On the Evolution of the tRNA-Dependent Amidotransferases, GatCAB and GatDE

Sheppard, Kelly; Söll, Dieter

doi:10.1016/j.jmb.2008.01.016

Cited by 52 publications

(94 citation statements)

References 69 publications

(52 reference statements)

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“…In keeping with the prediction that all archaeal GluRSs are nondiscriminating (32), the acceptor stem loop is indeed absent from all archaea, with only one exception. The Sulfolobus solfataricus GluRS has a similar loop (Fig.…”

Section: Thermautotrohpicussupporting

confidence: 76%

Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase

O’Donoghue

Sheppard

Nureki

et al. 2011

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

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The specificity of most aminoacyl-tRNA synthetases for an amino acid and cognate tRNA pair evolved before the divergence of the three domains of life. Glutaminyl-tRNA synthetase (GlnRS) evolved later and is derived from the archaeal-type nondiscriminating glutamyl-tRNA synthetase (GluRS), an enzyme with relaxed tRNA specificity capable of forming both Glu-tRNA Glu and Glu-tRNA Gln . The archaea lack GlnRS and use a specialized amidotransferase to convert Glu-tRNA Gln to Gln-tRNA Gln needed for protein synthesis. We show that the Methanothermobacter thermautotrophicus GluRS is active toward tRNA Glu and the two tRNA Gln isoacceptors the organism encodes, but with a significant catalytic preference for . The less active responds to the less common CAA codon for Gln. From a biochemical characterization of M. thermautotrophicus GluRS variants, we found that the evolution of tRNA specificity in GlnRS could be recapitulated by converting the M. thermautotrophicus GluRS to a tRNA Gln specific enzyme, solely through the addition of an acceptor stem loop present in bacterial GlnRS. One designed GluRS variant is also highly specific for the isoacceptor, which responds to the CAG codon, and shows no activity toward . Because it is now possible to eliminate particular codons from the genome of Escherichia coli , additional codons will become available for genetic code engineering. Isoacceptor-specific aminoacyl-tRNA synthetases will enable the reassignment of more open codons while preserving accurate encoding of the 20 canonical amino acids.

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Section: Thermautotrohpicussupporting

confidence: 76%

Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase

O’Donoghue

Sheppard

Nureki

et al. 2011

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

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“…In archaea, GatCAB is used only for Asn-tRNA Asn formation as GatDE forms Gln-tRNA Gln (16,17). Both AdTs likely were present in early archaea (40). The specificity of archaeal GatCAB for Asn-tRNA Asn synthesis might have enabled archaeal AspRS to coevolve with the AdT to form a thermostable complex in which GatCAB is not released following Asn-tRNA Asn synthesis.…”

Section: Sepcyse and Trnamentioning

confidence: 99%

“…Early bacteria likely emerged from the last universal common ancestral state (LUCAS) with just one AdT-GatCAB-for both Gln-tRNA Gln and Asn-tRNA Asn formation (40). After AsntRNA Asn formation in early bacteria, the release of GatCAB from bacterial ND-AspRS might be have been beneficial, because the free GatCAB could easily be repurposed for GlntRNA Gln formation with GluRS.…”

Section: Sepcyse and Trnamentioning

confidence: 99%

Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis

Suzuki

Nakamura

Kato

et al. 2014

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

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Many prokaryotes lack a tRNA synthetase to attach asparagine to its cognate tRNAAsn, and instead synthesize asparagine from tRNAAsn-bound aspartate. This conversion involves two enzymes: a nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) that forms Asp-tRNAAsn, and a heterotrimeric amidotransferase GatCAB that amidates Asp-tRNAAsn to form Asn-tRNAAsn for use in protein synthesis. ND-AspRS, GatCAB, and tRNAAsn may assemble in an ∼400-kDa complex, known as the Asn-transamidosome, which couples the two steps of asparagine biosynthesis in space and time to yield Asn-tRNAAsn. We report the 3.7-Å resolution crystal structure of the Pseudomonas aeruginosa Asn-transamidosome, which represents the most common machinery for asparagine biosynthesis in bacteria. We show that, in contrast to a previously described archaeal-type transamidosome, a bacteria-specific GAD domain of ND-AspRS provokes a principally new architecture of the complex. Both tRNAAsn molecules in the transamidosome simultaneously serve as substrates and scaffolds for the complex assembly. This architecture rationalizes an elevated dynamic and a greater turnover of ND-AspRS within bacterial-type transamidosomes, and possibly may explain a different evolutionary pathway of GatCAB in organisms with bacterial-type vs. archaeal-type Asn-transamidosomes. Importantly, because the two-step pathway for Asn-tRNAAsn formation evolutionarily preceded the direct attachment of Asn to tRNAAsn, our structure also may reflect the mechanism by which asparagine was initially added to the genetic code.

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“…We analyzed the phylogeny of GatB because this subunit is restricted to AdTs. The analysis showed that both GatBo and GatB are in the same bacterial clade and are not clustered with the archaeal GatB of the monospecific archaeal GatCAB AdTs (45). As a result, both GatCABs, GatCABo and GatCAB, will very likely display the same activities and specificities.…”

Section: Gatcabo Adt Is Able To Generate Both Asn-trna Asn and Gln-trnamentioning

confidence: 96%