Nucleic Acids in Chemistry and Biology

288 Chapter 7

O Ade -1

O O

V

RO

O Gua +1

O OH

O P

OR

O

O

O

O

N

N

N

N

O

N

N

N N

N

N

H H

N

N

N

N N

H

H

H

A 9

G 8

A 38

3.2Å

3.0Å

3.2Å

2.8Å

3.0Å

H

H

H

Figure 7.40 Transition state of the hairpin ribozyme. A crystal structure of the hairpin ribozyme bound to a
transition-state vanadate analogue suggests that reaction is facilitated by precise alignment of nucleobase
functional groups^27

7.6.3.1 Pseudoknots that Stimulate Ribosomal Frameshifting and Recoding. Although the ribo-

some typically maintains translation “in-frame”and reads each sequential triplet codon on mRNA in an
orderly fashion (Section 7.3), there are RNA structures that induce “recoding”of an mRNA reading frame
in order to produce two different proteins from the same RNA sequence. Usually, this is the result of 1
frameshifting, whereby the entire frame moves over by 1 nucleotide. This normally occurs at a “slippery
sequence” (i.e., AAAAAAA), that will bind A- and P-site tRNAs in the same manner, even after the frame
shifts by 1. This slippage normally occurs when the ribosome stalls after sensing particular downstream
RNA tertiary structures.^72
Viral genomes are remarkably compact. For example, multiple proteins are commonly encoded by over-
lapping framesof the same gene sequence. Retroviral gene expression depends on a specific type of bent
pseudoknot(Figure 7.41) that stimulates ribosomal frameshifting and thereby initiates synthesis of viral
proteases (pro) and polymerases (pol) from an mRNA sequence that overlaps with the region that encodes
structural proteins (gag).

7.6.3.2 The IRES of Hepatitis C Virus. Viruses commonly use RNA tertiary structures to “trick” the

host translation machinery into making viral proteins. During the first stages of normal eukaryotic trans-
lation, an initiation complex (the small ribosomal subunit and various factors) binds the 5
-cap structure
on mRNA and recognizes the adjacent start codon. Lacking cap structures, many viruses contain complex
tertiary structures at their 5
-termini, immediately upstream of the start codon. These 5
-UTRstructures
bind the small ribosomal subunit, allowing it to recognize the proper start codon and initiate the synthesis
of viral proteins. Structured elements in viral 5
-UTRs (and even in certain host mRNAs that lack caps)
are called internal ribosome entry sites (IRES), and they function by replacing protein factors that are nor-
mallyrequired for translation initiation.
One of the best characterized examples of a viral IRES is the 5
-UTR from HCV mRNA.^73 This RNA
element is
330 nucleotides in length, and it contains a four-way junction that adopts a tertiary fold that
is essential for ribosomal recognition. When the 40S subunit binds the IRES, it no longer requires eukary-
otic initiation factors A, B, G, or E and it initiates translation of the HCV polyprotein at an adjacent start
codon (Figure 7.42).

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