Indolmycin Resistance of Streptomyces coelicolor A3(2) by Induced Expression of One of Its Two Tryptophanyl-tRNA Synthetases

Kitabatake, Makoto; Ali, K.; Demain, Arnold L.; Sakamoto, Kensaku; Yokoyama, Shigeyuki; Söll, Dieter

doi:10.1074/jbc.m202639200

Cited by 51 publications

(59 citation statements)

References 34 publications

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“…In some cases aaRS duplicates with different tRNA substrate specificities are found in the same organism, presumably to provide versatility in the choice of certain aminoacyl-tRNA synthesis pathways (34,35). Both closely related (36) and highly diverged homologues have also been described that differ in their amino acid recognition properties (37,38). For example, several bacteria encode two distantly related forms of isoleucyl-tRNA synthetase, IleRS1 and IleRS2, the second of which confers resistance to pseudomonic acid A, a competitive inhibitor of isoleucine binding (39,40).…”

Section: Limiting the Addition Of Nonprotein Amino Acids To The Genetmentioning

confidence: 99%

Nonorthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogues to the genetic code

Jester

Levengood

Roy

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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Insertion of lysine during protein synthesis depends on the enzyme lysyl-tRNA synthetase (LysRS), which exists in two unrelated forms, LysRS1 and LysRS2. LysRS1 has been found in most archaea and some bacteria, and LysRS2 has been found in eukarya, most bacteria, and a few archaea, but the two proteins are almost never found together in a single organism. Comparison of structures of LysRS1 and LysRS2 complexed with lysine suggested significant differences in their potential to bind lysine analogues with backbone replacements. One such naturally occurring compound, the metabolic intermediate S-(2-aminoethyl)-L-cysteine, is a bactericidal agent incorporated during protein synthesis via LysRS2. In vitro tests showed that S-(2-aminoethyl)-L-cysteine is a poor substrate for LysRS1, and that it inhibits LysRS1 200-fold less effectively than it inhibits LysRS2. In vivo inhibition by S-(2-aminoethyl)-L-cysteine was investigated by replacing the endogenous LysRS2 of Bacillus subtilis with LysRS1 from the Lyme disease pathogen Borrelia burgdorferi. B. subtilis strains producing LysRS1 alone were relatively insensitive to growth inhibition by S-(2-aminoethyl)-L-cysteine, whereas a WT strain or merodiploid strains producing both LysRS1 and LysRS2 showed significant growth inhibition under the same conditions. These growth effects arising from differences in amino acid recognition could contribute to the distribution of LysRS1 and LysRS2 in different organisms. More broadly, these data demonstrate how diversity of the aminoacyltRNA synthetases prevents infiltration of the genetic code by noncanonical amino acids, thereby providing a natural reservoir of potential antibiotic resistance.

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Section: Limiting the Addition Of Nonprotein Amino Acids To The Genetmentioning

confidence: 99%

Nonorthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogues to the genetic code

Jester

Levengood

Roy

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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“…For example, mupirocin, an antibiotic produced by Pseudomonas fluorescens, selectively inhibits the prokaryotic isoleucyl-tRNA synthetases but has little or no effect on the eukaryotic enzymes (2,3). Indolmycin, a secondary metabolite of Streptomyces griseus and analogue of tryptophan, inhibits only one of the two tryptophanyl-tRNA synthetases in Streptomyces coelicolor (4).…”

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confidence: 99%

A Unique Hydrophobic Cluster Near the Active Site Contributes to Differences in Borrelidin Inhibition among Threonyl-tRNA Synthetases

Ruan

Bovee

Sacher

et al. 2005

Journal of Biological Chemistry

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Borrelidin, a compound with anti-microbial and antiangiogenic properties, is a known inhibitor of bacterial and eukaryal threonyl-tRNA synthetase (ThrRS). The inhibition mechanism of borrelidin is not well understood. Archaea contain archaeal and bacterial genre ThrRS enzymes that can be distinguished by their sequence. We explored species-specific borrelidin inhibition of ThrRSs. The activity of ThrRS from Sulfolobus solfataricus and Halobacterium sp. NRC-1 was inhibited by borrelidin, whereas ThrRS enzymes from Methanocaldococcus jannaschii and Archaeoglobus fulgidus were not. In Escherichia coli ThrRS, borrelidin binding induced a conformational change, and threonine was not activated as shown by ATP-PP i exchange and a transient kinetic assay measuring intrinsic tryptophan fluorescence changes. These assays further showed that borrelidin is a noncompetitive tight binding inhibitor of E. coli ThrRS with respect to threonine and ATP. Genetic selection of borrelidin-resistant mutants showed that borrelidin binds to a hydrophobic region (Thr-307, His-309, Cys-334, Pro-335, Leu-489, Leu-493) proximal to the zinc ion at the active site of the E. coli ThrRS. Mutating residue Leu-489 3 Trp reduced the space of the hydrophobic cluster and resulted in a 1500-fold increase of the K i value from 4 nM to 6 M. An alignment of ThrRS sequences showed that this cluster is conserved in most organisms except for some Archaea (e.g. M. jannaschii, A. fulgidus) and some pathogens (e.g. Helicobacter pylori). This study illustrates how one class of natural product inhibitors affects aminoacyl-tRNA synthetase function, providing potentially useful information for structure-based inhibitor design.Aminoacyl-tRNA synthetases (aaRSs) 1 catalyze the acylation of transfer RNAs with their cognate amino acids and are therefore essential enzymes for protein synthesis in all organisms (1). They display exquisite specificity in discriminating between similar amino acid or tRNA substrates. Even though the core architectures of the active sites of individual aaRSs are relatively conserved, protein sequence alignments showed significant divergence among the three domains of life. However, finely tuned structural differences between aaRS orthologs provide ample opportunities for the evolution of species-specific inhibitors of any given tRNA synthetase. For example, mupirocin, an antibiotic produced by Pseudomonas fluorescens, selectively inhibits the prokaryotic isoleucyl-tRNA synthetases but has little or no effect on the eukaryotic enzymes (2, 3). Indolmycin, a secondary metabolite of Streptomyces griseus and analogue of tryptophan, inhibits only one of the two tryptophanyl-tRNA synthetases in Streptomyces coelicolor (4).ThrRS is a class II aaRS containing an N-terminal editing domain, a C-terminal tRNA binding domain, and a zinc-binding catalytic domain with the class II conserved motifs 1, 2, and 3 that provide critical ATP binding determinants (5). ThrRSs from Chinese hamster ovary cells, Saccharomyces cerevisiae and Escherichia coli (revie...

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“…Some data suggest that SAV4725 may be involved in a mechanism that renders some Streptomyces strains, including S. avermitilis and S. coelicolor A3(2), naturally resistant to indolmycin, an antibiotic that inhibits tryptophanyl tRNA synthase (ref. 23 and data not shown). S. avermitilis and S. coelicolor A3(2) are naturally resistant to chloramphenicol.…”

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confidence: 99%

Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis

et al. 2003

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Species of the genus Streptomyces are of major pharmaceutical interest because they synthesize a variety of bioactive secondary metabolites. We have determined the complete nucleotide sequence of the linear chromosome of Streptomyces avermitilis. S. avermitilis produces avermectins, a group of antiparasitic agents used in human and veterinary medicine. The genome contains 9,025,608 bases (average GC content, 70.7%) and encodes at least 7,574 potential open reading frames (ORFs). Thirty-five percent of the ORFs (2,664) constitute 721 paralogous families. Thirty gene clusters related to secondary metabolite biosynthesis were identified, corresponding to 6.6% of the genome. Comparison with Streptomyces coelicolor A3(2) revealed that an internal 6.5-Mb region in the S. avermitilis genome was highly conserved with respect to gene order and content, and contained all known essential genes but showed perfectly asymmetric structure at the oriC center. In contrast, the terminal regions were not conserved and preferentially contained nonessential genes.

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Indolmycin Resistance of Streptomyces coelicolor A3(2) by Induced Expression of One of Its Two Tryptophanyl-tRNA Synthetases

Cited by 51 publications

References 34 publications

Nonorthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogues to the genetic code

Nonorthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogues to the genetic code

A Unique Hydrophobic Cluster Near the Active Site Contributes to Differences in Borrelidin Inhibition among Threonyl-tRNA Synthetases

Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis

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