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Chapter 27 : Modified Nucleosides in Translation

Author: James F. Curran1
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Affiliations: 1: Department of Biology, Wake Forest University, P.O. Box 7325, Winston-Salem, North Carolina 27109
Content Type: Monograph
Publication Year: 1998

Category: Microbial Genetics and Molecular Biology

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Abstract:

Cellular physiology is fundamentally dependent on the functions of translational apparatus, and these functions are dependent on modified nucleosides. This chapter examines the translational functions of modified nucleosides in the anticodon arm of tRNA. There are modifications at other positions within tRNA, but our knowledge of translational effects is limited to the modifications in the anticodon region. Emphasis is placed on the effects that the loss of specific modifications has on the activities of tRNA. Before considering the effects of modifications on translation, it is helpful to review certain aspects of the decoding process. Further work on the translational mechanism is needed to fully understand the roles of modified nucleosides in the important cellular process. The chapter discusses the effects of modified nucleosides at various positions in the anticodon arm. There are data on the translational effects of a subset of the modified nucleosides that occur within the anticodon arm. The chapter talks about a discussion of unmodified U34 because models for decoding by the modified forms are extended from those for unmodified U. Virtually all tRNAs contain modified nucleosides within the anticodon region, and it has become abundantly clear that they contribute to translation in a number of ways. The future looks very promising for the continued study and understanding of the roles that modified nucleosides play in the fundamentally important translational process.

Citation: Curran J. 1998. Modified Nucleosides in Translation, p 493-516. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch27

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Modified Nucleosides in Translation
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Citation: Curran J. 1998. Modified Nucleosides in Translation, p 493-516. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch27
/content/10.1128/9781555818296.chap27.fig27-1
Figure 1

Schematic structure of the tRNA anticodon arm. The ribbon structure of yeast tRNA is shown on the left. The anticodon arm (AC arm) is the bottom quarter of the molecule, and the anticodon nucleotides (AC) are indicated at the bottom. A detailed view of the AC arm is shown on the right. The stem includes the five base pairs on the top, and the loop contains seven nucleotides. The anticodon nucleotides are 36, 35, and 34, which read codon bases 1, 2, and 3, respectively. The U turn” in the backbone occurs between the highly conserved U33 and the 5′ end of the anticodon. All of the nucleotides discussed in the text are indicated. (Adapted from .)

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Image of Figure 1
Figure 1

Schematic structure of the tRNA anticodon arm. The ribbon structure of yeast tRNA is shown on the left. The anticodon arm (AC arm) is the bottom quarter of the molecule, and the anticodon nucleotides (AC) are indicated at the bottom. A detailed view of the AC arm is shown on the right. The stem includes the five base pairs on the top, and the loop contains seven nucleotides. The anticodon nucleotides are 36, 35, and 34, which read codon bases 1, 2, and 3, respectively. The U turn” in the backbone occurs between the highly conserved U33 and the 5′ end of the anticodon. All of the nucleotides discussed in the text are indicated. (Adapted from .)

Citation: Curran J. 1998. Modified Nucleosides in Translation, p 493-516. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch27
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Figure 2

Examples of base pair geometries that may occur at the wobble position. On the left are representatives of the four structures predicted by to function in decoding. For each base pair, the codon nucleotide is on the right and is fixed in the standard 3′-endo, A conformation (see the discussions in Li and Venclovas, 1992; ). The anticodon nucleotide may assume a “wobble” conformation. The boldface brackets indicate the positions of the N-glycosidic bonds for the Watson–Crick base pairs. Anticodon nucleotide wobble deviations from Watson–Crick geometry are indicated by curved arrows. At the top left is the G:C base pair, which is representative of the Watson–Crick base pairs (G:C, C:G, A:U, U:A, and I:C), all of which are geometrically equivalent. Just below are the U:G and G:U base pairs, in which the anticodon bases are slightly shifted into the major and minor grooves, respectively. The I:U base pair is geometrically equivalent to the G:U base pair. At the bottom left is the “long wobble” I:A base pair. On the right are two hypothetical schemes for base pairing between uridines. At the top right is the “short wobble” conformation favored by ). This base pair requires a 2′-endo conformation for the anticodon uridine. At the bottom right is the conformation preferred by ) in which a water molecule in the minor groove bridges between the uridine bases. This base pair does not require a 2′-endo conformation, but it does require a significant rotation of the anticodon base about the N-glycosidic bond (propeller twist). The propeller twist is not depicted in this two-dimensional diagram. (Adapted from .)

10.1128/9781555818296/fig27-2_thmb.gif
10.1128/9781555818296/fig27-2.gif
Image of Figure 2
Figure 2

Examples of base pair geometries that may occur at the wobble position. On the left are representatives of the four structures predicted by to function in decoding. For each base pair, the codon nucleotide is on the right and is fixed in the standard 3′-endo, A conformation (see the discussions in Li and Venclovas, 1992; ). The anticodon nucleotide may assume a “wobble” conformation. The boldface brackets indicate the positions of the N-glycosidic bonds for the Watson–Crick base pairs. Anticodon nucleotide wobble deviations from Watson–Crick geometry are indicated by curved arrows. At the top left is the G:C base pair, which is representative of the Watson–Crick base pairs (G:C, C:G, A:U, U:A, and I:C), all of which are geometrically equivalent. Just below are the U:G and G:U base pairs, in which the anticodon bases are slightly shifted into the major and minor grooves, respectively. The I:U base pair is geometrically equivalent to the G:U base pair. At the bottom left is the “long wobble” I:A base pair. On the right are two hypothetical schemes for base pairing between uridines. At the top right is the “short wobble” conformation favored by ). This base pair requires a 2′-endo conformation for the anticodon uridine. At the bottom right is the conformation preferred by ) in which a water molecule in the minor groove bridges between the uridine bases. This base pair does not require a 2′-endo conformation, but it does require a significant rotation of the anticodon base about the N-glycosidic bond (propeller twist). The propeller twist is not depicted in this two-dimensional diagram. (Adapted from .)

Citation: Curran J. 1998. Modified Nucleosides in Translation, p 493-516. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch27
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Figure 3

Frameshifting competes with normal translation at the RF2-programmed frameshift site. Shown is an example of an RF2 variant used to measure the relative rate of aa-tRNA selection at the leucine CUG codon. Prior to the frameshift (top) the peptidyl-tRNA is base paired to message CUU in the ribosomal Ρ site. The next triplet, CUG, is available for decoding in the A site. Normal translation occurs if tRNA binds productively at the A site, fixing the “0” reading frame. Alternatively, frameshifting occurs when the peptidyl-tRNA slips one nucleotide rightward onto UUC, fixing the “+1”reading frame. (For mechanistic details of the RF2-programmed frameshift, see ; and )

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10.1128/9781555818296/fig27-3.gif
Image of Figure 3
Figure 3

Frameshifting competes with normal translation at the RF2-programmed frameshift site. Shown is an example of an RF2 variant used to measure the relative rate of aa-tRNA selection at the leucine CUG codon. Prior to the frameshift (top) the peptidyl-tRNA is base paired to message CUU in the ribosomal Ρ site. The next triplet, CUG, is available for decoding in the A site. Normal translation occurs if tRNA binds productively at the A site, fixing the “0” reading frame. Alternatively, frameshifting occurs when the peptidyl-tRNA slips one nucleotide rightward onto UUC, fixing the “+1”reading frame. (For mechanistic details of the RF2-programmed frameshift, see ; and )

Citation: Curran J. 1998. Modified Nucleosides in Translation, p 493-516. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch27
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Tables

Modified Nucleosides in Translation
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Citation: Curran J. 1998. Modified Nucleosides in Translation, p 493-516. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch27
/content/10.1128/9781555818296.chap27.tab27-1
Table 1

Summary of the effects of modified nucleosides on translation

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10.1128/9781555818296/tab27-1.gif
Generic image for table
Table 1

Summary of the effects of modified nucleosides on translation

Citation: Curran J. 1998. Modified Nucleosides in Translation, p 493-516. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch27

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