Base pairing between the 3' end of 16S rRNA and mRNA is shown to be important for the programmed -1 frameshifting utilized'in decoding the Escherchia coli dnaX gene. This pairing is the same as the ShineDalgarno pairing used by prokaryotic ribosomes in selection of translation initiators, but for frameshifting the interaction occurs within elongating ribosomes. For dnaX -1 frameshifting, the 3' base of the Shine-Dalgarno sequence is 10 nucleotides 5' of the shift site. Previously, Shine-Dalgarno rRNA-mRNA pairing was shown to stimulate the + 1 frameshifting necessary for decoding the release factor 2 gene. However, in the release factor 2 gene, the Shine-Dalgarno sequence is located 3 nucleotides 5' of the shift site. When the Shine-Dalgarno sequence is moved to the same position relative to the dnaX shift site, it is inhibitory rather than stimulatory.Shine-Dalgarno interactions by elongating ribosomes are likely to be used in stimulating -1 frameshifting in the decoding of a variety of genes.Programmed ribosomal frameshifting is used for a variety of purposes in the decoding of a significant minority of genes in probably all organisms (1). For instance, in decoding the Escherichia coli dnaX gene, half of the ribosomes frameshift internally in the coding sequence and terminate to yield a short product (4, 10, 36). Accessory mRNA sequence elements, stimulators, serve to elevate the level of frameshifting at the shift site. In all known cases of -1 frameshifting, the stimulators are 3' to the shift site. The only known 5' stimulator is involved in + 1 frameshifting. In decoding the E. coli polypeptide chain release factor 2 (RF2), a Shine-Dalgarno (SD)-like sequence 5' of the shift site base pairs with its complement near the 3' end of 16S rRNA (8,(39)(40)(41). This is the same interaction that is well known to be crucial in selection of ribosome initiation sites. It is also known that ribosome binding to SD sequences can be independent of initiation (32, 38; see also reference 14). The involvement of the internal SD sequence in RF2 frameshifting shows that elongating ribosomes must unexpectedly be able to continuously scan mRNA for potential pairing.In this paper, we show that an upstream SD-like interaction can also mediate -1 frameshifting, as in expression of E. coli dnaX, which encodes DNA polymerase III subunits. E. coli DNA polymerase III consists of three core subunits and seven accessory subunits (20). Of the seven accessory subunits, T and ry are both translated from the same dnaX transcript. T is the 71-kDa full-length product of the dnaX gene translated entirely in the zero frame. ry is produced by a remarkably efficient (-50%) -1 ribosomal frameshift. After translating two-thirds of the gene, half of the ribosomes slip from the zero to the -1 frame. One codon later, the shifted ribosomes reach a UGA stop codon and produce the y (47-kDa) subunit (4, 10, 36).To date, two essential elements of the dnaX -1 frameshifting have been identified. These two cis elements are an A AAA AAG heptanucleotide shift s...

Three elements are crucial for the programmed frameshifting in translation of dnaX mRNA: a Shine-Dalgarno (SD)-like sequence, a double-shift site, and a 3' structure. The conformation of the mRNA containing these three elements was investigated using chemical and enzymatic probes. The probing data show that the structure is a specific stem-loop. The bottom half of the stem is more stable than the top half of the stem. The function of the stem-loop was further investigated by mutagenic analysis. Reducing the stability of the bottom half of the stem strongly effects frameshifting levels, whereas similar changes in the top half are not as effective. Stabilizing the top half of the stem gives increased frameshifting beyond the WT efficiency. The identity of the primary RNA sequence in the stem-loop is unimportant, provided that the overall structure is maintained. The calculated stabilities of the variant stem-loop structures correlate with frameshifting efficiency. The SD-interaction and the stem-loop element act independently to increase frameshifting in dnaX.

The and ␥ subunits of DNA polymerase III are both encoded by a single gene in Escherichia coli and Thermus thermophilus. ␥ is two-thirds the size of and shares virtually all its amino acid sequence with . E. coli and T. thermophilus have evolved very different mechanisms for setting the approximate 1:1 ratio between and ␥. Both mechanisms put ribosomes into alternate reading frames so that stop codons in the new frame serve to make the smaller ␥ protein. In E. coli, Ϸ50% of initiating ribosomes translate the dnaX mRNA conventionally to give , but the other 50% shift into the ؊1 reading frame at a specific site (A AAA AAG) in the mRNA to produce ␥. In T. thermophilus ribosomal frameshifting is not required: the dnaX mRNA is a heterogeneous population of molecules with different numbers of A residues arising from transcriptional slippage on a run of nine T residues in the DNA template. Translation of the subpopulation containing nine As (or ؉͞؊ multiples of three As) yields . The rest of the population of mRNAs (containing nine ؉͞؊ nonmultiples of three As) puts ribosomes into the alternate reading frames to produce the ␥ protein(s). It is surprising that two rather similar dnaX sequences in E. coli and T. thermophilus lead to very different mechanisms of expression.

Using a DNA construct, named Lama, derived from the murine parotid secretory protein (PSP) gene, we have obtained salivary gland specific gene expression in transgenic mice. Lama is a PSP minigene and allows analysis of the PSP gene 5' regulatory region by transgenesis. We show here that the regulatory region included in Lama with 4.6 kb of 5' flanking sequence is sufficient to direct expression specifically to the salivary glands. The expression level in the parotid gland is only about one percent of the PSP mRNA level, while that of the sublingual gland is near the PSP mRNA level. This suggests significant differences in the PSP gene regulation in the two glands. In addition, Lama is a secretory expression vector in which cDNAs or genomic fragments can be inserted. We demonstrate that the Lama construct can direct the expression of a heterologous cDNA encoding the C-terminal peptide of human factor Vil to salivary glands and that the corresponding peptide is secreted into saliva.