Proteins are synthesized according to a pattern of contiguous triplet codons. Once the reading frame is set, codons are translated in order, without overlap or punctuation, until a termination codon is encountered. Usually, the other two possible reading frames within a gene contain no useful genetic information. However, a few genes are structured so that ribosomes "hiccup" at a certain point in the translation of the mRNA, leading to a change in the reading frame from that point on. In some cases this appears to be a mechanism used to produce two or more related proteins from a single transcript or to regulate the synthesis of a protein.

The best-documented example occurs in the translation of the mRNA for the gag and pol genes of the Rous sarcoma virus (see Fig. 25-31). The two genes overlap, with pol encoded by the reading frame in which each codon is offset to the left by one base pair (-1 reading frame) relative to gag (Fig. 1). The product of the pol gene (reverse transcriptase; p. 882) is translated initially as a larger gag pol fusion protein using the same mRNA used for the gag protein alone. This fusion protein is later trimmed to the mature reverse transcriptase by proteolytic digestion. The large fusion protein is produced by a translational frameshift that occurs in the overlap region and allows the ribosome to bypass the UAG termination codon at the end of the gag gene (shown in red in Fig. 1). This frameshift occurs in about 5% of the translation events, so that the gag pol fusion protein, and ultimately reverse transcriptase, is synthesized at the appropriate level for efficient replication of the viral genome-about 20-fold less than the gag protein. A similar mechanism is used to produce both the τ and γ subunits of E. coli DNA polymerase III from dnaX gene transcripts (see Table 24-2).

An example of the use of this mechanism for regulation occurs in the gene for E. coli release factor 2 (RF₂), a protein required for termination of protein synthesis at the termination codons UAA and UGA (described later in this chapter). The 26th codon of the gene for RF₂ is UGA, which would normally halt protein synthesis. The remainder of the gene is in the +1 reading frame (off set one base pair to the right) relative to this UGA codon. Low levels of RF₂ lead to a translational pause at this codon, because UGA is not recognized as a termination codon unless RFz binds to it. The absence of RF₂ prevents the termination of protein synthesis at this UGA and allows time for a frameshift so that UGA plus the C that follows it (UGAC) is read as GAC = Asp. Translation then proceeds in the new reading frame to complete synthesis of RF₂. In this way, RF₂ regulates its own synthesis in a feedback loop.

An especially unusual frameshifting mechanism occurs through the editing of mRNAs prior to translation. The genes in mitochondrial DNA that encode the cytochrome oxidase subunit II in some protists do not have open reading frames that correspond precisely to the protein product. Instead, the codons specifying the amino terminus of the protein are in a different reading frame from the codons specifying the carboxyl terminus. The problem is corrected not on the ribosome, but by a posttranscriptional editing process in which four uridines are added to create three new codons and shift the reading frame so that the entire gene can be translated directly, as shown in Figure 2a; the

added uridine residues are shown in red. Only a small part of the gene (the region affected by editing) is shown. Neither the function nor mechanism of this editing process is understood. A special class of RNA molecules encoded by these mitochondria have been detected that have sequences complementary to the final, edited mRNAs. These appear to act as templates for the editing process and are referred to as guide RNAs (Fig. 2b). Note that the base pairing involves a number of G=U base pairs (symbolized by blue dots), which are common in RNA molecules.

Figure 1 The gag pol overlap region in Rous sarcoma virus.

Figure 2 RNA editing of the transcript of the cytochrome oxidase subunit II gene from mitochondria of Trypanosoma brucei.

A distinct form of RNA editing occurs in the gene for the apolipoprotein B component of lowdensity lipoprotein in vertebrates. One form of apo lipoprotein B, called apoB-100 (Mr 513,000), is synthesized in the liver. A second form, apoB-48 (M,. 250,000), is synthesized in the intestine. Both are synthesized from an mRNA produced from the gene for apoB-100. A cytosine deaminase enzyme found only in the intestine binds to the mRNA at codon 2,153 (CAA = Gln) and converts the C to a U to introduce the termination codon UAA at this position. The apoB-48 produced in the intestine from the modified mRNA is simply an abbreviated form (corresponding to the amino-terminal half) of apoB-100 (Fig. 3). This reaction permits the synthesis of two different proteins from one gene in a tissue-specific manner.

Figure 3 RNA editing of the transcript of the gene for the apolipoprotein B-100 component of lowdensity lipoprotein.