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Category: Microbial Genetics and Molecular Biology
tRNA Discrimination in Aminoacylation, Page 1 of 2
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The recognition of a tRNA by its aminoacyl-tRNA synthetase is a classic example of the specificity often encountered in biology. Each of the 20 aminoacyl-tRNA synthetases in a cell must distinguish its own set of isoacceptor tRNAs from the many noncognate tRNAs and efficiently catalyze the covalent attachment of the correct amino acid to the 3' end of only these species. Ultimately, the fate of the cell rests on this interaction, as there are no subsequent proof-reading steps in protein synthesis whereby the amino acid is matched against the anticodon to ensure that the proper amino acid is inserted in response to a given codon. How an aminoacyl-tRNA synthetase is able to select its tRNA substrates from a pool of noncognate species sharing similar tertiary structure has been the focus of over 20 years of research. Recent technical refinements in the types of assays used to study this interaction have contributed a wealth of new information to this field, allowing the identification of nucleotides conferring a particular amino acid acceptor identity for a number of tRNAs. The goal of this chapter is to summarize these more recent developments in tRNA recognition.
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(A) Cloverleaf structure of a typical class I tRNA, numbered according to Sprinzl et al. ( 152 ). Bases conserved in all E. coli tRNAs are included. (B) Three-dimensional structure of yeast tRNAPhe ( 54 , 110 ).
(A) Cloverleaf structure of a typical class I tRNA, numbered according to Sprinzl et al. ( 152 ). Bases conserved in all E. coli tRNAs are included. (B) Three-dimensional structure of yeast tRNAPhe ( 54 , 110 ).
Major recognition elements of E. coli tRNAMet (A), tRNAAla (B), yeast tRNAAsp (C), and tRNAGln (D).
Major recognition elements of E. coli tRNAMet (A), tRNAAla (B), yeast tRNAAsp (C), and tRNAGln (D).
Kinetic effect of nucleotide substitutions of E. coli, yeast, and human tRNAPhe on aminoacylation by the cognate synthetase ( 6 , 7 , 85 , 119 – 121 , 159 ). The numbers shown refer to the fold reduction in k cat /K m on substitution at that site. Where variable effects of aminoacylation were observed, kinetic data for the nucleotide substitution causing the largest defect are shown.
Kinetic effect of nucleotide substitutions of E. coli, yeast, and human tRNAPhe on aminoacylation by the cognate synthetase ( 6 , 7 , 85 , 119 – 121 , 159 ). The numbers shown refer to the fold reduction in k cat /K m on substitution at that site. Where variable effects of aminoacylation were observed, kinetic data for the nucleotide substitution causing the largest defect are shown.
Role of the anticodon in recognition of tRNAs
a Ec,Escherichia coli; Sc, Saccharomyces cerevisiae; L, lysidine; H, Human; Bov, bovine; Q, queuosine; and W, wheat germ.
b The tRNAAsn amber( 89 ) and opal94 suppressors are inactive in vivo.
c Anticodon is required for in vivo identity ( 89 ).
d 34 , 35 , and 36 refer to positions of the three anticodon nucleotides.
e See text for additional references.
f Based on the fact that serine isoacceptor tRNAs contain base changes at all three positions of the anticodon.
g Additional anticodon recognition sites may exist.
h Data using the tRNA-like structure from TYMV RNA.
Role of the anticodon in recognition of tRNAs
a Ec,Escherichia coli; Sc, Saccharomyces cerevisiae; L, lysidine; H, Human; Bov, bovine; Q, queuosine; and W, wheat germ.
b The tRNAAsn amber( 89 ) and opal94 suppressors are inactive in vivo.
c Anticodon is required for in vivo identity ( 89 ).
d 34 , 35 , and 36 refer to positions of the three anticodon nucleotides.
e See text for additional references.
f Based on the fact that serine isoacceptor tRNAs contain base changes at all three positions of the anticodon.
g Additional anticodon recognition sites may exist.
h Data using the tRNA-like structure from TYMV RNA.
E. coli amber-suppressor tRNAs classified according to their amino acid acceptor identities a
a Data from reference 89 and additional references therein.
b Also known as trpT (SuUAG).
c Also known as glnV(SuUAG), serU(SuUAG), and tyrT (SuUAG), respectively.
E. coli amber-suppressor tRNAs classified according to their amino acid acceptor identities a
a Data from reference 89 and additional references therein.
b Also known as trpT (SuUAG).
c Also known as glnV(SuUAG), serU(SuUAG), and tyrT (SuUAG), respectively.
Role of discriminator base in identity of E. coli tRNAs
Role of discriminator base in identity of E. coli tRNAs
Summary of known recognition elements for some tRNAs a
a Additional as yet unidentified recognition elements may also be present. See Table 1 for abbreviations.
b See text for additional references.
c See Table 3 for additional references.
d See Table 1 for additional references.
Summary of known recognition elements for some tRNAs a
a Additional as yet unidentified recognition elements may also be present. See Table 1 for abbreviations.
b See text for additional references.
c See Table 3 for additional references.
d See Table 1 for additional references.