Identity determinants of E.coli tryptophan tRNA

O’Donoghue²,

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

et al. 2013

283

312

The composition of the human microbiota is recognized as an important factor in human health and disease. Many of our cohabitating microbes belong to phylum-level divisions for which there are no cultivated representatives and are only represented by small subunit rRNA sequences. For one such taxon (SR1), which includes bacteria with elevated abundance in periodontitis, we provide a single-cell genome sequence from a healthy oral sample. SR1 bacteria use a unique genetic code. In-frame TGA (opal) codons are found in most genes (85%), often at loci normally encoding conserved glycine residues. UGA appears not to function as a stop codon and is in equilibrium with the canonical GGN glycine codons, displaying strain-specific variation across the human population. SR1 encodes a divergent tRNA Gly UCA with an opal-decoding anticodon. SR1 glycyl-tRNA synthetase acylates tRNA Gly UCA with glycine in vitro with similar activity compared with normal tRNA Gly UCC . Coexpression of SR1 glycyl-tRNA synthetase and tRNA Gly UCA in Escherichia coli yields significant β-galactosidase activity in vivo from a lacZ gene containing an in-frame TGA codon. Comparative genomic analysis with Human Microbiome Project data revealed that the human body harbors a striking diversity of SR1 bacteria. This is a surprising finding because SR1 is most closely related to bacteria that live in anoxic and thermal environments. Some of these bacteria share common genetic and metabolic features with SR1, including UGA to glycine reassignment and an archaeal-type ribulose-1,5-bisphosphate carboxylase (RubisCO) involved in AMP recycling. UGA codon reassignment renders SR1 genes untranslatable by other bacteria, which impacts horizontal gene transfer within the human microbiota.

Section: Resultsmentioning

confidence: 99%

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

O’Donoghue²,

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

et al. 2013

283

312

Journal of Biological Chemistry

“…Support of such a notion comes from the fact that high conservation of nucleotides in this region of bacterial tRNAs Ser cannot be detected; contrary to that, the G30:C40 base pair is absolutely conserved among archaeal tRNA Ser species. This position has been identified as an identity determinant for human phenylalanyl-tRNA synthetase (40 tRNA Ser Recognition in M. barkeri 48782 tors, it makes the largest contribution to serine identity, as confirmed by different experimental approaches (9,17,41). Despite direct contacts that have been observed between T. thermophilus SerRS and the variable arm stem (7), sequence alterations of the variable arm only insignificantly affected the serylation efficiency (27).…”

Section: Barkeri Possesses Two Functional Serrs Enzymes-bothmentioning

confidence: 88%

Differential Modes of Transfer RNASer Recognition in Methanosarcina barkeri

Korenčić

Polycarpo

Weygand-Đurašević

et al. 2004

Two dissimilar seryl-transfer RNA (tRNA) synthetases (SerRSs) exist in Methanosarcina barkeri, one of bacterial type and the other resembling SerRSs present only in some methanogenic archaea. To investigate the requirements of these enzymes for tRNA Ser recognition, serylation of variant transcripts of M. barkeri tRNA Ser was kinetically analyzed in vitro with pure enzyme preparations. Characteristically for the serine system, the length of the variable arm was shown to be crucial for both enzymes, as was the identity of the discriminator base (G73). Moreover, a novel determinant for the specific tRNA Ser recognition was identified as the anticodon stem base pair G30:C40; its contribution to the efficiency of serylation was remarkable for both SerRSs. However, despite these similarities, the two SerRSs do not possess a uniform mode of tRNA Ser recognition, and additional determinants are necessary for serylation specificity by the methanogenic enzyme. In particular, the methanogenic SerRS relies on G1:C72 identity and on the number of unpaired nucleotides at the base of the variable stem for tRNA Ser recognition, unlike its bacterial type counterpart. We propose that such a distinction between the two enzymes in tRNA Ser identity determinants reflects their evolutionary pathways, hence attesting to their diversity.To maintain translational accuracy, aminoacyl-transfer RNA (tRNA) 1 synthetases are highly selective toward their amino acid and tRNA substrates. In the process of tRNA recognition, the cognate and non-cognate substrates are discriminated according to characteristic nucleotides in certain positions of the tRNA, specific for the tRNA/synthetase system.

“…Several technical advances are settling the problem of how aminoacyl-tRNA synthetase can specifically recognize cognate tRNAs from a pool of various tRNA species sharing a similar tertiary structure (1)(2)(3). These studies have indicated that a relatively small number of nucleotides specify the amino acid acceptor identity of tRNA, which usually include the anticodon nucleotides and the discriminator base at position 73 (the base preceding the 3' terminal CCA) as major recognition sites (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). In addition to these major recognition nucleotides, structural features are often recognized by cognate aminoacyl-tRNA synthetase (20)(21)(22).…”

Section: Introductionmentioning

confidence: 99%

Identity elements ofSaccharomyces cerevisiaetRNA^His

Nameki¹,

Asahara²,

Shimizu³

et al. 1995

Nucl Acids Res

Self Cite

Recognition of tRNAHiS by Saccharomyces cerevisiae histidyl-tRNA synthetase was studied using in vitro transcripts. Histidine tRNA is unique in possessing an extra nucleotide, G.1, at the 5' end. Mutation studies indicate that this irregular secondary structure at the end of the acceptor stem is important for aminoacylation with histidine, while the requirement of either base of this extra base pair is smaller than that in Escherichia coil. The anticodon was also found to be required for histidylation. The regions involved in histidylation are essentially the same as those in E.coli, whereas the proportion of the contributions of the two portions distant from each other, the anticodon and the end of the acceptor stem, makes a substantial difference between the two systems.