Infection of Salmonella typhimurium with coliphage Mu d1 (Apr lac): construction of pyr::lac gene fusions

Purine utilization by Klebsiella oxytoca M5al: genes for ring-oxidizing and -opening enzymes

The enterobacterium Klebsiella oxytoca uses a variety of inorganic and organic nitrogen sources, including purines, nitrogen-rich compounds that are widespread in the biosphere. We have identified a 23-gene cluster that encodes the enzymes for utilizing purines as the sole nitrogen source. Growth and complementation tests with insertion mutants, combined with sequence comparisons, reveal functions for the products of these genes. Here, we report our characterization of 12 genes, one encoding guanine deaminase and the others encoding enzymes for converting (hypo)xanthine to allantoate. Conventionally, xanthine dehydrogenase, a broadly distributed molybdoflavoenzyme, catalyzes sequential hydroxylation reactions to convert hypoxanthine via xanthine to urate. Our results show that these reactions in K. oxytoca are catalyzed by a two-component oxygenase (HpxE-HpxD enzyme) homologous to Rieske nonheme iron aromatic-ring-hydroxylating systems, such as phthalate dioxygenase. Our results also reveal previously undescribed enzymes involved in urate oxidation to allantoin, catalyzed by a flavoprotein monooxygenase (HpxO enzyme), and in allantoin conversion to allantoate, which involves allantoin racemase (HpxA enzyme). The pathway also includes the recently described PuuE allantoinase (HpxB enzyme). The HpxE-HpxD and HpxO enzymes were discovered independently by de la Riva et al. (L. de la Riva, J. Badia, J. Aguilar, R. A. Bender, and L. Baldoma, J. Bacteriol. 190:7892-7903, 2008). Thus, several enzymes in this K. oxytoca purine utilization pathway differ from those in other microorganisms. Isofunctional homologs of these enzymes apparently are encoded by other species, including Acinetobacter, Burkholderia, Pseudomonas, Saccharomyces, and Xanthomonas.

Mu dI1(Ap lac) mutagenesis of Yersinia pestis plasmid pFra and identification of temperature-regulated loci associated with virulence

The F1 capsule of Yersinia pestis, encoded by the 100 kb plasmid pFra, is often assumed to be essential for full virulence of Y. pestis. However, virulent strains of Y. pestis that are F1- and either pFra+ or pFra- have been reported. To assess the role of pFra-encoded factors in virulence, mutants in pFra with insertions of the defective transposing bacteriophage Mu dl(Ap lac) were obtained, by using the wild type (wt) and the pLcr-cured derivative of strain C092. Mutants that exhibited temperature regulation of lactose fermentation and retarded electrophoretic mobility of pFra were selected. A total of 15 insertion mutants were isolated in the wt strain (12 of which had a single insertion in the genome, in pFra); and 24 mutants in the isogenic pLcr- derivative. Four of the pLcr+ mutants, and none of the pLcr- mutants, were F1-. All F1- mutants were decreased in virulence for mice compared to the wt parent; and five of the F1+ mutants also were significantly attenuated in mice. Fusion end-joints of insert DNA were cloned into Escherichia coli by using pMLB524, a vector for rescuing operon fusions of lacZ. Recombinants were obtained which contained pFra inserts ranging from < 2kb to approximately 36 kb, and the insertions occurred at several sites on pFra. All of the four F1- mutants tested mapped within the F1 capsule operon (caf1). The remaining five attenuated mutants sequenced were F1+ and mapped outside of but near the operon. Sequencing and complete analysis of the pFra insertions mutants could facilitate identification of new potential virulence factors.

Regulation of Raoultella terrigena comb.nov. phytase expression

Phytases catalyze the release of phosphate from phytate (myo-inositol hexakisphosphate) to inositol polyphosphates. Raoultella terrigena comb.nov. phytase activity is known to increase markedly after cells reach the stationary phase. In this study, phytase activity measurements made on single batch cultures indicated that specific enzyme activity was subject to catabolite repression. Cyclic AMP (cAMP) showed a positive effect in expression during exponential growth and a negative effect during stationary phase. RpoS exhibited the opposite effect during both growth phases; the induction to stationary phase decreased twofold in the rpoS::Tn10 mutant, but the effect of RpoS was not clearly determined. Two phy::MudI1734 mutants, MW49 and MW52, were isolated. These formed small colonies in comparison with the MW25 parent strain when plated on Luria-Bertani (LB) or LB supplemented with glucose. They did not grow in minimal media or under anaerobiosis, but did grow aerobically on LB and LB glucose at a lower rate than did MW25. The beta-galactosidase activity level in these mutants increased three to four fold during stationary growth in LB glucose and during anaerobiosis. Addition of cAMP during the exponential growth of MW52 on LB glucose provoked a decrease in beta-galactosidase activity during the stationary phase, confirming its negative effect on phytase expression during stationary growth.

NtrC is required for control of Klebsiella pneumoniae NifL activity

In response to molecular oxygen and/or fixed nitrogen, the product of the Klebsiella pneumoniae nitrogen fixation L (nifL) gene inhibits NifA-mediated transcriptional activation. Nitrogen regulation of NifL function occurs at two levels: transcription of the nifLA operon is regulated by the general Ntr system, and the activity of NifL is controlled by an unknown mechanism. We have studied the regulation of NifL activity in Escherichia coli and Salmonella typhimurium by monitoring its inhibition of NifA-mediated expression of a K. pneumoniae phi(nifH'-'lacZ) fusion. The activity of the NifL protein transcribed from the tac promoter is regulated well in response to changes of oxygen and/or nitrogen status, indicating that no nif- or K. pneumoniae-specific product is required. Unexpectedly, strains carrying ntrC (glnG) null alleles failed to release NifL inhibition, despite the fact that synthesis of NifL was no longer under Ntr control. Additional evidence indicated that it is indeed the transcriptional activation capacity of NtrC, rather than its repression capacity, that is needed, and hence it is a plausible hypothesis that NtrC activates transcription of a gene(s) whose product(s) in turn functions to relieve NifL inhibition under nitrogen-limiting conditions.

Utilization of orotate as a pyrimidine source by Salmonella typhimurium and Escherichia coli requires the dicarboxylate transport protein encoded by dctA

Mutants deficient in orotate utilization (initially termed out mutants) were isolated by selection for resistance to 5-fluoroorotate (FOA), and the mutations of 12 independently obtained isolates were found to map at 79 to 80 min on the Salmonella typhimurium chromosome. A gene complementing the mutations was cloned and sequenced and found to possess extensive sequence identity to characterized genes for C4-dicarboxylate transport (dctA) in Rhizobium species and to the sequence inferred to be the dctA gene of Escherichia coli. The mutants were unable to utilize succinate, malate, or fumarate as sole carbon source, an expected phenotype of dctA mutants, and introduction of the cloned DNA resulted in restoration of both C4-dicarboxylate and orotate utilization. Further, succinate was found to compete with orotate for entry into the cell. The S. typhimurium dctA gene encodes a highly hydrophobic polypeptide of 45.4 kDa, and the polypeptide was found to be enriched in the membrane fraction of minicells harboring a dctA+ plasmid. The DNA immediately upstream of the deduced -35 region contains a putative cyclic AMP-cyclic AMP receptor protein complex binding site, thus affording an explanation for the more effective utilization of orotate with glycerol than with glucose as carbon source. The E. coli dctA gene was cloned from a lambda vector and shown to complement C4-dicarboxylate and orotate utilization in FOA-resistant mutants of both E. coli and S. typhimurium. The accumulated results demonstrate that the dctA gene product, in addition to transporting C4-dicarboxylates, mediates the transport of orotate, a cyclic monocarboxylate.

Isolation and characterization of adenylate kinase (adk) mutations in Salmonella typhimurium which block the ability of glycine betaine to function as an osmoprotectant

Mutants of Salmonella typhimurium that were not protected by glycine betaine (GB) but could still use proline as an osmoprotectant in media of high osmolality were isolated. The mutations responsible for this phenotype proved to be alleles of the adenylate kinase (adk) gene, as shown by genetic mapping, sequencing of the cloned mutant alleles, complementation with the Escherichia coli adk gene, and assay of Adk enzyme activity in crude extracts. One of the mutations was in the untranslated leader of the adk mRNA, a second was in the putative Shine-Dalgarno sequence, and a third was in the coding region of the gene. The loss of osmoprotection by GB was shown to be due to the fact that the accumulation of this solute actually resulted in a severe inhibition of growth in the adk mutants. The addition of GB in the presence of 0.5 M NaCl resulted in a rapid decline in the ATP pool and a dramatic increase in the AMP pool in the mutants. Proline, which is not toxic to the adk mutants, did not have any significant effects on the cellular levels of ATP and AMP. The mutants exhibited two different phenotypes with respect to the utilization of other osmoprotectants: they were also inhibited by propiothiobetaine, L-carnitine, and gamma-butyrobetaine, but they were stimulated normally in media of high osmolality by proline, choline-O-sulfate, and stachydrine.

Genetic evidence that promoter P2 is the physiologically significant promoter for the pyrBI operon of Escherichia coli K-12

The pyrBI operon of Escherichia coli K-12 encodes the two nonidentical subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase (ATCase). Expression of this operon is negatively regulated by pyrimidine availability primarily through UTP-sensitive transcriptional attenuation and, to a lesser extent, at the level of transcriptional initiation. Previous studies indicated that the pyrBI operon was transcribed from tandem sigma 70 promoters designated P1 and P2, with the large majority of transcription initiated at the more downstream promoter P2. To more clearly define the roles of these promoters, mutations that severely impair or inactivate individual promoters were constructed in the chromosomal pyrBI operon, and their effects on ATCase synthesis were measured. In cells grown under conditions of either pyrimidine excess or pyrimidine limitation, more than 99% of all ATCase synthesis was directed by transcripts initiated at promoter P2, indicating that it is the only physiologically significant pyrBI promoter. However, mutations that effectively inactivate promoter P1 caused a 15% reduction in ATCase levels, apparently by inhibiting transcription from promoter P2 by an unknown mechanism. Support for this explanation was provided by the demonstration that little, if any, transcriptional initiation occurred at promoter P1 in a transcriptional fusion vector whereas a high level of transcription was initiated at promoter P2 in an equivalent construction. Our results also provide evidence for pyrimidine-mediated regulation of transcriptional initiation at promoter P2 over a severalfold range and show that cells can grow reasonably well with very low levels of ATCase, apparently because of changes in the concentration of allosteric effectors that increase the specific activity of the enzyme.

Light emission from a Mudlux transcriptional fusion in Salmonella typhimurium is stimulated by hydrogen peroxide and by interaction with the mouse macrophage cell line J774.2

Hydrogen peroxide is known to induce a multigenic response in Salmonella typhimurium cells. We have used a Mudlux transcriptional reporter system to identify and isolate fusions in the virulent strain SL1344 which respond to hydrogen peroxide in vitro by light production, and one of these fusions, MPG203, has been further characterized. Transient light production was observed from MPG203 at levels of hydrogen peroxide as low as 10 microM. However, high levels of this toxic oxidizing agent resulted in light suppression, particularly at low bacterial densities. This fusion was also shown to produce light following adhesion to cells of the mouse macrophage cell line J774.2. Furthermore, the response was greatly reduced in the presence of catalase, directly implicating hydrogen peroxide as the eliciting agent and suggesting the involvement of the hydrogen peroxide-induced bacterial stress response in the infection process. Chemiluminescence studies also indicated that inhibition of the respiratory burst may occur as the infection ratio is increased. In addition, the level of light produced from bacteria within individual macrophage cells was shown to vary.

Molecular genetic analysis of the Escherichia coli phoP locus

We have cloned the Escherichia coli phoP gene, a member of the family of environmentally responsive two-component systems, and found its deduced amino acid sequence to be 93% identical to that of the Salmonella typhimurium homolog, which encodes a major virulence regulator necessary for intramacrophage survival and resistance to cationic peptides of phagocytic cells. The phoP gene was mapped to kilobase 1202 on the Kohara map (25-min region) of the E. coli genome (Y. Kohara, K. Akiyama, and K. Isono, Cell 50:495-508, 1987) and found to be transcribed in a counterclockwise direction. Both E. coli and S. typhimurium phoP mutants were more sensitive than their isogenic wild-type strains to the frog-derived antibacterial peptide magainin 2, suggesting a role for PhoP in the response to various stresses in both enteric species.

Transcriptional organization of the rfaGBIJ locus of Salmonella typhimurium

The transcriptional organization of the rfaGBIJ gene cluster of Salmonella typhimurium was studied by using lacZ and cat transcriptional probes. The results indicated that the leftward end of the gene cluster (rfaG-rfaB-rfaI) is an operon that is transcribed from one or more promoters that lie upstream of rfaG. The results further indicated that the product of the rfaH (sfrB) gene acts as a positive regulator of transcription of the entire rfaGBIJ cluster. At least one site required for the RfaH-mediated transcriptional regulation lies within or very close to the upstream promoter.

Suppression of the abnormal phenotype of Salmonella typhimurium rfaH mutants by mutations in the gene for transcription termination factor Rho

Mutations in the rfaH gene have previously been shown to cause premature termination of transcription of the traYZ operon of the F factor and also to prevent expression of the rfaGBIJ gene cluster of Salmonella typhimurium. In the present study, mutants were selected for their ability to restore the normal pattern of rfaGBIJ function. On the basis of this initial section, several classes of extragenic suppressor mutants were isolated that completely or partially corrected the Tra- and Rfa- phenotypes of the prototype rfaH mutant. The suppressor mutations included mutations in rho and mutations that mapped in or close to rpoBC. Other suppressor mutations were located elsewhere on the chromosome, presumably identifying other genes that play a role in the RfaH-mediated transcriptional regulation.

Analysis of the host ranges of transposon bacteriophages Mu, MuhP1, and D108 by use of lipopolysaccharide mutants of Salmonella typhimurium LT2

The lipopolysaccharide receptors for the mutator bacteriophages Mu, MuhP1, and D108 were investigated with lipopolysaccharide mutants of Salmonella typhimurium LT2. Mu adsorbed only to mutants lacking the terminal O antigen but retaining the main chain sugars of the core; the side chain N-acetylglucosamine was not required. MuhP1 and D108 adsorbed partially to cells with the same receptors but adsorbed well only to cells with shorter lipopolysaccharides of the Rc and Rd1 chemotypes.

Genetic evidence that NarL function is not required for nitrate regulation of nitrate assimilation in Klebsiella pneumoniae M5al

We cloned the narL gene, required for nitrate induction of respiratory nitrate reductase synthesis, from Klebsiella pneumoniae. The E. coli narL gene product shares sequence similarity with the response regulator proteins of two-component regulatory systems. We found that narL(+)-containing plasmids restored nitrate regulation of anaerobic respiratory gene expression in appropriate Escherichia coli hosts. The K. pneumoniae narL region encoded a protein whose migration in Laemmli gels was indistinguishable from that of the narL product of E. coli. We constructed a narL::Km mutant of K. pneumoniae. This mutation abolished nitrate induction of respiratory nitrate reductase synthesis but had no effect on nitrate induction of assimilatory nitrate and nitrite reductase synthesis. We conclude that K. pneumoniae has distinct nitrate-responsive regulators for controlling respiratory and assimilatory gene expression.

Nucleotide sequence of the transcriptional control region of the osmotically regulated proU operon of Salmonella typhimurium and identification of the 5' endpoint of the proU mRNA

Southern blot analysis of 15 proU transposon insertions in Salmonella typhimurium indicated that this operon is at least 3 kilobase pairs in length. The nucleotide sequence of 1.5-kilobase-pair fragment that contains the transcriptional control region of the proU operon and the coding sequences specifying 290 amino acids of the first structural gene of the operon was determined. The predicted amino acid sequence of the product of this gene shows extensive similarity to the HisP, MalK, and other proteins that are inner membrane-associated components of binding protein-dependent transport systems. S1 mapping and primer extension analysis of the proU mRNAs revealed several species with different 5' ends. Two of these endpoints are sufficiently close to sequences that have weak similarities to the consensus -35 and -10 promoter sequences that they are likely to define two transcription start sites. However, we cannot rule out the possibility that some or all of the 5' endpoints detected arose as a result of the degradation of a longer mRNA. The expression of proU-lacZ operon fusions located on plasmids was normal in S. typhimurium regardless of the plasmid copy number. The sequences mediating normal, osmoregulated expression of the proU operon were shown by subcloning to be contained on an 815-base-pair fragment. A 350-base-pair subclone of this fragment placed onto a lacZ expression vector directed a high-level constitutive expression of beta-galactosidase, suggesting that there is a site for negative regulation in the proU transcriptional control region which has been deleted in the construction of this plasmid.

Genetic regulation of nitrate assimilation in Klebsiella pneumoniae M5al

We isolated Mu dI1734 insertion mutants of Klebsiella pneumoniae that were unable to assimilate nitrate or nitrite as the sole nitrogen source during aerobic growth (Nas- phenotype). The mutants were not altered in respiratory (anaerobic) nitrate and nitrite reduction or in general nitrogen control. The mutations were linked and thus defined a single locus (nas) containing genes required for nitrate assimilation. beta-Galactosidase synthesis in nas+/phi(nas-lacZ) merodiploid strains was induced by nitrate or nitrite and was inhibited by exogenous ammonia or by anaerobiosis. beta-Galactosidase synthesis in phi(nas-lacZ) haploid (Nas-) strains was nearly constitutive during nitrogen-limited aerobic growth and uninducible during anaerobic growth. A general nitrogen control regulatory mutation (ntrB4) allowed nitrate induction of phi(nas-lacZ) expression during anaerobic growth. This and other results suggest that the apparent anaerobic inhibition of phi(nas-lacZ) expression was due to general nitrogen control, exerted in response to ammonia generated by anaerobic (respiratory) nitrate reduction.

Role of the ribosome in suppressing transcriptional termination at the pyrBI attenuator of Escherichia coli K-12

Pyrimidine-mediated regulation of pyrBI operon expression in Escherichia coli K-12 occurs primarily by an attenuation control mechanism. Previous studies have suggested a model for attenuation control in which low intracellular levels of UTP cause close coupling of transcription and translation within the pyrBI leader region. This close coupling apparently prevents transcriptional termination at an attenuator (a rho-independent transcriptional terminator) located 23 base pairs before the pyrBI structural genes within an open reading frame for a 44-amino acid leader polypeptide. Presumably, a ribosome involved in the synthesis of the leader polypeptide disrupts or precludes the formation of the attenuator-encoded RNA hairpin, which is required for transcriptional termination. In this study, we examined the role of the ribosome in inhibiting transcriptional termination at the pyrBI attenuator. Using oligonucleotide-directed mutagenesis, we systematically introduced termination codons into the reading frame for the leader polypeptide to determine the distance a ribosome must translate to suppress transcriptional termination. These mutations were incorporated individually into a pyrB::lacZ gene fusion, which was then introduced into the E. coli chromosome. The resulting fusion strains were used to measure the effect of each mutation on pyrB::lacZ expression. The results show that a ribosome must translate to within 14-16 nucleotides of the attenuator-encoded RNA hairpin to inhibit transcriptional termination efficiently, which indicates a direct interaction between the ribosome and the termination hairpin sequence as proposed in the present model. Additional results indicate that factors not included in the present model for attenuation control contribute to the expression and regulation of the pyrBI operon.

Operon structure of flagellar genes in Salmonella typhimurium

In Salmonella typhimurium, more than 40 genes have been shown to be involved in flagellar formation and function and almost all of them have been assigned to three regions of the chromosome, termed region I, region II, and region III. In the present study, a large number of transposon-insertion mutants in these flagellar genes were isolated using Tn10 and Mud1. The flaV gene was found to be a strong hot spot for Tn10 insertion. Complementation analysis of the polarity effects exerted by the transposon-insertion mutants defined 13 different flagellar operons; 3 in region I, 4 in region II, and 6 in region III. These results are compared with the reported arrangement of the corresponding genes in Escherichia coli.

Unmasking of bacteriophage Mu lipopolysaccharide receptors in Salmonella enteritidis confers sensitivity to Mu and permits Mu mutagenesis

The human pathogen Salmonella enteritidis 3b was found to be highly resistant to phage P22 and Mu derivatives. The Mu sensitivity (musA1) allele from Salmonella typhimurium could be transferred to S. enteritidis 3b at low frequency by cotransduction with hisG::Tn10. Sensitivity to Mu resulted in a large reduction in the number of lipopolysaccharide core-region oligosaccharides that were substituted with O-antigen polysaccharide. The residual high-molecular-weight lipopolysaccharide appeared to be a hybrid displaying O antigens which were immunologically related to those of S. typhimurium and not to those of S. enteritidis. Consequently, Mu d1(Ap lac) could then be transduced into Mus strains forming stable lysogens. On temperature induction, Mu transposition could easily be used to generate mutations in genes coding for cell surface antigens including fimbriae, lipopolysaccharide, and flagella.

In vivo functional characterization of a yeast nucleotide sequence: construction of a mini-Mu derivative adapted to yeast

We have constructed a derivative of the bacteriophage Mu (called MudIIZZ1), which contains the lacZ gene coding for beta-galactosidase (beta Gal) and markers suited for yeast transformation (2 mu circle replication origin and LEU2). This new transposon is an efficient tool for studying the expression of cloned yeast nucleotide sequences through beta Gal-protein fusions. It is also adapted for one-step disruption experiments so that a functional map of the same sequence can be drawn. We have used this MudIIZZ1 transposon to study a 5-kb DNA fragment which had been cloned by complementation of a cold-sensitive respiration-deficient phenotype. By testing the expression of the beta Gal fusions and the disruption phenotype, we have confirmed the presence of a gene required for mitochondrial functions, and revealed another two open reading frames in the same fragment; one of these also interferes with mitochondrial biogenesis. The method is fast and reliable, and has potential for more general purposes which are discussed.

Use of lambda vehicles to isolate ompC-lacZ gene fusions in Salmonella typhimurium LT2

A novel plasmid vector, pAMH70 carrying both the lamB and nusA genes of Escherichia coli K12 was constructed. Introduction of this plasmid into Salmonella typhimurium LT2 renders this bacterium both sensitive to lambda adsorption and able to sustain growth and lysogenization by lambda. Using this strain as a recipient, stable gene fusions to the gene encoding a major outer membrane porin protein OmpC, were constructed with a lambda vehicle lambda placMu. To confirm the actual site of fusions they were genetically mapped and transducing phages carrying the ompC-lacZ fusion were isolated and relysogenized. The fusions were also shown to be to ompC by their regulatory properties.

In vivo formation of gene fusions in Pseudomonas putida and construction of versatile broad-host-range vectors for direct subcloning of Mu d1 and Mu d2 fusions

The Mu d1 and Mu d2 prophages were integrated into the conjugative broad-host-range plasmid R751. The two plasmids were then transferred into Pseudomonas putida, and derivatives carrying intact Mu prophages were recovered. After induction of Mu at 42 degrees C, both operon and gene fusions were observed on 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-Gal) plates. Broad-host-range vectors were constructed which allow direct cloning of both operon or gene fusions and their analysis in Escherichia coli and P. putida. By using one of these vectors, two operon fusions were isolated from the P. putida chromosome and comparatively analyzed in E. coli and P. putida.

High frequency generalized transduction by miniMu plasmid phage

Deletion derivatives of phage Mu which replicate as multicopy plasmids, and also transpose and package like Mu, have been developed for the in vivo cloning of bacterial genes. We show here that these miniMu plasmid phage are also efficient at generalized transduction and that both in vivo cloning and generalized transduction of a given gene can be accomplished in a single experiment.

Molecular characterization of the oligopeptide permease of Salmonella typhimurium

The oligopeptide permease (Opp) of Salmonella typhimurium is a periplasmic binding protein-dependent transport system and handles any peptides containing from two to five amino acid residues. Opp plays an important nutritional role and is also required for the recycling of cell wall peptides. We have determined the nucleotide sequence of the opp operon. In addition to the four opp genes identified previously by genetic means (oppABCD) a fifth gene, oppF, is shown to be cotranscribed as part of the opp operon. Using reverse genetics, we show that oppF also encodes an essential component of the Opp transport system. The five proteins, OppABCDF, are shown to be the only proteins required for Opp function. Regulation of opp expression and of the differential expression of genes within the operon is investigated. We have devised a simple means of constructing lacZ gene fusions to any S. typhimurium chromosomal gene in vivo, using derivatives of bacteriophage Mu. Using this procedure, opp-lacZ gene fusions were selected. The resultant Opp-LacZ hybrid proteins were used to show that OppB, OppC and OppD are membrane-associated proteins. A detailed comparison of the Opp components with those of other binding protein-dependent transport systems provides insight into the mechanisms and evolution of these transport systems.

Cloning of genes from members of the family Enterobacteriaceae with mini-Mu bacteriophage containing plasmid replicons

An in vivo cloning system that uses derivatives of the Escherichia coli bacteriophage Mu with plasmid replicons has been extended to five different species of the family Enterobacteriaceae. Mu and these mini-Mu replicon elements were introduced into strains of E. coli, Shigella flexneri, Salmonella typhimurium, Citrobacter freundii, and Proteus mirabilis by infection, by transformation, or by conjugation with newly constructed broad-host-range plasmids containing insertions of these elements. Lysates from these cells, lysogenic for Mu and mini-Mu elements, were used to infect sensitive recipient strains of E. coli, S. typhimurium, and C. freundii. Drug-resistant transductants had mini-Mu replicon elements with inserts of different DNA sequences. All of the lysogens made could be induced to yield high phage titers, including those coming from strains that were resistant to Mu and Mu derivatives. Clones of 10 particular genes were isolated by their ability to complement specific mutations in the recipient strains, even in the presence of the E. coli K-12 restriction system. Some of the mini-Mu replicon elements used contained lac gene fusing segments and resulted in fusions of the lac operon to control regions in the cloned sequences.

Isolation of point mutations in bacteriophage Mu attachment regions cloned in a lambda::mini-Mu phage

Twenty-one derivatives of a lambda::mini-Mu phage containing point mutations in the Mu attachment regions were isolated after mutD mutagenesis and selection for relief from Mu-specific replicative interference of lambda growth. DNA sequence analysis revealed that the single left-end mutant had suffered a T----C transition at position 1 of the Mu sequence, while the remaining 20 right-end mutants contained single base-pair insertions or deletions within the terminal 19 base pairs. A genetic assay showed that the right-end mutations revealed by sequencing were necessary for relief of the replicative inhibition of lambda growth. The properties of these mutants suggest that the terminal 2-base-pair and subterminal 8-base-pair inverted repeats are important for Mu-specific replicative transposition.

crp genes of Shigella flexneri, Salmonella typhimurium, and Escherichia coli

The complete nucleotide sequences of the Salmonella typhimurium LT2 and Shigella flexneri 2B crp genes were determined and compared with those of the Escherichia coli K-12 crp gene. The Shigella flexneri gene was almost like the E. coli crp gene, with only four silent base pair changes. The S. typhimurium and E. coli crp genes presented a higher degree of divergence in their nucleotide sequence with 77 changes, but the corresponding amino acid sequences presented only one amino acid difference. The nucleotide sequences of the crp genes diverged to the same extent as in the other genes, trp, ompA, metJ, and araC, which are structural or regulatory genes. An analysis of the amino acid divergence, however, revealed that the catabolite gene activator protein, the crp gene product, is the most conserved protein observed so far. Comparison of codon usage in S. typhimurium and E. coli for all genes sequenced in both organisms showed that their patterns were similar. Comparison of the regulatory regions of the S. typhimurium and E. coli crp genes showed that the most conserved sequences were those known to be essential for the expression of E. coli crp.

Reversion and immobilization of phage Mud1 cts (Apr lac) insertion mutations in Salmonella typhimurium

Phage Mud1 cts (Apr lac), or Mud1, insertion mutations may be accompanied by adjacent deletion formation which can complicate use of lac fusions generated with this phage for gene regulatory studies. As for phage Mu insertion mutations, phage Mud1 insertions fail to revert at significant frequency (whether or not accompanied by an adjacent deletion). We describe isolation of revertible (X mutant) derivatives of phage Mud1 in Salmonella typhimurium. The X mutant derivatives allow use of reversion as a simple test to determine whether a Mud1 insertion has occurred precisely without an adjacent deletion that may have fused the lac genes to a promoter outside of the gene of interest. In addition, a simple method for stabilizing Mud1 generated lac fusions against subsequent transposition is described.

Virulence genes regulated at the transcriptional level by Ca2+ in Yersinia pestis include structural genes for outer membrane proteins

Yersinia pestis, the causative agent of plague, has a virulence determinant called the low-Ca2+ response (Lcr+ phenotype) that confers on the bacterium Ca2+ dependence for growth at 37 degrees C and expression of V antigen. This virulence determinant is common to the three species of Yersinia and is mediated by Lcr plasmids (called pCD in Y. pestis). In this study, we generated insertions of Mu dI1(Ap lac) in pCD1 of Y. pestis KIM, screened for cells showing transcriptional regulation by Ca2+, and obtained inserts that define at least four pCD1 genes. Their patterns of transcription under different growth conditions closely paralleled the pattern of expression of the V antigen. We tested for expression of Lcr-specific yersinial outer membrane proteins (Yops) by the pCD1::Mu dI1(Ap lac) plasmids. Four of the inserts each eliminated expression of a different Yop; one of these Yops was unique to Y. pestis. Two of the insertions affecting Yops caused avirulence, and one caused strongly decreased virulence of Y. pestis in mice. These data indicate that Yops, like the V antigen, are virulence attributes regulated in the low-Ca2+ response.

Osmoregulation of gene expression in Salmonella typhimurium: proU encodes an osmotically induced betaine transport system

Previous evidence has indicated that a gene, proU, is involved in the response of bacterial cells to growth at high osmolarity. Using Mu-mediated lacZ operon fusions we found that transcription of the proU gene of Salmonella typhimurium is stimulated over 100-fold in response to increases in external osmolarity. Our evidence suggests that changes in turgor pressure are responsible for these alterations in gene expression. Expression of proU is independent of the ompR gene, known to be involved in osmoregulation of porin expression. Thus, there must be at least two distinct mechanisms by which external osmolarity can influence gene expression. We show that there are relatively few genes in the cell which are under such osmotic control. The proU gene is shown to encode a high-affinity transport system (Km = 1.3 microM) for the osmoprotectant betaine, which is accumulated to high concentrations in response to osmotic stress. Even when fully induced, this transport system is only able to function in medium of high osmolarity. Thus, betaine transport is regulated by osmotic pressure at two levels: the induction of expression and by modulation of activity of the transport proteins. We have previously shown that the proP gene encodes a lower-affinity betaine transport system (J. Cairney, I. R. Booth, and C. F. Higgins, J. Bacteriol., 164:1218-1223, 1985). In proP proU strains, no saturable betaine uptake could be detected although there was a low-level nonsaturable component at high substrate concentrations. Thus, S. typhimurium has two genetically distinct pathways for betaine uptake, a constitutive low-affinity system (proP) and an osmotically induced high-affinity system (proU).

Role of translation and attenuation in the control of pyrBI operon expression in Escherichia coli K-12

Expression of the pyrBI operon of Escherichia coli K-12, which encodes the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase, is negatively regulated by the intracellular levels of UTP. Previous experiments suggested a unique model for regulation of operon expression in which low UTP levels cause close coupling of transcription and translation of the pyrBI leader region. This close coupling suppresses transcriptional termination at an attenuator preceding the structural genes. In this study, we examined the regulatory role of translation and attenuation in operon expression. To determine whether the leader region is translated, we constructed a plasmid, designated pBHM17, in which the pyrBI promoter(s) and the first 11 codons for a putative 44-amino acid leader polypeptide are fused to codon 9 of lacZ. A transformant carrying this plasmid synthesized a beta-galactosidase fusion protein with the amino-terminal sequence of the leader polypeptide, demonstrating that the signals required for leader polypeptide synthesis function in vivo. Synthesis of the fusion protein was nearly insensitive to pyrimidine availability. In uracil-grown cells, the level of fusion protein synthesis encoded by plasmid pBHM17 was much greater than that encoded by a similar plasmid containing a pyrB::lacZ gene fusion, in which the pyrBI promoter-regulatory region is intact. These results indicate that the downstream leader sequence which includes the attenuator is required for regulation and functions as a transcriptional barrier. Oligonucleotide-directed mutagenesis was used to change the ATG leader polypeptide initiation codon of the intact pyrBI operon to ACG, which was shown to strongly inhibit translational initiation. This mutation greatly reduced operon expression and regulation as predicted by the attenuation control model.

Toxicity of the pyrimidine biosynthetic pathway intermediate carbamyl aspartate in Salmonella typhimurium

Growth of Salmonella typhimurium pyrC or pyrD auxotrophs was severely inhibited in media that caused derepressed pyr gene expression. No such inhibition was observed with derepressed pyrA and pyrB auxotrophs. Growth inhibition was not due to the depletion of essential pyrimidine biosynthetic pathway intermediates or substrates. This result and the pattern of inhibition indicated that the accumulation of the pyrimidine biosynthetic pathway intermediate carbamyl aspartate was toxic. This intermediate is synthesized by the sequential action of the first two enzymes of the pathway encoded by pyrA and pyrB and is a substrate for the pyrC gene product. It should accumulate to high levels in pyrC or pyrD mutants when expression of the pyrA and pyrB genes is elevated. The introduction of either a pyrA or pyrB mutation into a pyrC strain eliminated the observed growth inhibition. Additionally, a direct correlation was shown between the severity of growth inhibition of a pyrC auxotroph and the levels of the enzymes that synthesize carbamyl aspartate. The mechanism of carbamyl aspartate toxicity was not identified, but many potential sites of growth inhibition were excluded. Carbamyl aspartate toxicity was shown to be useful as a phenotypic trait for classifying pyrimidine auxotrophs and may also be useful for positive selection of pyrA or pyrB mutants. Finally, we discuss ways of overcoming growth inhibition of pyrC and pyrD mutants under derepressing conditions.

Osmotic regulation of L-proline transport in Salmonella typhimurium

The transport of proline is important for the adaptation of Salmonella typhimurium to osmotic stress because exogenous proline permits the growth of the organism in media of elevated osmotic strength that would otherwise be toxic. Measurements of the rate of [3H]proline transport in S. typhimurium indicated that the organism has two distinct proline permeases, the ProU and the ProP systems, whose activities increase more than fivefold as a consequence of growth in media containing 0.3 M NaCl or 0.47 M sucrose. Transport via a third proline permease, the PutP system, is not affected by the osmotic strength of the medium. We constructed strains that carry fusions of lacZ to proU or proP, genes that are required for the two osmotically stimulated proline transport systems. Assays of beta-galactosidase revealed that the transcription of the proU gene is increased more than 10-fold as a result of exposure of the cells to 0.3 M NaCl, 0.47 M sucrose, or equivalent concentrations of other solutes that are not freely diffusible across the cytoplasmic membrane. Increased transcription cannot be triggered by methanol, ethanol, and glycerol, substances that are freely diffusible across the membrane, suggesting that the signal for increased transcription might be an osmotic gradient across the cytoplasmic membrane. The proP gene does not show transcriptional regulation of sufficient magnitude to account for the stimulation of [3H]proline transport. Thus, the osmotic stimulation of the ProP system might be mediated by some posttranscriptional event.

Oxygen regulation in Salmonella typhimurium

Regulation by oxygen of the peptidase T (pepT) locus of Salmonella typhimurium was studied by measuring beta-galactosidase levels in strains containing a pepT::Mu d1(Apr lac) operon fusion. beta-Galactosidase was induced in anaerobic cultures and late-exponential and stationary-phase aerated cultures. Peptidase T activity also was induced under these growth conditions. pepT+ but not pepT strains will utilize as amino acid sources the tripeptides Leu-Leu-Leu and Leu-Gly-Gly only when grown anaerobically. Mutations at two loci, oxrA and oxrB (oxygen regulation) prevent induction of the pepT locus. The oxrA locus is homologous to the fnr locus of Escherichia coli. We have isolated 12 independent Mu d1 insertions (oxd::Mu d1, oxygen dependent) that show induction of beta-galactosidase in anaerobic cultures and stationary-phase aerated cultures. These insertions fall into nine classes based on map location. All of the oxd::Mu d1 insertions are regulated by oxrA and oxrB and therefore define a global regulon that responds to oxygen limitation.

Genetic analysis of the low calcium response in Yersinia pestis mu d1(Ap lac) insertion mutants

Yersinia pestis strain KIM requires plasmid pCD1 for expression of the low calcium response, plague virulence antigen V, and virulence. We constructed Mu d1(Ap lac) insertion mutants of this plasmid which were unable to express the low calcium response. The insertions mapped to a 17-kilobase region of the plasmid. By determining the orientation of the insertions and examining beta-galactosidase production from the Mu d1 lac genes, we determined that this region contains three units of transcription, one of which is transcribed in a direction opposite the direction of transcription of the other two. Transcription of at least two of these units was induced significantly at 37 degrees C compared with 26 degrees C. Ca2+ (2.5 mM) and ATP (18 mM) had no significant effect on the level of expression of the Mu d1 lac genes of these mutants. All insertions in the region strongly reduced production of the V antigen. Insertions from each unit of transcription also reduced virulence in mice.

Proline uptake through the major transport system of Salmonella typhimurium is coupled to sodium ions

Strains of Salmonella typhimurium deficient in one or more of the proline transport systems have been constructed and used to study the mechanism of energy coupling to transport. Proline uptake through the major proline permease (PP-I, putP) is shown to be absolutely coupled to Na+ ions and not to H+ ions as has previously been assumed. Transport through the minor proline permease (PP-II, proP), however, is unaffected by the presence or absence of Na+. The effect of Na+ on the kinetics of proline uptake shows that external Na+ increases the Vmax for transport. It seems probable that proline transport through PP-I is also coupled to Na+ ions in Escherichia coli.

Characterization of mutations that lie in the promoter-regulatory region for glnA, the structural gene encoding glutamine synthetase

In enteric bacteria products of nitrogen regulatory genes ntrA, ntrB and ntrC are known to regulate transcription both positively and negatively at glnA, the structural gene encoding glutamine synthetase [L-glutamate:ammonia-ligase (ADP-forming), EC 6.3.1.2]. We have characterized two types of cis-acting mutations in the glnA promoter-regulatory region. One type, which we have called promoter Up [glnAp (Up)], elevates transcription of glnA to high levels without need for ntr-mediated activation but leaves expression sensitive to ntr-mediated repression. The other type renders glnA transcription insensitive to repression but leaves it normally responsive to activation. Properties of the two types of promoter-regulatory mutations suggest that sites for ntr-mediated activation of glnA transcription are functionally distinct from sites for ntr-mediated repression.

Anaerobic and leucine-dependent expression of a peptide transport gene in Salmonella typhimurium

Using Mu d1-mediated lac operon fusions, we studied the transcriptional regulation of the genes encoding two peptide transport systems, the oligopeptide permease and the tripeptide permease. The four opp genes were found to be constitutively expressed, whereas the genes encoding the tripeptide permease are under a complex set of regulatory controls. Two loci, tppA and tppB, are required for tripeptide permease function. Locus tppA is shown to be a positive regulator of tppB expression. In addition, tppB expression is specifically induced by exogeneous leucine or by anaerobiosis. Anaerobic induction of tppB is independent of the fnr gene product which is required for the anaerobic expression of several respiratory enzymes. Thus, there must be at least two distinct pathways for the anaerobic regulation of gene expression.

Bacteriophage Mu d1(Apr lac) generates vir-lac operon fusions in Shigella flexneri 2a

Previous studies have demonstrated that expression of virulence in Shigella spp. is controlled by growth temperature. To study the regulation of virulence (vir) genes, we set out to develop a rapid, easily-assayed phenotype with which to measure expression of virulence. This report described a procedure for isolating vir-lac operon fusions in S. flexneri 2a by using the specialized transducing bacteriophage Mu d1(Apr lac) of Casadaban and Cohen (M. Casadaban and S. N. Cohen, Proc. Natl. Acad. Sci. U.S.A. 76:4530-4533, 1976). Mu d1(Apr lac) lysogens were isolated and screened for loss of virulence and for temperature-dependent expression of the lactose genes on Mu d1(Apr lac). A recombinant plasmid carrying the Mu immunity gene was also introduced into lysogens of interest to stabilize the Mu d1(Apr lac) insertion and prevent possible thermal induction at 37 degrees C. The mutant which we isolated failed to penetrate tissue culture cells in the assay for virulence and produced almost 15-fold more beta-galactosidase when grown at 37 degrees C than when grown at 30 degrees C. The site of insertion of Mu d1(Apr lac) in this strain was shown to be in the 140-megadalton plasmid pSf2a140, which is known to be associated with virulence. P1L4-mediated transduction of the insertion into a virulent recipient demonstrated genetic linkage of Mu d1(Apr lac) with loss of virulence and temperature-dependent expression of beta-galactosidase. All of these features fulfill the phenotype expected for a Mu d1(Apr lac)-induced vir-lac operon fusion. This mutant provides us with a means of measuring expression of a gene function required for virulence by assaying for beta-galactosidase. The insertion will also serve as a starting point for mapping of genes on pSf2a140 which are necessary for expression of virulence.

Isolation and characterization of lac fusions to two nitrogen-regulated promoters

Mud1 (Ap, lac, cts)-mediated fusions to argTr and dhuA, two transport operon promoters in Salmonella typhimurium, were isolated and characterized in order to investigate the regulation of these promoters. Using these fusions we showed that these promoters are under nitrogen regulation and that this effect, as well as the response to a promoter-up mutation in dhuA, is at the transcriptional level. We utilized the fusions to determine that the histidine transport operon does not contain any internal promoters. The fusions were also used to screen the promoters for additional modes of regulation: argTr was found to respond to carbon regulation in addition to nitrogen regulation, while dhuA does not. The argTr promoter contains a sequence with good homology to the consensus sequence determined for the cAMP receptor protein binding site. Neither promoter responds to sulfur or phosphate regulation.

Mutagenesis of Erwinia carotovora subsp. carotovora with bacteriophage Mu d1 (Apr lac cts62): construction of his-lac gene fusions

The bacteriophage Mu d1(Apr lac cts62 ) obtained from an Escherichia coli double lysogen carrying the defective Mu d1 phage and a Mu-P1 hybrid phage was utilized as a vector for phage mutagenesis in Erwinia carotovora subsp. carotovora. Among ampicillin-resistant transductants. 1.4% were auxotrophs. The synthesis of beta-galactosidase was derepressed upon starvation for histidine in two different his-lac fusion strains.

Plasmid insertion mutagenesis and lac gene fusion with mini-mu bacteriophage transposons

Small bacteriophage Mu transposable elements containing the lac operon structural genes were constructed to facilitate the isolation and use of Mu insertions and lac gene fusions. These mini-Mu elements have selectable genes for either ampicillin or kanamycin resistance and can be used to form both transcriptional and translational lac gene fusions. Some of the mini-Mu-lac elements constructed are deleted for the Mu A and B transposition genes and form stable insertions that cannot undergo transposition unless complemented for these functions. A procedure was developed for selecting mini-Mu insertions specifically into plasmids, including commonly used high-copy-number cloning vectors such as pBR322. Mu insertions in pBR322 were found to be distributed around the plasmid, but insertions in certain regions occurred more frequently than in others.

Gratuitous repression of avtA in Escherichia coli and Salmonella typhimurium

avtA , which encodes transaminase C (alanine-valine transaminase), is repressed by excess-L-alanine or L-leucine, and also by limitation for any of a number of amino acids in Escherichia coli and Salmonella typhimurium. Amino acid limitation causes repression by promoting the accumulation of L-alanine or L-leucine or both. avtA is also repressed by L-alpha-aminobutyric acid and other nonprotein amino acids which are structurally similar to L-alanine. We hypothesize that L-alanine and L-alpha-aminobutyric acid, whose syntheses are catalyzed by transaminase C, are the true corepressors of avtA . Repression by structural analogs of the true corepressors is termed gratuitous repression.

Facile and gentle method for quantitative lysis of Escherichia coli and Salmonella typhimurium

Garrett et al. (Mol. Gen. Genet. 182:326-331, 1981) constructed strains of Escherichia coli harboring derivatives of plasmid pBR322 that carry the lysis genes (S, R, and Rz) of phage lambda. The plasmid construction placed the genes under control of the lactose operon operator-promotor (and thus of lac repressor). Induction of E. coli strains carrying these plasmids resulted in rapid lysis of the culture unless the S gene was defective, in which case the cells grew normally. A freeze-thaw treatment of induced cells carrying an S- plasmid gave quantitative lysis of either E. coli or Salmonella typhimurium cells under exceptionally gentle conditions. The method was equally effective on exponential phase cells and stationary phase cells and was readily extended to a large number of independent cultures.

A modified nucleotide in tRNA as a possible regulator of aerobiosis: synthesis of cis-2-methyl-thioribosylzeatin in the tRNA of Salmonella

The state of modification of the adenosine residue (A37), found adjacent to the anticodon in tRNAs that recognize codons beginning with U, varies in Salmonella bacteria grown under different physiological conditions. In aerobically grown bacteria, these tRNAs contain ms2io6A and in bacteria grown anaerobically they contain its precursor, ms2i6A. The hydroxylation of the isopentenyl (i6-) side chain of ms2i6A does not occur in the absence of oxygen. When the bacteria are grown under iron or cysteine limitation the tRNAs contain predominantly i6A, rather than ms2i6A, ms2io6A, or io6A. The bacteria do not methylthiolate (ms2-) the i6A under these conditions. A Salmonella miaA mutant lacking the isopentenylation enzyme contains an A37 rather than any of the modified forms. Some of the biosynthetic pathways of the amino acids corresponding to ms2i6A containing tRNAs (phe, tyr, trp, ser, leu, cys) are known to have altered regulation depending on the state of modification of nucleoside A37. This regulation appears to be effected through attenuation. We hypothesize that these varying states of modification are related to electron-acceptor pathways in anaerobic or aerobic growth. The role of ms2io6-adenine (the cytokinin hormone in plants) and i6-adenine (an activator of the cell cycle in animal cells) is discussed as related to the role of modifying enzymes in regulation.