tRNA Discrimination in Aminoacylation

Leo Pallanck; Marie Pak; Ladonne H. Schulman

doi:10.1128/9781555818333.ch18

Chapter 18 : tRNA Discrimination in Aminoacylation

Authors: Leo Pallanck¹, Marie Pak², Ladonne H. Schulman

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Affiliations: 1: Department of Genetics, University of Wisconsin, Madison, 445 Henry Hall, Madison, Wisconsin 53706; 2: Laboratory of Molecular Genetics/NIC,NICHD Building 6B, Room 3B-309, Bethesda, Maryland 20892

Content Type: Monograph

Publication Year: 1995

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555818333

Chapter DOI: 10.1128/9781555818333.ch18

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Abstract:

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.

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

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tRNA Discrimination in Aminoacylation

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Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

/content/10.1128/9781555818333.chap18.fig18-1

Figure 1

(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 ).

10.1128/9781555818333/fig18-1_thmb.gif

10.1128/9781555818333/fig18-1.gif

Figure 1

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

/content/10.1128/9781555818333.chap18.fig18-2

Figure 2

Major recognition elements of E. coli tRNAMet (A), tRNAAla (B), yeast tRNAAsp (C), and tRNAGln (D).

10.1128/9781555818333/fig18-2_thmb.gif

10.1128/9781555818333/fig18-2.gif

Figure 2

Major recognition elements of E. coli tRNAMet (A), tRNAAla (B), yeast tRNAAsp (C), and tRNAGln (D).

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

/content/10.1128/9781555818333.chap18.fig18-3

Figure 3

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.

10.1128/9781555818333/fig18-3_thmb.gif

10.1128/9781555818333/fig18-3.gif

Figure 3

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

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Tables

tRNA Discrimination in Aminoacylation

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

/content/10.1128/9781555818333.chap18.tab18-1

Table 1

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.

10.1128/9781555818333/tab18-1_thmb.gif

10.1128/9781555818333/tab18-1.gif

Table 1

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.

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

/content/10.1128/9781555818333.chap18.tab18-2

Table 2

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.

10.1128/9781555818333/tab18-2_thmb.gif

10.1128/9781555818333/tab18-2.gif

Table 2

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.

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

/content/10.1128/9781555818333.chap18.tab18-3

Table 3

Role of discriminator base in identity of E. coli tRNAs

10.1128/9781555818333/tab18-3_thmb.gif

10.1128/9781555818333/tab18-3.gif

Table 3

Role of discriminator base in identity of E. coli tRNAs

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

/content/10.1128/9781555818333.chap18.tab18-4

Table 4

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.

10.1128/9781555818333/tab18-4_thmb.gif

10.1128/9781555818333/tab18-4.gif

Table 4

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.

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18