Rapid selection of aminoacyl-tRNAs based on biotinylation of alpha-NH2 group of charged amino acids

Site-Specific Introduction of Alanines for the Nuclear Magnetic Resonance Investigation of Low-Complexity Regions and Large Biomolecular Assemblies

Nuclear magnetic resonance (NMR) studies of large biomolecular machines and highly repetitive proteins remain challenging due to the difficulty of assigning frequencies to individual nuclei. Here, we present an efficient strategy to address this challenge by engineering a Pyrococcus horikoshii tRNA/alanyl-tRNA synthetase pair that enables the incorporation of up to three isotopically labeled alanine residues in a site-specific manner using in vitro protein expression. The general applicability of this approach for NMR assignment has been demonstrated by introducing isotopically labeled alanines into four distinct proteins: huntingtin exon-1, HMA8 ATPase, the 300 kDa molecular chaperone ClpP, and the alanine-rich Phox2B transcription factor. For large protein assemblies, our labeling approach enabled unambiguous assignments while avoiding potential artifacts induced by site-specific mutations. When applied to Phox2B, which contains two poly-alanine tracts of nine and twenty alanines, we observed that the helical stability is strongly dependent on the homorepeat length. The capacity to selectively introduce alanines with distinct labeling patterns is a powerful tool to probe structure and dynamics of challenging biomolecular systems.

The tRNA identity landscape for aminoacylation and beyond

tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.

Ribosomal Synthesis of Peptides Bearing Noncanonical Backbone Structures via Chemical Posttranslational Modifications

Noncanonical peptide backbone structures, such as heterocycles and non-α-amino acids, are characteristic building blocks present in peptidic natural products. To achieve ribosomal synthesis of designer peptides bearing such noncanonical backbone structures, we have devised translation-compatible precursor residues and their chemical posttranslational modification processes. In this chapter, we describe the detailed procedures for the in vitro translation of peptides containing the precursor residues by means of genetic code reprogramming technology and posttranslational generation of objective noncanonical backbone structures.

In vitro selection and characterization of a novel Zn(II)-dependent phosphorothiolate thiolesterase ribozyme

Here we present the in vitro selection of a novel ribozyme specific for Zn2+-dependent catalysis on hydrolysis of a phosphorothiolate thiolester bond. The ribozyme, called the TW17 ribozyme, was evolved and selected from an artificial RNA pool covalently linked to a biotin-containing substrate through the phosphorothiolate thiolester bond. The secondary structure for the evolved ribozyme consisted of three major helices and three loops. Biochemical and chemical studies of ribozyme-catalyzed reaction products provided evidence that the ribozyme specifically catalyzes hydrolysis of the phosphorothiolate thiolester linkage. A successful ribozyme construct with active catalysis in trans further supported the determined ribozyme structure and indicated the potential of the ribozyme for multiple-substrate turnover. The ribozyme also requires Zn2+ and Mg2+ for maximal catalysis. The TW17 ribozyme, in the presence of Zn2+ and Mg2+, conferred a rate enhancement of at least 5 orders of magnitude when compared to the estimated rate of the uncatalyzed reaction. The ribozyme completely lost catalytic activity in the absence of Zn2+, like Zn2+-dependent protein hydrolases. The discovery and characterization of the TW17 ribozyme suggest additional roles for Zn2+ in ribozyme catalysts.

Rapid and simple ribozymic aminoacylation using three conserved nucleotides

Selection-amplification finds new RNA enzymes (ribozymes) among randomized RNAs with flanking unvaried sequences (primer complements). Precise removal of 3'-primer before reaction selected aminoacylation from PheAMP in three cycles, yielding active RNAs (k(cat) = 12-20 min(-1)) using only three conserved nucleotides, acting independently of divalent ions. This unusually simple RNA active site encouraged study of the reaction via molecular mechanics-based free energy minimization. On this basis, we suggest a chemical path for RNA-catalyzed transaminoacylation. Site modeling also predicted new features, L-stereoselectivity, 2'-regioselectivity, independence of amino acid side chain, and phosphorylated activating group, that were subsequently verified. The same selection also showed that RNA aminoacylation from adenylate is simpler than from CoA thioester, potentially rationalizing translational activation by adenylates. The simplicity of this active site suggests a general route to small ribozymes.

New catalytic structures from an existing ribozyme

Although protein enzymes with new catalytic activities can arise from existing scaffolds, less is known about the origin of ribozymes with new activities. Furthermore, mechanisms by which new macromolecular folds arise are not well characterized for either protein or RNA. Here we investigate how readily ribozymes with new catalytic activities and folds can arise from an existing ribozyme scaffold. Using in vitro selection, we isolated 23 distinct kinase ribozymes from a pool of sequence variants of an aminoacylase parent ribozyme. Analysis of these new kinases showed that ribozymes with new folds and biochemical activities can be found within a short mutational distance of a given ribozyme. However, the probability of finding such ribozymes increases considerably as the mutational distance from the parental ribozyme increases, indicating a need to escape the fold of the parent.

Uniform binding of aminoacylated transfer RNAs to the ribosomal A and P sites

The association and dissociation rate constants of eight different E. coli aminoacyl-tRNAs (aa-tRNAs) for E. coli ribosomes programmed with mRNAs of defined sequences were determined. Identical association and dissociation rate constants were observed for all eight aa-tRNAs in both the ribosomal A and P sites despite substantial differences in tRNA sequence, the type of esterified amino acid, and posttranscriptional modifications. These results indicate that the overall binding of all aa-tRNAs to the ribosome is uniform. However, when either the esterified amino acid or the tRNA modifications were removed, binding was no longer uniform. These results suggest that differences in tRNA sequences and tRNA modifications have evolved to offset differential thermodynamic contributions of the esterified amino acid and the codon-anticodon interaction so that ribosomal binding of all aa-tRNAs remains uniform.

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.

An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp

The product of the Escherichia coli yadB gene is homologous to the N-terminal part of bacterial glutamyl-tRNA synthetases (GluRSs), including the Rossmann fold with the acceptor-binding domain and the stem-contact fold. This GluRS-like protein, which lacks the anticodon-binding domain, does not use tRNA(Glu) as substrate in vitro nor in vivo, but aminoacylates tRNA(Asp) with glutamate. The yadB gene is expressed in wild-type E. coli as an operon with the dksA gene, which encodes a protein involved in the general stress response by means of its action at the translational level. The fate of the glutamylated tRNA(Asp) is not known, but its incapacity to bind elongation factor Tu suggests that it is not involved in ribosomal protein synthesis. Genes homologous to yadB are present only in bacteria, mostly in Proteobacteria. Sequence alignments and phylogenetic analyses show that the YadB proteins form a distinct monophyletic group related to the bacterial and organellar GluRSs (alpha-type GlxRSs superfamily) with ubiquitous function as suggested by the similar functional properties of the YadB homologue from Neisseria meningitidis.

Genomic investigation of the system for selenocysteine incorporation in the bacterial domain

The elucidation of nearly 100 bacterial genomes has made it possible to categorize them into two groups, according to the presence or absence of a selenocysteine (Sec) tRNA. In the group with the tRNA, a Sec incorporation system like that of Escherichia coli would be expected. However, for the other group, the following question has been left unsolved. Is it reasonable to assume that bacteria without the tRNA lack the entire Sec system, and do such bacteria exist commonly? To explore it experimentally, we chose Bacillus subtilis, a representative eubacterium for which a Sec tRNA has not been found. First, we reviewed the genome to search for the tRNA gene. Second, we examined the possible expression of an unknown tRNA. Third, we examined Sec-related enzymes and proteins in B. subtilis cell extracts. Fourth, the B. subtilis and E. coli seryl-tRNA synthetases were expressed, and the specificity was analyzed. Consequently, all of the data showed negative results about the existence of the Sec system in B. subtilis. Additionally, we discuss the possibility of predicting the existence or absence of the system in each bacterial organism by using the Sec tRNA and seryl-tRNA synthetase as indicators.

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.

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.

Recognition of tRNA backbone for aminoacylation with cysteine: evolution from Escherichia coli to human

The underlying basis of the genetic code is specific aminoacylation of tRNAs by aminoacyl-tRNA synthetases. Although the code is conserved, bases in tRNA that establish aminoacylation are not necessarily conserved. Even when the bases are conserved, positions of backbone groups that contribute to aminoacylation may vary. We show here that, although the Escherichia coli and human cysteinyl-tRNA synthetases both recognize the same bases (U73 and the GCA anticodon) of tRNA for aminoacylation, they have different emphasis on the tRNA backbone. The E. coli enzyme recognizes two clusters of phosphate groups. One is at A36 in the anticodon and the other is in the core of the tRNA structure and includes phosphate groups at positions 9, 12, 14, and 60. Metal-ion rescue experiments show that those at positions 9, 12, and 60 are involved with binding divalent metal ions that are important for aminoacylation. The E. coli enzyme also recognizes 2'-hydroxyl groups within the same two clusters: at positions 33, 35, and 36 in the anticodon loop, and at positions 49, 55, and 61 in the core. The human enzyme, by contrast, recognizes few phosphate or 2'-hydroxy groups for aminoacylation. The evolution from the backbone-dependent recognition by the E. coli enzyme to the backbone-independent recognition by the human enzyme demonstrates a previously unrecognized shift that nonetheless has preserved the specificity for aminoacylation with cysteine.

Manipulation of tRNA properties by structure-based and combinatorial in vitro approaches

The wide knowledge accumulated over the years on the structure and function of transfer RNAs (tRNAs) has allowed molecular biologists to decipher the rules underlying the function and the architecture of these molecules. These rules will be discussed and the implications for manipulating tRNA properties by structure-based and combinatorial in vitro approaches reviewed. Since most of the signals conferring function to tRNAs are located on the two distal extremities of their three-dimensional L shape, this implies that the structure of the RNA domain connecting these two extremities can be of different architecture and/or can be modified without disturbing individual functions. This concept is first supported by the existence in nature of RNAs of peculiar structures having tRNA properties, as well as by engineering experiments on natural tRNAs. The concept is further illustrated by examples of RNAs designed by combinatorial methods. The different procedures used to select RNAs or tRNA-mimics interacting with aminoacyl-tRNA synthetases or with elongation factors and to select tRNA-mimics aminoacylated by synthetases are presented, as well as the functional and structural characteristics of the selected molecules. Production and characteristics of aptameric RNAs fulfilling aminoacyl-tRNA synthetase functions and of RNAs selected to have affinities for amino acids are also described. Finally, properties of RNAs obtained by either the structure-based or the combinatorial methods are discussed in the light of the origin and evolution of the translation machinery, but also with a view to obtain new inhibitors targeting specific steps in translation.

Structure-Function Analysis of RNAs Generated by In Vivo and In Vitro Selection

Today, the concept of Darwinian evolution plays a significant role in studying structure-function relationships concerning known molecules and in helping to design previously unknown molecules with desired functionalities. Results from

A single amidotransferase forms asparaginyl-tRNA and glutaminyl-tRNA in Chlamydia trachomatis

Aminoacyl-tRNA is generally formed by aminoacyl-tRNA synthetases, a family of 20 enzymes essential for accurate protein synthesis. However, most bacteria generate one of the two amide aminoacyl-tRNAs, Asn-tRNA or Gln-tRNA, by transamidation of mischarged Asp-tRNA(Asn) or Glu-tRNA(Gln) catalyzed by a heterotrimeric amidotransferase (encoded by the gatA, gatB, and gatC genes). The Chlamydia trachomatis genome sequence reveals genes for 18 synthetases, whereas those for asparaginyl-tRNA synthetase and glutaminyl-tRNA synthetase are absent. Yet the genome harbors three gat genes in an operon-like arrangement (gatCAB). We reasoned that Chlamydia uses the gatCAB-encoded amidotransferase to generate both Asn-tRNA and Gln-tRNA. C. trachomatis aspartyl-tRNA synthetase and glutamyl-tRNA synthetase were shown to be non-discriminating synthetases that form the misacylated tRNA(Asn) and tRNA(Gln) species. A preparation of pure heterotrimeric recombinant C. trachomatis amidotransferase converted Asp-tRNA(Asn) and Glu-tRNA(Gln) into Asn-tRNA and Gln-tRNA, respectively. The enzyme used glutamine, asparagine, or ammonia as amide donors in the presence of either ATP or GTP. These results suggest that C. trachomatis employs the dual specificity gatCAB-encoded amidotransferase and 18 aminoacyl-tRNA synthetases to create the complete set of 20 aminoacyl-tRNAs.

Study on construction of a cDNA library corresponding to an amino acid-specific tRNA and influence of the modified nucleotide upon nucleotide misincorporations in reverse transcription

The construction of a cDNA library corresponding to an amino acid-specific tRNA and the influence of the modified nucleotide in the tRNA upon misincorporation in reverse transcription were investigated. The distinctive feature of the constructive strategy is that the cDNA library was prepared in connection with the charging activity of the tRNA. The aminoacyl-tRNA was captured selectively by using a biotin-avidin system. After hydrolysis of the ester bond, the tRNA was collected as an amino acid-specific tRNA pool, and a poly(A) tail was attached to the CCA terminus for reverse transcription. To the 3'-terminus of the transcribed cDNA, poly (dC) was added by terminal deoxynucleotidyl transferase, and the cDNA was amplified by PCR. The double-stranded cDNA was used for transformation of Escherichia coli JM109. Sequence analyses of the obtained clones bearing the tRNA genes revealed that a few nucleotide substitutions occurred at the location where the modified nucleotides exist. Among them, it was noteworthy that 1-methyladenosine (m(1)A22) in the D-loop of Bacillus subtilis tRNA(Ser) was recognized as G in the reverse transcription and the result revealed different tendency of the misincorporation, which has been shown in the study of HIV-1 reverse transcription.

A new reporter gene system suited for cell-free protein synthesis and high-throughput screening in small reaction volumes

The properties of M-hirudin as a new reporter gene system were examined using rabbit reticulocyte lysate for cell-free protein expression. In contrast to the luciferase gene, in vitro translation of M-hirudin is highly robust against changes in concentrations of K+ (and Rb+). In addition, M-hirudin can be detected very sensitively using a reasonably priced fluorimetric thrombin assay. To show that the new reporter gene system is well suited for (u)HTS-applications, cell-free synthesis as well as the fluorimetric assay of M-hirudin were carried out in nanotiter and microtiter plates, respectively.

Cation radius effects on cell-free translation in rabbit reticulocyte lysate

The effect of monovalent cation concentrations on the translation was examined in the rabbit reticulocyte cell-free system. The translation of standard reporter gene luciferase was studied using different concentrations of LiCl, NaCl, KCl, RbCl, CsCl, NH(4)Cl, and (CH(3))(4)NCl and the acetates of Na(+), K(+), and NH4(+). Only the salts of K(+), Rb(+), and NH4(+) and to some minor extent of Cs(+) significantly supported translation. Optimum concentrations were dependent on the cation used. Optimum concentrations ranged between 40 mM (NH(4)Ac), 80 mM (KCl, NH(4)Cl), and 100 mM (RbCl, KAc). The maximum efficiency of translation depends on the ionic radius of the cation used. KCl and RbCl were superior to all other salts tested in stimulating in vitro translation. The results were confirmed, using a second reporter system, M-hirudin. Here, however, broad optima were observed with RbCl being slightly superior to KCl in supporting translation.

An in vitro evolved precursor tRNA with aminoacylation activity

A set of catalysts for aminoacyl-tRNA synthesis is an essential component for translation. The RNA world hypothesis postulates that RNA catalysts could have played this role. Here we show an in vitro evolved precursor tRNA consisting of two domains, a catalytic 5'-leader sequence and an aminoacyl-acceptor tRNA. The 5'-leader sequence domain selectively self-charges phenylalanine on the 3'-terminus of the tRNA domain. This cis-acting ribozyme is susceptible to RNase P RNA, generating the corresponding 5'-leader segment and the mature tRNA. Moreover, the 5'-leader segment is able to aminoacylate the mature tRNA in trans. Mutational studies have revealed that C(74) and C(75) at the tRNA aminoacyl-acceptor end form base pairs with G71 and G70 of the trans-acting ribozyme. Such Watson-Crick base pairing with tRNA has been observed in RNase P RNA and 23S rRNA, suggesting that all three ribozymes use a similar mechanism for the recognition of the aminoacyl-acceptor end. Our demonstrations indicate that catalytic precursor tRNAs could have provided the foundations for the genetic coding system in the proto-translation system.

RNA analysis by ion-pair reversed-phase high performance liquid chromatography

Ion-pair reversed-phase high performance liquid chromatography (IP RP HPLC) is presented as a new, superior method for the analysis of RNA. IP RP HPLC provides a fast and reliable alternative to classical methods of RNA analysis, including separation of different RNA species, quantification and purification. RNA is stable under the analysis conditions used; degradation of RNA during the analyses was not observed. The versatility of IP RP HPLC for RNA analysis is demonstrated. Components of an RNA ladder, ranging in size from 155 to 1770 nt, were resolved. RNA transcripts of up to 5219 nt were analyzed, their integrity determined and they were quantified and purified. Purification of mRNA from total RNA is described, separating mouse rRNA from poly(A)(+) mRNA. IP RP HPLC is also suitable for the separation and purification of DIG-labeled from unlabeled RNA. RNA purified by IP RP HPLC exhibits improved stability.

In vitro selection of RNAs aminoacylated by Escherichia coli leucyl-tRNA synthetase

To investigate systematically the RNA sequences necessary for aminoacylation by Escherichia coli leucyl-tRNA synthetase, RNAs with leucylation activity were isolated by in vitro selection from a library of tRNALeu variants possessing randomized sequences in the D-loop, the variable arm, and the T-loop. After two rounds of selection, most of the selected variants showed the following features: (1) the tertiary interaction between nucleotides at positions 15 and 48 was A15-U48; (2) the continuous G18G19 sequence, which is invariant in canonical tRNAs, appeared at the fixed position in the D-loop; and (3) the nucleotide at position 20a in the D-loop was A. These selected nucleotides and their positions, concentrating on the hinge region of tRNA, were identical to those of native tRNALeu. In contrast, although the long variable arm is the most characteristic of the tRNALeu structure, the primary and secondary structures were not correlated with the leucylation activity. These findings indicate that A15-U48, A20a, and G18G19 located at specific positions are involved in the tertiary folding of leucine-accepting tRNA molecules. With increases in the selection cycle, the D-loop sequence and the secondary structure of the variable arm became similar to those of tRNALeu, suggesting that tRNALeu represents an optimized RNA sequence for leucylation.

tRNA mimics

Mimics recapitulating the structural features of tRNAs are involved in biological processes other than ribosome-dependent protein synthesis. A knowledge of the rules underlying the architecture and function of tRNAs allows the design of non-natural mimics. The study of these mimics sheds light upon links between replication, translation and metabolic pathways, leads to biotechnological applications, and provides experimental and conceptual tools for the exploration of primordial evolutionary processes.