Role of DNA regions flanking the tryptophan promoter of Escherichia coli. I. Insertion of synthetic oligonucleotides

Analysis of regulation of the ilvGMEDA operon by using leader-attenuator-galK gene fusions

Five of the genes for the biosynthesis of isoleucine and valine form the ilvGMEDA operon of Escherichia coli K-12. Expression of the operon responds to changes in the availability of isoleucine, leucine, and valine (ILV). Addition of an excess of all three amino acids results in reduced expression of the operon, whereas limitation for one of the three amino acids causes an increase in expression. The operon is preceded by a leader-attenuator which clearly regulates the increased expression that occurs due to reduced aminoacylation of tRNA. To assess the factors that result in the reduced expression of this operon upon the addition of ILV, a series of plasmids were constructed in which the ilv regulatory region was fused to galK. In response to addition of the amino acids, expression of the galK gene fused to the leader-attenuator decreased five- to sevenfold, instead of the twofold observed for the chromosomal operon. A deletion analysis with these plasmids indicated that the ILV-specific decrease in expression required an intact leader-attenuator but not ilvGp2 or the DNA that precedes this promoter. This conclusion was supported by both S1 nuclease analysis of transcription initiation and determination of galK mRNA levels by RNA-RNA hybridization.

Point mutations in a pBR322-based expression plasmid resulting in increased synthesis of bovine growth hormone in Escherichia coli

The bGH cDNA coding for bovine growth hormone (bGH) is expressed poorly in Escherichia coli using a pBR322-based expression plasmid. Random mutagenesis of the plasmid gave rise to two types of plasmid mutants which increased the expression of bGH. One class had single base changes in the first four codons of the bGH sequence. The second class had single base changes in regions of the plasmid involved in controlling plasmid replication but had little effect on plasmid copy number.

Physical identification of an internal promoter, ilvAp, in the distal portion of the ilvGMEDA operon

It has been previously demonstrated that the ilvGMEDA operon is expressed in vivo from the promoters ilvGp2 and ilvEp. An additional internal promoter is identified and designated ilvAp. This internal promoter, which allows independent expression of ilvA, has been analyzed both in vivo and in vitro. Our results indicate that: (1) ilvAp exists in both Escherichia coli K-12 and Salmonella typhimurium, as demonstrated by fusion to the galK reporter gene; (2) ilvAp is located in the distal coding sequence of ilvD; (3) the ilvAp sequences are not identical for these two bacterial species; (4) transcription from ilvAp of E. coli K-12 was demonstrated; (5) expression from ilvAp responds to the availability of oxygen; (6) potential 3' 5'-cyclic AMP receptor protein binding sites exist adjacent to ilvAp.

Point mutations that affect translation initiation of the transposon Tn10 tetA gene

Single base-pair changes affecting the 5' untranslated leader of the tetracycline-resistance gene (tetA) mRNA resulted in increased or decreased levels in expression of tetA-lacZ protein fusions. The base changes affected the rate of initiation of translation of tetA mRNA because operon fusions revealed that the mutations had little or no effect on transcription. The translational efficiency of wild-type and mutant tetA mRNAs varied by more than a factor of 2000. The observed variations could be correlated with stabilization and destabilization of RNA secondary structures. These structures, located 5' from the translation start codon, sequester the Shine-Dalgarno sequence.

Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters

Expression of the genes determining the subunits of Escherichia coli DNA gyrase (gyrA and gyrB) is known to be induced by relaxation of the template DNA. In this paper we report a deletion analysis of the gyrA and gyrB promoter regions. We find that a DNA sequence 20 base pairs long that includes the -10 consensus region, the transcription start point, and the first few transcribed bases is responsible for the property of induction by DNA relaxation. We propose a model for relaxation-stimulated transcription in which promoter clearance is the rate-limiting step.

AUU-to-AUG mutation in the initiator codon of the translation initiation factor IF3 abolishes translational autocontrol of its own gene (infC) in vivo

We previously showed that Escherichia coli translation initiation factor IF3 regulates the expression of its own gene infC at the translational level in vivo. Here we create two alterations in the infC gene and test their effects on translational autocontrol of infC expression in vivo by measuring beta-galactosidase activity expressed from infC-lacZ gene fusions under conditions of up to 4-fold derepression or 3-fold repression of infC expression. Replacement of the infC promoter with the trp promoter deletes 120 nucleotides of the infC mRNA 5' to the translation initiation site without affecting autogenous translational control. Mutation of the unusual AUU initiator codon of infC to the more common AUG initiator codon abolishes translation initiation factor IF3-dependent repression and derepression of infC expression in vivo. These results establish the AUU initiator codon of infC as an essential cis-acting element in autogenous translational control of translation initiation factor IF3 expression in vivo.

Formation of MboII vectors and cassettes using asymmetric MboII linkers

Class-IIS restriction endonucleases such as MboII cleave DNA at a specified distance away from their recognition sequences. This feature was exploited to cleave DNA at previously inaccessible locations by preparing special asymmetric linker/adapters containing the MboII recognition sequence. These could be joined to DNA fragments and subsequently cleaved by MboII. Attachment of a 3' phosphate to one of the two different oligodeoxynucleotides comprising the asymmetric duplex prevented ligation at the improper end of the linker. Plasmids were constructed containing a unique BamHI or BclI site between the recognition and cleavage site of MboII. These sites were used to introduce a foreign fragment into the plasmid at a position permitting MboII to cleave within the newly inserted fragment. Once cleaved at the unique MboII site, another DNA fragment was inserted. DNA was thus inserted at a sequence not previously accessible to specific cleavage by a restriction enzyme. A cassette containing an identifiable marker, the lac operator, between two oppositely oriented MboII/BamHI linkers was made and tested in a random insertion linker mutagenesis experiment.

Analysis and comparison of the internal promoter, pE, of the ilvGMEDA operons from Escherichia coli K-12 and Salmonella typhimurium

It was previously determined that the distal portion of the ilvGMEDA operon was expressed despite the insertion of transposons into ilvG and ilvE. This observation suggested the existence of internal promoters upstream of ilvE (pE) and ilvD (pD). The internal promoter pE, responsible for part of ilvEDA expression, has been analyzed both in vivo and in vitro. Our results indicate that: pE exists in both E. coli K-12 and S. typhimurium; pE is located in the distal end of the ilvM coding sequence; the pE sequence is highly conserved in the two bacteria; the amino acid sequence of the ilvM gene product is 93% homologous between the two bacteria; transcription from pE can be demonstrated both in vivo and in vitro; the efficiency of pE is essentially equivalent in the two bacteria.

The effect of nalidixic acid on expression from related E. coli promoters

The effect of the DNA gyrase inhibitor, nalidixic acid, on expression from E. coli promoters was studied using the pKO-1, galactokinase expression vector system. Expression from a series of related hybrid promoters, tet promoter variants and the trp promoter flanked by oligonucleotide blocks was measured after incubation with nalidixic acid. Expression from the pBR322 tet promoter and tet promoter mutants within the -10 region was reduced after the drug treatment. The lacUV5, trp, and tettrp promoters were essentially unaffected while the trplac and the trptet promoters were stimulated. Studies of the trp promoter flanked by upstream or downstream oligonucleotide blocks revealed similar responses to the trp promoter parent control plasmids.

Construction and characterization of pBR322-derived plasmids with deletions of the RNA I region

A region upstream from the origin of replication in ColE1-type plasmids has been shown to be necessary for replication. Two RNA transcripts are produced from this area, RNA II, which yields the primer for DNA polymerase initiation at the origin and RNA I, which is complementary to the 5' end of RNA II and acts to inhibit primer formation. We have constructed plasmids which do not possess the nucleotide sequence for RNA I, or the normal 5' terminus and promoter of RNA II. The RNA II analog, in these plasmids, is believed to be synthesized by the readthrough transcription of the upstream trimethoprim-resistant dihydrofolate reductase (DHFR) gene at a level comparable to that produced by the tryptophan promoter. These plasmids have a copy number of about tenfold higher than that of pBR322 during logarithmic growth and are compatible with other ColE1-type plasmids. These plasmids are stably maintained in several strains when selective pressure is present and the plasmids are stably maintained during exponential growth in W3110 strains without selective pressure. In all strains examined, the dimeric form of the plasmid was lost from cells much more rapidly than those containing the monomeric form.

Use of bacterial DHFR-II fusion proteins to elicit specific antibodies

Plasmids containing the coding region of the type II dihydrofolate reductase (DHFR) specified by R388 have been used to alter the amino acid (aa) sequence at the C-terminus of this protein. These plasmids have a unique cloning site in the C-terminal portion of the 78-aa coding region. Insertions of DNA fragments into this site produced plasmids that code for proteins with 6- to 80-aa extensions. The vectors were constructed to terminate translation in all three phases beyond the position of insertion of foreign DNA. Random DNA fragments from the major sperm protein (MSP) gene of Caenorhabditis elegans produced by DNase I cleavage were inserted into these vectors. Cell extracts from colonies containing MSP sequences were examined by gel electrophoresis and immunoblotting. One of the hybrid DHFR-MSP proteins was isolated and antibody was prepared to it. This antibody preparation reacted with MSP in immunoblots of purified MSP and whole cell extracts of the worm. A rapid purification procedure for the DHFR is presented.

A convenient technique to compare the efficiency of promoters in Escherichia coli

We describe a technique which allows one to insert any promoter in front of the chromosomal malPQ operon. This can be done easily by using only one plasmid, one strain, and two simple selections. Properties of the final chromosomal fusion are such that the level of amylomaltase, the product of the malQ gene, measures quantitatively the efficiency of the inserted promoter. This method was utilized to compare the efficiency of four well-known promoters: lacZp, trp, tac, lambdaPR and three malT activated promoters: malPp, malkP and malEp.

In vitro characterization of hybrid promoters and altered tryptophan operon promoters

This study examines the in vitro interaction of hybrid and altered Escherichia coli promoters and other promoters with purified E. coli RNA polymerase. Three parameters of polymerase activity were examined: the time for open complex formation; the temperature of transitions; and the time required for productive initiation. The results indicate the rate of in vitro binding as measured by the filter binding technique does not completely correlate with the in vivo activities among these diverse promoters. Transition temperatures ranged from 13 to 27 degrees C with the lowest transition temperatures associated with the relatively weak in vivo beta-lactamase and anti-tet promoters. The productive initiation studies showed a dependence on labeled nucleoside triphosphate concentration when that nucleotide was present early and frequently in the transcript. Promoters containing the -10 region of the lac promoter had slow productive initiation rates while trp -10 promoter derivatives were generally very fast. In the promoters studied here, a trend was noted between the binding rate and transition temperature studies in that the promoters with the lower transition temperatures tended to bind more rapidly.

Transcription termination signal for the cat-86 indicator gene in a Bacillus subtilis promoter-cloning plasmid

Plasmid pPL703 is a promoter-cloning plasmid for Bacillus subtilis consisting of the promoter-less cat-86 gene inserted between the EcoRI and BamHI sites of pUB110. The orientation of cat-86 in pPL703 is opposite to that of two major transcript species that occur within the pUB110 vector portion of pPL703. Therefore, transcripts initiated in cloned promoters which activate cat-86 expression presumably must terminate prior to entering the vector portion of pPL703 to permit stable maintenance of promoter-containing derivatives in host cells. We have identified an apparent Rho-independent transcription terminator 35 bp 3' to the cat-86 coding sequence. A restriction fragment spanning the terminator is 90% efficient in terminating transcription in both B. subtilis and Escherichia coli. The structure of the cat-86 transcription termination site is similar to Rho-independent termination sites identified in E. coli.

Role of DNA regions flanking the tryptophan promoter of Escherichia coli. II. Insertion of lac operator fragments

To examine the effect of introducing protein-binding sites around a promoter upon expression from that promoter, a series of altered tryptophan promoter plasmids have been constructed. In these derivatives of pKO-1 (a galK-expression, promoter-assay vector), the trp promoter has been introduced into the vector, such that the galK expression is dependent on the trp promoter. Unique restriction sites have been introduced adjacent to the trp promoter for the insertion of other DNA fragments. The DNA-binding site (a lac operator (lacO) fragment of 33 bp) for the lactose repressor was inserted into the trp promoter-pKO plasmids at various defined locations from -52 to +58 relative to the start site of transcription. Strains bearing tryptophan promoter-lactose operator plasmid derivatives were assayed for galactokinase activity in Escherichia coli C600 and JM103 (a lacIQ strain) to observe the effect of lac repressor binding and removal. In those plasmids where the lac repressor was downstream from the promoter, expression was diminished by the presence of the lactose repressor and galactokinase activity could be induced by addition of IPTG. An analogous lac promoter plasmid was repressed over 90%, and the plasmid containing the lacO fragment at +2 exhibited up to 80% repression; 40-50% repression was observed when the lacO was placed at positions +27 and +58. Placement of the lacO at the upstream locations -39 and -52 produced lower repression. To examine the effects of more than one operator surrounding the promoter, plasmids were constructed that had a lacO at -39 or -52 and, in addition, had an operator downstream.+2