Characterization of yeast seryl-tRNA synthetase active site mutants with improved discrimination against substrate analogues

An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in Escherichia coli

We report the development of the orthogonal amber-suppressor pair Archaeoglobus fulgidus seryl-tRNA (Af-tRNA^Ser)/Methanosarcina mazei seryl-tRNA synthetase (MmSerRS) in Escherichia coli. Furthermore, the crystal structure of MmSerRS was solved at 1.45 Å resolution, which should enable structure-guided engineering of its active site to genetically encode small, polar noncanonical amino acids (ncAAs).

Genetic evidence for a noncanonical function of seryl-tRNA synthetase in vascular development

In a recent genetic screen, we identified mutations in genes important for vascular development and maintenance in zebrafish (Jin et al. Dev Biol. 2007;307:29-42). Mutations [corrected] at the adrasteia (adr) locus cause a pronounced dilatation of the aortic arch vessels as well as aberrant patterning of the hindbrain capillaries and, to a lesser extent, intersomitic vessels. This dilatation of the aortic arch vessels does not appear to be caused by increased cell proliferation but is dependent on vascular endothelial growth factor (Vegf) signaling. By positional cloning, we isolated seryl-tRNA synthetase (sars) as the gene affected by the adr mutations. Small interfering RNA knockdown experiments in human umbilical vein endothelial cell cultures indicate that SARS also regulates endothelial sprouting. These analyses of zebrafish and human endothelial cells reveal a new noncanonical function of Sars in endothelial development.

Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate

Aminoacyl-tRNA synthetase forms an enzyme-bound intermediate, aminoacyladenylate in the amino-acid activation reaction. This reaction is monitored by measuring the ATP-PPi exchange reason in which [(32)P]PPi is incorporated into ATP. We previously reported that L-lysine hydroxamate completely inhibited the L-lysine-dependent ATP-PPi exchange reaction catalysed by lysyl-tRNA synthetase from Bacillus stearothermophilus (BsLysRS). Several experiments suggested that BsLysRS can adenylate L-lysine hydroxamate, but the enzyme-bound lysyladenylate-like compound does not undergo the nucleophilic attack of PPi. This contrasts with the two reports for seryl-tRNA synthetase (SerRS): (i) L-serine hydroxamate was utilized by yeast SerRS as a substrate in the ATP-PPi exchange; and (ii) a seryladenylate-like compound was formed from L-serine hydroxamate in the crystal structure of Thermus thermophilus SerRS. To gain clues about the mechanistic difference, we have determined the crystal structures of two complexes of BsLysRS with the adenylate of L-lysine hydroxamate and with 5'-O-[N-(L-Lysyl)sulphamoyl] adenosine. The comparisons of the two BsLysRS structures and the above SerRS structure revealed the specific side-chain shift of Glu411 of BsLysRS in the complex with the adenylate of L-lysine hydroxamate. In support of other structural comparisons, the result suggested that Glu411 plays a key role in the arrangement of PPi for the nucleophilic attack.

Antibacterial 5'-O-(N-dipeptidyl)-sulfamoyladenosines

The aminoacyl-tRNA synthetase (aaRS) class of enzymes is a validated target for antimicrobial development. Aminoacyl analogues of 5'-O-(N-L-aminoacyl)-sulfamoyladenosines are known to be potent inhibitors of aaRS, but whole cell antibacterial activity of these compounds is very limited, and poor penetration into bacteria has been proposed as the main reason for this. Aiming to find derivatives that better penetrate bacteria, we developed a simple and short method to prepare dipeptidyl-derivatives of 5'-O-(N-L-aminoacyl)-sulfamoyladenosines, and used this method to prepare 18 5'-O-(N-dipeptidyl)-sulfamoyladenosines. The antibacterial activity of these derivatives and a number of reference compounds against S. aureus, E. faecalis and E. coli was determined. Several of the new derivatives showed improved antibacterial activity and an altered spectrum of antibacterial activity.

Aminoacyl-tRNA synthetase inhibitors as potent and synergistic immunosuppressants

The aminoacyl-tRNA synthetase family of enzymes is the target of many antibacterials and inhibitors of eukaryotic hyperproliferation. In screening analogues of 5'-O-(N-L-aminoacyl)-sulfamoyladenosine containing all 20 proteinogenic amino acids, we found these compounds to have potent immunosuppressive activity. Also, we found that combinations of these compounds inhibited the immune response synergistically. Based on these data, analogues with modifications at the aminoacyl and ribose moieties were designed and evaluated, and several of these showed high immunosuppressive potency, with one compound having an IC50 of 80 nM, when tested in a cellular mixed lymphocyte reaction assay. Apart from showing the potential of aminoacyl-tRNA synthetase inhibitors as immunosuppressants, the current study also provides arguments for careful evaluation of the immunosuppressive activity of developmental antibacterials that target these enzymes.

Hydrolysis of non-cognate aminoacyl-adenylates by a class II aminoacyl-tRNA synthetase lacking an editing domain

Aminoacyl-tRNA synthetases, a group of enzymes catalyzing aminoacyl-tRNA formation, may possess inherent editing activity to clear mistakes arising through the selection of non-cognate amino acid. It is generally assumed that both editing substrates, non-cognate aminoacyl-adenylate and misacylated tRNA, are hydrolyzed at the same editing domain, distant from the active site. Here, we present the first example of an aminoacyl-tRNA synthetase (seryl-tRNA synthetase) that naturally lacks an editing domain, but possesses a hydrolytic activity toward non-cognate aminoacyl-adenylates. Our data reveal that tRNA-independent pre-transfer editing may proceed within the enzyme active site without shuttling the non-cognate aminoacyl-adenylate intermediate to the remote editing site.

Selective inhibition of divergent seryl-tRNA synthetases by serine analogues

Seryl-tRNA synthetases (SerRSs) fall into two distinct evolutionary groups of enzymes, bacterial and methanogenic. These two types of SerRSs display only minimal sequence similarity, primarily within the class II conserved motifs, and possess distinct modes of tRNA(Ser) recognition. In order to determine whether the two types of SerRSs also differ in their recognition of the serine substrate, we compared the sensitivity of the representative methanogenic and bacterial-type SerRSs to serine hydroxamate and two previously unidentified inhibitors, serinamide and serine methyl ester. Our kinetic data showed selective inhibition of the methanogenic SerRS by serinamide, suggesting a lack of mechanistic uniformity in serine recognition between the evolutionarily distinct SerRSs.

Synthesis of chemically stabilized phosmidosine analogues and the structure--activity relationship of phosmidosine

Phosmidosine is known to have potent antitumor activity and the unique property of stopping cell growth at the G(1) phase in the cell cycle. However, this natural product having N-prolylphosphoramidate and O-methyl ester linkages on the 5'-phosphoryl residue is unstable under basic conditions and even during the chemical synthesis due to its inherent methyl transfer activity. To find stable derivatives of phosmidosine, a variety of phosmidosine analogues 1a-d replaced by longer alkyl groups in place of the methyl group on the phosphoramidate linkage were synthesized by reaction of alkyl N-(N-tritylprolyl)phosphorodiamidite derivatives 7a-d with an 8-oxoadenosine derivative 4 protected with acid-labile protecting groups. Consequently, the O-ethyl ester derivative 1b was found to be sufficiently stable in aqueous solution. When the prolyl group was replaced by other aminoacyl moieties, the reaction of N-tritylaminoacylamide derivatives 25a-d with an appropriately protected 8-oxoadenosine 5'-(ethyl phosphoramidite) derivative 9 gave better results than the above coupling reaction. A phosphoramidothioate derivative 17 and several simple compounds such as 11, 13, and 15 lacking partial structures of phosmidosine were also synthesized. The antitumor activities of these modified analogues were extensively studied to clarify the structure-activity relationship of phosmidosine. As a result, the two diastereoisomers of longer alkyl-containing phosmidosine analogues both proved to have similar antitumor activities. Replacement of l-proline with other l-amino acids or d-proline resulted in considerable decrease of the antitumor activity. The non-nucleotidic materials 13 did not show any antitumor activity, but a simple core compound of 11 exhibited weak cytotoxicity. The phosphoramidothioate derivative 17 maintained essentially a similar antitumor activity, but the efficiency decreased slightly.

Maize seryl-tRNA synthetase: specificity of substrate recognition by the organellar enzyme

In our study of seryl-tRNA formation in maize, we investigated the enzymes involved in serylation. Only two dissimilar seryl-tRNA synthetase (SerRS) cDNA clones were identified in the Zea mays EST (expressed sequence tag) databases. One encodes a seryl-tRNA synthetase, which presumably functions in the organelles (SerZMm), while the other synthetase product is more similar to eukaryotic cytosolic counterparts (SerZMc). The expression of SerZMm in Saccharomyces cerevisiae resulted in complementation of mutant respiratory phenotype, caused by a disruption of the nuclear gene, presumably encoding yeast mitochondrial seryl-tRNA synthetase (SerSCm). Purified mature SerZMm displays tRNA-assisted serine activation and aminoacylates maize mitochondrial and chloroplast tRNA(Ser) transcripts with similar efficiencies, raising the possibility that only two isoforms of seryl-tRNA synthetase may be sufficient to catalyze seryl-tRNA(Ser) formation in three cellular compartments of Zea mays. Phylogenetic analysis suggests that SerZMm is of mitochondrial origin.