Construction of phi80 dhis carrying Salmonella typhimurium histidine operon mutations

Structural and functional conservation of histidinol dehydrogenase between plants and microbes

The partial amino acid sequence of histidinol dehydrogenase (L-histidinol:NAD+ oxidoreductase, EC 1.1.1.23) from cabbage was determined from peptide fragments of the purified protein. The relative positions of these peptides were deduced by aligning their sequences with the sequence of the HIS4C gene product of Saccharomyces cerevisiae. cDNA encoding histidinol dehydrogenase was then amplified from a library using a polymerase chain reaction primed with degenerate oligonucleotide pools of known position and orientation. By using this amplified fragment as a probe, an apparently full-length cDNA clone was isolated that is predicted to encode a proenzyme having a putative 31-amino acid chloroplast transit peptide and a mature molecular mass of 47.5 kDa. The predicted protein sequence was 51% identical to the yeast enzyme and 49% identical to the Escherichia coli enzyme. Expression of the cDNA clone in an E. coli his operon deletion strain rendered the mutant able to grow in the presence of histidinol.

Structure and function of the Salmonella typhimurium and Escherichia coli K-12 histidine operons

We have determined the complete nucleotide sequence of the histidine operons of Escherichia coli and of Salmonella typhimurium. This structural information enabled us to investigate the expression and organization of the histidine operon. The proteins coded by each of the putative histidine cistrons were identified by subcloning appropriate DNA fragments and by analyzing the polypeptides synthesized in minicells. A structural comparison of the gene products was performed. The histidine messenger RNA molecules produced in vivo and the internal transcription initiation sites were identified by Northern blot analysis and S1 nuclease mapping. A comparative analysis of the different transcriptional and translational control elements within the two operons reveals a remarkable preservation for most of them except for the intercistronic region between the first (hisG) and second (hisD) structural genes and for the rho-independent terminator of transcription at the end of the operon. Overall, the operon structure is very compact and its expression appears to be regulated at several levels.

Nucleotide sequence of the Escherichia coli hisD gene and of the Escherichia coli and Salmonella typhimurium hisIE region

In this paper we report the nucleotide sequence of the hisD gene of Escherichia coli and of the his IE region of both E. coli and Salmonella typhimurium. The hisD gene codes for a bifunctional enzyme, L-histidinol:NAD+ oxidoreductase, of 434 amino acids with a molecular mass of 46,199 daltons. We established that the hisIE region of both S. typhimurium and E. coli is composed of a single gene and not, as previously believed, of two separate genes. The derived amino acid sequence indicates that the hisIE gene codes for a bifunctional protein of 203 amino acids with an approximate molecular mass of 22,700 daltons. We also determined the nucleotide sequence of a deletion mutant in S. typhimurium which abolishes the hisF and hisI functions but retains the hisE function. We deduced that the mutant produces a chimeric protein fusing the aminoterminal region of the upstream hisF gene to the carboxyl-terminal domain of the hisIE gene which encodes for the hisE function. In view of these results the structural and functional organization of the histidine operon in enteric bacteria needs to be revised. The operon is composed of only 8 genes and the pathway leading to the biosynthesis of the amino acid requires 11 enzymatic steps.

The hisD-hisC gene border of the Salmonella typhimurium histidine operon

We have sequenced the hisD-hisC gene border of the Salmonella typhimurium histidine operon. The translation termination codon of the hisD gene overlaps with the translation initiation codon of the hisC gene in the manner AUGA. The Shine-Dalgarno sequence of the hisC gene is contained entirely within hisD and there is no intercistronic space since all of the bases are utilized in coding. Two mutations that alter the hisD-hisC gene border are analyzed. Both mutations simultaneously abolish the termination codon of hisD and modify the initiation codon of hisC. One of the mutations changes the hisC initiation codon from AUG to AUU. The AUU codon is 10 to 20% as efficient as AUG for initiation of translation of the hisC gene. The mutant hisC ribosome binding site is compared to the ribosome binding site of the Escherichia coli infC gene which has been reported to contain an AUU initiation codon. The role of overlapping termination/initiation codons in regulating translation of polycistronic mRNAs in bacterial operons is discussed.

Use of M13mp phages to study gene regulation, structure and function: cloning and recombinational analysis of genes of the Salmonella typhimurium histidine operon

A restriction map was determined for a phi 80 lambda dhis transducing phage DNA carrying the Salmonella typhimurium histidine operon. DNA fragments containing the promoter/regulatory region and the first two structural genes of the histidine operon (hisOGD) were identified by their ability to direct regulated synthesis of histidinol dehydrogenase (product of hisD) in a coupled in vitro protein synthesizing system. A 3.1-kb SalI-EcoRI restriction fragment containing the hisOGD region, was subcloned into phage M13mp8 and M13mp9 RF DNAs. Methods are described for shuttling mutant and wild-type bacterial DNA sequences between the M13mp::his phage and host bacterial genomes. Of novel importance is the use of the phage M13 gene II amber mutation to obtain integration of the M13mp::his phage genome into the homologous his region of the bacterial chromosome following transduction of recipients lacking an amber suppressor. This method can be used to facilitate allele replacement with genes carried on M13 transducing phages.

DNA sequence changes of mutations in the histidine operon control region that decrease attenuation

The DNA sequence changes of 18 (9 different) mutations in the control region of the histidine operon of Salmonella typhimurium are presented. All of these mutations increase the level of expression of the operon, presumably by decreasing transcription termination at the attenuator. Five of the mutations were previously isolated hisO mutations, and the other four were isolated here as His+ pseudorevertants of His- stop codon mutations in the leader peptide gene. Only two mutations, O1242 and O3154, directly affect the terminator stem of the leader RNA. One mutation, O1202, creates a strong new stem that would compete with the terminator stem. Most of the other mutations damage other RNA stems. Their effect can best be explained by, and they thus provide supporting evidence for, the prevailing model of attenuator regulation involving alternative, competing RNA stems in the leader RNA. Two mutations that do not appear to significantly affect an RNA stem directly, including a deletion of three of the seven consecutive histidine codons, are best explained as effects of a translating ribosome upon the RNA stem structures, even though the histidine codons are not translated in the pseudorevertants.

Gene organization in the distal part of the Salmonella typhimurium histidine operon and determination and sequence of the operon transcription terminator

Several transducing phages, carrying different deletions of the Salmonella typhimurium histidine operon were constructed and mapped. These phages were used to obtain fragments of DNA comprising different regions of the operon, which were subcloned in plasmid vectors. The recombinant plasmids allowed the construction of a physical and restriction map of the histidine operon. The presence of the different genes on individual fragments was confirmed by complementation tests. The transcription termination site of the histidine operon has been established by S1 mapping and sequence analysis. The entire operon measures about 7100 base pairs and the last six structural genes are contained in 3450 bases of genetic materials.

Cloning and restriction map of the first part of the histidine operon of Salmonella typhimurium

The first part of the histidine operon of Salmonella typhimurium, hisGpeaGD, has been cloned onto the vector plasmid mini-ColE1 (pVH51). The resulting plasmid, pWB91, has a single EcoRI site and is 11,500 base pairs in size. The HindII restriction map was determined by the method of two-dimensional cross-annealing between a partial digest pattern and a complete digest pattern. The restriction fragment containing the genetic control region was identified with the aid of the small (35-base pair) internal deletion 01242 and the observation that heteroduplexed restriction fragments containing this deletion have markedly reduced mobility on polyacrylamide gels. The genetic control region was then mapped in more detail with other restriction enzymes. The genetic orientation of the restriction map was determined with the aid of several deletions of integral HindII fragments generated in vitro.

Mutation spoT of Escherichia coli increases expression of the histidine operon deleted for the attenuator

F'-episomes carrying the Salmonella typhimurium wild-type or attenuator-deleted histidine (his) operons were introduced into Escherichia coli strains containing relA or spoT single and double mutations known to affect guanosine 3'-diphosphate 5'-diphosphate (ppGpp) and guanosine 3'-triphosphate 5'-diphosphate (pppGpp) levels. Expression of the his operon and expression of the gene for 6-phosphogluconate dehydrogenase (gnd) were measured during balanced growth in amino acid-rich and minimal media. The data were consistent with the interpretation that ppGpp is a positive effector of his operon expression, whereas pppGpp is not an essential effector. The conclusion that his operon expression is maximally stimulated at a lower than maximum intracellular ppGpp concentration was further confirmed. Neither ppGpp nor pppGpp appeared to influence gnd gene expression. The metabolic regulation of the E. coli his operon was found to be similar to the ppGpp-meidated metabolic regulation of the S. typhimurium his operon.

Construction and expression of a hybrid plasmid containing the Escherichia coli thrA and thrB genes

In vitro recombination techniques were used to clone the Escherichia coli thrA and thrB structural genes in the plasmid vector pBR322. The chimeric plasmid was analyzed and characterized genetically, by restriction mapping and DNA sequencing. The limited expression of the threonine biosynthetic enzymes in the strain carrying the recombinant plasmid is discussed.

Positive control of lac operon expression in vitro by guanosine 5'-diphosphate 3'-diphosphate

Maximal expression of the Escherichia coli lactose operon in a coupled in vitro transcription-translation system from a Salmonella typhimurium relA mutant was strongly dependent upon addition of guanosine 5'-diphosphate 3'-diphosphate (ppGpp). Without added ppGpp, at saturating 3',5'-cyclic AMP (cAMP) concentrations, synthesis of beta-galactosidase (beta-D-galactoside galactohydrolase, EC 3.2.1.23) was reproducibly only 5-7% of that which can be obtained with 0.5-0.8 mM ppGpp. Experiments in which transcription was uncoupled from translation indicated that this 14- to 20-fold stimulation by ppGpp occurred at the level of transcription. When coupled beta-galactosidase synthesis was primed with a template containing a well-characterized mutant lac promoter (lacP(r)L8UV5), the dependence on ppGpp was greatly reduced. This result provides an important experimental control previously unavailable for verifying the significance of ppGpp effects on gene regulation in vitro; it indicates that activation of lacP(+) expression by ppGpp is specifically an effect of increased transcription initiations. Furthermore, the large ppGpp stimulation of lacP(+) DNA enabled the level of expression of this template to approach that of lacP(r)L8UV5 DNA, an observation expected from results in vivo but not obtained with other transcription-translation systems in vitro. The importance of these results is considered with respect to previous ideas on the physiological role of ppGpp as a supercontrol molecule in bacterial regulation.

Construction of an M13 histidine-transducing phage: a single-stranded cloning vehicle with one EcoRI site

In order to create a ready source of single-stranded DNA for DNA sequence determination by the dideoxy chain-termination method, the promoter-proximal part of the histidine operon, the hisOGD region of Salmonella typhimurium, was cloned onto the single-stranded phage M13. Both orientations of the his DNA were cloned to supply DNA template for sequencing of each strand. Insertion was achieved at an HaeIII site in the intergenic region (IR) of M13, and a single EcoRI site was purposely regenerated at one boundary of the his DNA insert. Infected colonies, not plaques, were selected using the hisD gene as a selective marker. The single RI site and the hisD marker for auxotrophic selection represent improvements on the wild type M13 as a single-stranded vector for cloning other DNA.

Plasmid detection and sizing in single colony lysates

A simple and contained procedure for the rapid assay of the presence and size of plasmids similar to Col El is described. Bacteria are picked from an agar plate with a toothpick, lysed with dodecyl sulfate and heat, and placed directly on an agarose gel for electrophoresis.

Genetic characterization of a phi80 transducing bacteriophage carrying the histidine operon of Salmonella typhimurium

A phi 80 transducing phage, phi 80imm lambdadhis, carrying the Salmonella his-gnd region, was characterized by immunity studies, tonB deletion analysis, and marker rescue analysis. Phi 80imm lambdadhis retains the phage immunity region of the phi 80-lambda hybrid phage from which it was derived. Bacterial genes replace most late phage genes. Deletion analysis shows the prophage gene order to be immlambda-his-gnd and indicates the orientation of the his operon to be hisOGDCBHAFIE-gnd. The structure of phi 80imm lambdadhis is remarkably similar to two independently isolated phi 80 phages that carry the his-gnd region of Escherichia coli and that, like phi80imm lambdahis, were derived by directed gene transposition to the tonB locus. A derivative of phi 80imm lambdadhis that is phi 80 immune is also reported.

Guanosine 5'-diphosphate 3'-diphosphate (ppGpp): positive effector for histidine operon transcription and general signal for amino-acid deficiency

Maximal expression of the histidine operon of Salmonella typhimurium in a coupled in vitro transcription-translation system is strongly dependent upon addition of guanosine 5'-diphosphate 3'-diphosphate (ppGpp). This requirement for ppGpp is exerted at the level of transcription through a mechanism distinct from the his-operon-specific regulatory mechanism. In vivo derepression of the his operon is markedly defective when histidine starvation is imposed on a relA mutant--unable to rapidly increase synthesis of ppGpp--growing in amino-acid-rich medium. Increased sensitivity of relA mutants to growth inhibition by a number of amino-acid analogs suggests that ppGpp is generally important in adjusting expression of amino-acid-producing systems. Analysis of these findings leads us to propose that ppGpp is a positive effector in a system that enables the cell to balance endogenous amino-acid production with environmental conditions of amino-acid availability, and to compensate efficiently for transient changes in these conditions. We propose a unifying theory of the role of ppGpp as the general signal molecule (alarmone) in a "super-control" which senses an amino-acid deficiency and redirects the cell's economy in response.

Specific binding of the first enzyme for histidine biosynthesis to the DNA of histidine operon

Studies were done to examine direct binding of the first enzyme of the histidine biosynthetic pathway (phosphoribosyltransferase) to 32P-labeled phi80dhis DNA and competition of this binding by unlabeled homologous DNA and by various preparations of unlabeled heterologous DNA, including that from a defective phi80 bacteriophage carrying the histidine operon with a deletion of part of its operator region. Our findings show that phosphoribosyltransferase binds specifically to site in or near the regulatory region of the histidine operon. The stability of the complex formed by interaction of the enzyme with the DNA was markedly decreased by the substrates of the enzyme and was slightly increased by the allosteric inhibitor, histidine. These findings are consistent with previous data that indicate that phosphoribosyltransferase plays a role in regulating expression of the histidine operon.

Histidine regulation in Salmonella typhimurium: an activator attenuator model of gene regulation

An activator-attenuator model of positive control, a s opposed to the classic repressor-operator model of negative control, is proposed for the major operon-specific mechanism governing expression of the histidine gene cluster of Salmonella typhimurium. Evidence for this mechanism is derived from experiments performed with a coupled in vitro transcription-translation system, as well as with a minimal in vitro transcription system [Kasai, T. (1974) Nature 249, 523--527]. The product (G enzyme, or N-1-[5'-phosphoribosyl]adenosine triphosphate:pyrophosphate phosphoribosyltransferase; EC 2.4.2.17) of the first structural gene (hisG) of the histidine operon is not involved in the positive control mechanism. However, a possible role for G enzyme as an accessory negative control element interacting at the attenuator can be accommodated in our model. The operon-specific mechanism works in conjunction with an independent mechanism involving guanosine 5'-diphosphate 3'-diphosphate (ppGpp) which appears to be a positive effector involved in regulating amino-acid-producing systems, in general [Stephens, J.C., Artz, S.W. & Ames, B.N. (1975) Proc. Nat. Acad. Sci. USA, in press].