Function independence of microhelix aminoacylation from anticodon binding in a class I tRNA synthetase

Effect of a domain-spanning disulfide on aminoacyl-tRNA synthetase activity

Enzymes regulated by allostery undergo conformational rearrangement upon binding effector molecules. For modular proteins, a flexible interface may mediate reorientation of the protein domains and transmit binding events to activate catalysis at a distance. Aminoacyl-tRNA synthetases (aaRSs) that use tRNA anticodons as identity elements can be considered allosteric enzymes in which aminoacylation of the tRNA acceptor stem is enhanced upon anticodon binding. We reasoned that anticodon-triggered conformational change might be restricted upon introduction of a disulfide linkage near the core of an aaRS. Here we show that a double cysteine mutation engineered at the Escherichia coli MetRS domain interface spontaneously generates a disulfide linkage. This disulfide clamp has no effect on methionyl adenylate formation but reduces the level of tRNA(Met) aminoacylation approximately 2-fold. Activity is restored upon chemical reduction of the disulfide, demonstrating that E. coli MetRS requires a flexible interface domain for full catalytic efficiency.

Domain-domain communication in aminoacyl-tRNA synthetases

Aminoacyl-tRNA synthetases are modular proteins, with domains that have distinct roles in the aminoacylation reaction. The catalytic core is responsible for aminoacyl adenylate formation and transfer of the amino acid to the 3' end of the bound transfer RNA (tRNA). Appended and inserted domains contact portions of the tRNA outside the acceptor site and contribute to the efficiency and specificity of aminoacylation. Some aminoacyl-tRNA synthetases also have distinct editing activities that are localized to unique domains. Efficient aminoacylation and editing require communication between RNA-binding and catalytic domains, and can be considered as a signal transduction system. Here, evidence for domain-domain communication in aminoacyl-tRNA synthetases is summarized, together with insights from structural analysis.

Biochemical and phylogenetic analyses of methionyl-tRNA synthetase isolated from a pathogenic microorganism, Mycobacterium tuberculosis

Mycobacterium tuberculosis methionyl-tRNA synthetase (MetRS) has been cloned and characterized. The protein contains class I signature sequences but lacks the Zn2+ binding motif and the C-terminal dimerization appendix that are found in MetRSs from several organisms including E. coli MetRS. Consistent with these features, the enzyme behaved as a monomer in a gel filtration chromatography and did not contain the bound Zn2+. Nonetheless, it was active to the tRNAMet of E. coli as determined by in vivo genetic complementation and in vitro reaction. Phylogenetic analysis separated the M. tuberculosis and E. coli MetRSs into prokaryote and eukaryote-archaea group, respectively. This result is consistent with the taxonomic locations of the organism but is an interesting contrast to the case of its paralogous protein, isoleucyl-tRNA synthetase, and suggests that the two enzymes evolved in separate idiosyncratic pathways.

Abnormal proteins enhance stress-induced cell death

The effect of abnormal proteins on cell viability was studied using artificially cleaved polypeptides. Escherichia coli methionyl-tRNA synthetase (MetRS) consists of two distinct domains and its activity is essential for cell viability. The polypeptide chain was split by linker insertion and expressed as two fragments. Two pairs of polypeptides, one split within the N-terminal domain and another at the junction of the two domains retained aminoacylation activity. The in vitro activities of these split mutants were enhanced by the presence of chaperonin, GroESL. However, cells containing these split polypeptides became sensitive to conditions that induce GroESL. The results of this work suggest that an abnormally generated protein can cause cell death under stressful conditions.

Affinity coelectrophoresis for dissecting protein-RNA domain-domain interactions in a tRNA synthetase system

The class I methionyl tRNA synthetase has a conserved N-terminal nucleotide binding fold which contains the active site, and a largely non-conserved C-terminal anticodon binding domain. At the C-terminal end of the anticodon binding domain is a peptide which curls back into the N-terminal nucleotide binding fold near the active site. We showed that a mutation in this peptide disrupts aminoacylation and binding of a 7 base pair microhelix substrate based on the acceptor stem of tRNA(fMet). The novel technique of affinity coelectrophoresis was applied to this system for the first time to determine dissociation constants of wild-type and mutant MetRS for small RNA substrates. A description and evaluation of this technique for measuring weak protein-nucleic acid interactions is presented here, in the context of the methionyl tRNA synthetase system.

Switching recognition of two tRNA synthetases with an amino acid swap in a designed peptide

The genetic code is based on specific interactions between transfer RNA (tRNA) synthetases and their cognate tRNAs. The anticodons for methionine and isoleucine tRNAs differ by a single nucleotide, and changing this nucleotide in an isoleucine tRNA is sufficient to change aminoacylation specificity to methionine. Results of combinatorial mutagenesis of an anticodon-binding-helix loop peptide were used to design a hybrid sequence composed of amino acid residues from methionyl- and isoleucyl-tRNA synthetases. When the hybrid sequence was transplanted into isoleucyl-tRNA synthetase, active enzyme was generated in vivo and in vitro. The transplanted peptide did not confer function to methionyl-tRNA synthetase, but the substitution of a single amino acid within the transplanted peptide conferred methionylation and prevented isoleucylation. Thus, the swap of a single amino acid in the transplanted peptide switches specificity between anticodons that differ by one nucleotide.

Thiol ligation of two zinc atoms to a class I tRNA synthetase: evidence for unshared thiols and role in amino acid binding and utilization

Class I tRNA synthetases generally contain a characteristic N-terminal catalytic core joined to a C-terminal domain that is idiosyncratic to the enzyme. The closely related class I Escherichia coli methionyl- and isoleucyl-tRNA synthetases each have a single zinc atom coordinated to ligands contained in the catalytic domain. Isoleucyl-tRNA synthetase has a second, functionally essential, zinc bound to ligands at the C-terminal end of the 939 amino acid polypeptide. Recent evidence suggested that this structure curls back and interacts directly or indirectly with the active site. We show here by X-ray absorption spectroscopy that the average Zn environment contains predominantly sulfur ligands with a Zn-S distance of 2.33 A. A model with eight coordinated thiolates divided between two Zn(Cys)4 structures best fit the data which are not consistent with a thiolate-bridged Zn2(Cys)6 structure joining the C-terminal end with the N-terminal active site domain. We also show that zinc bound to the N-terminal catalytic core is important specifically for amino acid binding and utilization, although a direct interaction with zinc is unlikely. We suggest that, in addition to idiosyncratic sequences for tRNA acceptor helix interactions incorporated into the class-defining catalytic domain common to class I enzymes, the architecture of at least some parts of the amino acid binding sites may differ from enzyme to enzyme and include motifs that bind zinc.

An RNA binding site in a tRNA synthetase with a reduced set of amino acids

A 30 amino acid helix-loop of known structure on the surface of the C-terminal domain of the class I Escherichia coli methionine tRNA synthetase is essential for methionine tRNA anticodon discrimination. Replacing this 30 amino acid peptide with a previously described sequence containing residues from the wild-type protein imbedded in a sequence matrix of mostly alanines and serines, we used a combinatorial mutagenesis and selection strategy to define residual wild-type residues that are not replaceable with alanine or serine, because they are needed for specific recognition of methionine tRNA. Four were identified, of which three have functional side chains (Asn, Arg, Lys). These four and a fifth (Trp) that was previously identified are located at the end of the helix and within the loop, lie on the same side of the structure, and span a distance of about 20 A. We conclude that, within the alanine, serine sequence matrix, only a few non-alanine, non-serine residues in the specificity-determining part of the structure are essential.

Dissection of a class II tRNA synthetase: determinants for minihelix recognition are tightly associated with domain for amino acid activation

The ten class II aminoacyl-tRNA synthetases are large homo- and hetero-oligomeric proteins that share three conserved sequence motifs. Within this class, Escherichia coli alanyl-tRNA synthetase is the only homotetramer and is comprised of subunits of 875 amino acids. The enzyme aminoacylates sequence-specific RNA oligonucleotides that recreate as few as four base pairs of the acceptor stem of tRNA(Ala). A monomeric 461 amino acid N-terminal fragment (461N) was previously shown to have full adenylate synthesis activity. However, fragment 461N has significant, but reduced, efficiency of charging of tRNA(Ala), when compared to native enzyme [Ho, C., Jasin, M., & Schimmel, P. (1985) Science 229, 389-393]. We show here that, in contrast, the fragment and the native enzyme aminoacylate a 12 base pair acceptor-T psi C stem minihelix and a four base pair RNA tetraloop with the same efficiency. We also show that fragment 461N makes footprint contacts both on and outside the acceptor helix of bound tRNA(Ala). With one possible exception, the contacts observed with fragment 461N are identical to those seen with the native enzyme. In spite of contacts outside the acceptor helix, fragment 461N charges the native tRNA, minihelix, and tetraloop with similar efficiency. Thus, all minihelix contacts required for activation for charging are tightly associated with the adenylate synthesis domain and, at least in the fragment, are not influenced by additional RNA-protein contacts outside the minihelix domain.(ABSTRACT TRUNCATED AT 250 WORDS)

Aminoacylation of RNA minihelices: implications for tRNA synthetase structural design and evolution

The genetic code is based on the aminoacylation of tRNA with amino acids catalyzed by the aminoacyl-tRNA synthetases. The synthetases are constructed from discrete domains and all synthetases possess a core catalytic domain that catalyzes amino acid activation, binds the acceptor stem of tRNA, and transfers the amino acid to tRNA. Fused to the core domain are additional domains that mediate RNA interactions distal to the acceptor stem. Several synthetases catalyze the aminoacylation of RNA oligonucleotide substrates that recreate only the tRNA acceptor stems. In one case, a relatively small catalytic domain catalyzes the aminoacylation of these substrates independent of the rest of the protein. Thus, the active site domain may represent a primordial synthetase in which polypeptide insertions that mediate RNA acceptor stem interactions are tightly integrated with determinants for aminoacyl adenylate synthesis. The relationship between nucleotide sequences in small RNA oligonucleotides and the specific amino acids that are attached to these oligonucleotides could constitute a second genetic code.