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Domain 4:

Synthesis and Processing of Macromolecules

Structural Basis for the Decoding Mechanism

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  • Author: Steven T. Gregory1
  • Editor: Susan T. Lovett2
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912; 2: Brandeis University, Waltham, MA
  • Received 06 March 2008 Accepted 15 May 2008 Published 02 January 2009
  • Address correspondence to Steven T. Gregory Steven_Gregory@Brown.edu
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  • Abstract:

    The bacterial ribosome is a complex macromolecular machine that deciphers the genetic code with remarkable fidelity. During the elongation phase of protein synthesis, the ribosome selects aminoacyl-tRNAs as dictated by the canonical base pairing between the anticodon of the tRNA and the codon of the messenger RNA. The ribosome's participation in tRNA selection is active rather than passive, using conformational changes of conserved bases of 16S rRNA to directly monitor the geometry of codon-anticodon base pairing. The tRNA selection process is divided into an initial selection step and a subsequent proofreading step, with the utilization of two sequential steps increasing the discriminating power of the ribosome far beyond that which could be achieved based on the thermodynamics of codon-anticodon base pairing stability. The accuracy of decoding is impaired by a number of antibiotics and can be either increased or decreased by various mutations in either subunit of the ribosome, in elongation factor Tu, and in tRNA. In this chapter we will review our current understanding of various forces that determine the accuracy of decoding by the bacterial ribosome.

  • Citation: Gregory S. 2009. Structural Basis for the Decoding Mechanism, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.5.4

Key Concept Ranking

DNA Polymerase III
0.48756284
Elongation Factor Tu
0.43391627
0.48756284

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ecosalplus.2.5.4.citations
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/content/journal/ecosalplus/10.1128/ecosalplus.2.5.4
2009-01-02
2017-06-24

Abstract:

The bacterial ribosome is a complex macromolecular machine that deciphers the genetic code with remarkable fidelity. During the elongation phase of protein synthesis, the ribosome selects aminoacyl-tRNAs as dictated by the canonical base pairing between the anticodon of the tRNA and the codon of the messenger RNA. The ribosome's participation in tRNA selection is active rather than passive, using conformational changes of conserved bases of 16S rRNA to directly monitor the geometry of codon-anticodon base pairing. The tRNA selection process is divided into an initial selection step and a subsequent proofreading step, with the utilization of two sequential steps increasing the discriminating power of the ribosome far beyond that which could be achieved based on the thermodynamics of codon-anticodon base pairing stability. The accuracy of decoding is impaired by a number of antibiotics and can be either increased or decreased by various mutations in either subunit of the ribosome, in elongation factor Tu, and in tRNA. In this chapter we will review our current understanding of various forces that determine the accuracy of decoding by the bacterial ribosome.

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Figures

Image of Figure 1
Figure 1

The 70S ribosome is represented by pairs of large ellipses, and tRNAs are represented by hooks. EF-Tu is depicted as an oval, a pentagon, and a rectangle to represent conformational changes (conf change) occurring in sequential steps. Elemental rate constants for the individual steps are indicated as k through k.

Citation: Gregory S. 2009. Structural Basis for the Decoding Mechanism, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.5.4
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Image of Figure 2
Figure 2

Upon the binding of cognate aminoacyl-tRNA, interprotein contacts at the interface of S4 and S5 are broken (red spheres), while new contacts (red spheres) are established between S12 and parts of 16S rRNA, including helix 44 (cyan). The domain closure is facilitated by the error-inducing antibiotics streptomycin (Sm; orange sticks and spheres) and paromomycin (Pm; green sticks and spheres). This figure is based on data from Protein Data Bank file 1FJG.

Citation: Gregory S. 2009. Structural Basis for the Decoding Mechanism, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.5.4
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Image of Figure 3
Figure 3

(A) In the vacant 30S subunit, A1492 and A1493 are stacked within helix 44 and G530 is in the configuration. (B) The most prominent changes upon tRNA binding are a rotation of the universally conserved A1492 and A1493 out from helix 44 toward the minor groove of the codon-anticodon minihelix. G530 shifts to the configuration and interacts with A1492 and the codon-anticodon minihelix. C1054 also rotates about the glycosidic bond to interact with the ASL. 16S rRNA is shown in blue, mRNA is shown in green, and the tRNA ASL analog is shown in purple. For clarity, the only residues of 16S rRNA shown are those directly involved in monitoring codon-anticodon recognition.

Citation: Gregory S. 2009. Structural Basis for the Decoding Mechanism, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.5.4
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Image of Figure 4
Figure 4

S12 is shown in blue, with residues altered in mutant forms shown as red sticks and spheres. 16S rRNA residues are shown as cyan sticks and spheres, and streptomycin (Sm) is shown as orange sticks and spheres. K53 is located some distance from streptomycin, and mutations of this residue probably act by interfering with domain closure due to the loss of contact with C1412 ( 42 ). The only S12 residue which directly contacts streptomycin is K42 ( 76 ).

Citation: Gregory S. 2009. Structural Basis for the Decoding Mechanism, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.5.4
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Image of Figure 5
Figure 5

Secondary structure elements are expanded to show sequence details around sites of mutations. SmR, streptomycin resistance; SuUGA, suppressor of UGA nonsense mutations; SuΔ1916, suppressor of the growth defect of the Δ1916 mutation in 23S rRNA (see text); , ribosomal ambiguity mutation.

Citation: Gregory S. 2009. Structural Basis for the Decoding Mechanism, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.5.4
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Image of Figure 6
Figure 6

Secondary structure elements are expanded to show sequence details around sites of mutations. SuUGA, suppressor of UGA nonsense mutations; Su , suppressor of the frameshift mutation; , ribosomal ambiguity mutation.

Citation: Gregory S. 2009. Structural Basis for the Decoding Mechanism, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.5.4
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