the same extent as tRNA's that functioned normally as donors in the peptidyltransferase reaction, at least in the absence of competing peptidyl-tRNA species. Two peptidyl-tRNA's lacking an amino group were also tested. In comparison with N-acetyl-L-phenylalanyl-tRNA(Phe) it was found that trans-cinnamyl-tRNA(Phe) and 3-phenylpropionyl-tRNA(Phe)'s formed dipeptides to the extent of 53 and 80%, respectively, when L-phenylalanyl-tRNA(Phe)was used as the acceptor tRNA. N-Acetyl-beta-phenylalanyl-tRNA(Phe) was found to be the most efficient donor substrate studied. Both isomers transferred N-acetyl-beta-phenylalanine to L-phenylalanyl-tRNA(Phe); the nature of the dipeptides formed in each case was verified by HPLC in comparison with authentic synthetic samples. Further, the rate and extent of peptide bond formation in each case exceeded that observed with the control tRNA, N-acetyl-L-phenylalanyl-tRNA(Phe).

Controlled degradation of yeast tRNAPhe by spleen phosphodiesterase in the presence of ethidium bromide

Degradation of yeast tRNAPhe with spleen phosphodiesterase in the presence of ethidium bromide has been studied. It was found that in the presence of the intercalating dye, the digestion is halted after a limited number of nucleotides is removed. Possible explanations of the observed phenomenon in connection with tRNA-ethidium bromide complex formation are discussed.