Demonstration of the early--late switch in vitro with bacteriophage T7 DNA as template

An unstructured mRNA region and a 5' hairpin represent important elements of the E. coli translation initiation signal determined by using the bacteriophage T7 gene 1 translation start site

Gene 1 of bacteriophage T7 early region--the RNA polymerase gene--is very actively translated during the infectious cycle of this phage. A 29 base pair fragment of its ribosome binding site containing the initiation triplet, the Shine-Dalgarno sequence (S-D), 10 nucleotides (nt) upstream and 6 nt downstream of these central elements was cloned into a vector to control the expression of the mouse dihydrofolate reductase gene (dhfr). Although all essential parts of this translation initiation region (TIR) should be present, this fragment showed only very low activity. Computer analysis revealed a potentially inhibitory hairpin binding the S-D sequence into its stem base paired to vector-derived upstream sequences. Mutational alterations demonstrated that this hairpin was not responsible for the low activity. However, addition of 21 nt of the T7 gene 1 upstream sequence to the 29 base pair fragment were capable of increasing the translational efficiency by one order of magnitude. Computer analysis of this sequence, including nucleotide shuffling, revealed that it contains a highly unstructured region lacking mRNA secondary structures but with a hairpin at its 5' end, here formed solely by T7 sequences. There was not much difference in activity whether the mRNA included or lacked vector-derived sequences upstream of the hairpin. Such highly unstructured mRNA regions were found in all very efficiently expressed T7 genes without any obvious sequence homologies. The delta G values of these regions were higher, i.e. potential secondary structural elements were fewer, than in TIR of genes from E. coli. This is likely due to the fact that T7 as a lytic phage is relying for successful infection on much stronger signals which a cell cannot afford because of the indispensable balanced equilibria of its interdependent biochemical processes. When the 5' ends of efficient T7 gene mRNA are formed by the action of RNase III they generally start with an unstructured region. Efficiently expressed T7 genes within a polycistronic mRNA, however, always contain a hairpin preceding the structure free sequence. We suggest that the formation of this 5' hairpin is releasing enough energy to keep the unstructured regions free of secondary RNA structures for sufficient time to give ribosomes and factors a good chance for binding to the TIR. In addition, sequences further downstream of the start codon give rise to an additional increase in efficiency of the TIR by almost two orders of magnitude.

Primary structures of Escherichia coli pyruvate formate-lyase and pyruvate-formate-lyase-activating enzyme deduced from the DNA nucleotide sequences

The structural gene of pyruvate formate-lyase (pfl) and that of pyruvate-formate-lyase-activating enzyme were shown to be adjacent on the chromosomal map of Escherichia coli. DNA sequencing was performed along a stretch of 3592 nucleotides to obtain the amino acid sequences of both proteins. The derived primary structures (759 and 245 residues) were confirmed by partial structure analyses on the purified proteins. The open reading frames are separated by a 194-nucleotide stretch, and their flanking regions include signal elements that are compatible with separate control of protein synthesis from the two genes.

Only one out of the three strong ribosomal binding sites of the early region of bacteriophage T7 exhibits high translational efficiency in fragments of about 30 base pairs

Within the early region of bacteriophage T7 three genes, 0.3, 1 and 1.3, are most efficiently expressed. They belong to the strongest initiation signals of Escherichia coli. In the T7 wild-type situation the proteins are produced with a molar ratio of gene 1:1.3:0.3 protein = 1:3.9:9.7. DNA fragments of about 30 base pairs comprising the ribosomal binding sites (RBS) of these genes were synthesized and cloned into derivatives of the pDS1 vector ribosomal binding sites (RBS) of these genes were synthesized and cloned into two derivatives of the pDS1 vector just upstream of the mouse dihydrofolate reductase gene. Although all tested RBS fragments contained an initiation triplet, a Shine-Dalgarno sequence and some nucleotides upstream and downstream of this region, only the gene 1.3 RBS fragment showed high efficiency whereas those of genes 0.3 and 1 were at the border of significance. The amount of synthesized mRNA was about the same for all three constructs. A major influence of vector-derived sequences on the RBS activity could be ruled out. The high translational activity of the short 1.3 gene RBS seems to be largely due to its primary structure. The other two RBSs studied require much longer sequences for high activity.

More than 150 nucleotides flanking the initiation codon contribute to the efficiency of the ribosomal binding site from bacteriophage T7 gene 1

The ribosomal binding site (RBS) from gene 1 of bacteriophage T7 was isolated on fragments of differing length and cloned upstream of the mouse dihydrofolate reductase gene to control the translation of its sequence. A 29 base pair sequence containing all elements generally believed to be essential for the RBS's showed extremely low activity. Additional upstream and downstream sequences were required to obtain a several orders of magnitude higher efficiency. By contrast, areas further downstream than +112 nucleotides from the initiator proved to be inhibitory, whereas the presence of an upstream RNaseIII cleavage site showed a strong stimulatory effect. This suggests that tertiary structures are involved in the function of the RBS studied. The efficient RBS's were complexed by ribosomes at much lower concentrations of the mRNA than the weak ones.

Isolation and the 5'-end nucleotide sequence of Bacillus licheniformis alpha-amylase gene

We have isolated and determined the 5'-end nucleotide sequence of the alpha-amylase gene from Bacillus licheniformis ATCC 14580. The alpha-amylase produced by this strain is thermostable and of liquefying type. The gene was originally cloned in a bacteriophage lambda 1059 vector. A subclone containing a 5.3 X 10(3)-base insert in pBR322 was further characterized. The nucleotide sequence coding for the 5' end of the structural gene together with the sequence coding for the upstream control regions was determined. The deduced N-terminal amino acid sequence was identical with the previously published amino acid sequence of B. licheniformis alpha-amylase. There was also very strong homology to the N-terminal sequence of Bacillus amyloliquefaciens alpha-amylase. The Mr of the thermostable alpha-amylase, as determined in vitro in a cell-free transcription/translation system of Escherichia coli, was about 55 000.

Differential stimulation by polyamines of phage DNA-directed in vitro synthesis of proteins

The effect of polyamines on T7- and lambda rifd18 DNA-directed synthesis of proteins in an Escherichia coli cell-free system has been studied. When T7 DNA was used as a template, the degree of stimulation by spermidine of protein synthesis was larger with T7 RNA polymerase than with Mr 42 K protein, while the synthesis of Mr 13.5 K protein was not stimulated significantly by spermidine. The synthesis of T7 RNA polymerase was stimulated approx. 10-fold by 1 mM spermidine. When lambda rifd18 DNA was used as a template, the synthesis of beta beta' subunits of RNA polymerase was stimulated greatly by spermidine, while the synthesis of elongation factor Tu and ribosomal proteins was not stimulated significantly by spermidine. Spermidine stimulation of T7 DNA-directed synthesis of T7 RNA polymerase was at the level of both translation and transcription. The degree of stimulation by spermidine was greater at the level of translation. Putrescine stimulated the synthesis of T7 RNA polymerase and Mr 42 K protein to a small degree at the level of translation.

Nucleotide sequence of the promoter and NH2-terminal signal peptide region of the alpha-amylase gene from Bacillus amyloliquefaciens

We have isolated and partially sequenced the gene coding for alpha-amylase (EC 3.2.1.1) from Bacillus amyloliquefaciens by molecular cloning in the plasmid pUB110 using Bacillus subtilis as a host. The nucleotide sequence of the NH2-terminal region of the cloned gene was determined and found to contain a 31-residue-long stretch of amino acids preceding the NH2-terminal sequence of the extracellular alpha-amylase. Within this sequence there is a 15-residue-long stretch of uncharged amino acids similar to that found at the NH2 terminus of other precursors to exported proteins. This "signal sequence" is probably removed in conjunction with the translocation of alpha-amylase through the cytoplasmic membrane. In vitro labeling of alpha-amylase with radioactive amino acids in a coupled transcription-translation system followed by partial sequencing established the exact location of the NH2 terminus of the alpha-amylase gene. The nucleotide sequence preceding the NH2 terminus has properties resembling the RNA-polymerase- and ribosome-binding sites found at the 5' terminus of many prokaryotic genes.