Specialized transduction of the Salmonella hut operons by coliphage lambda: deletion analysis of the hut operons employing lambda-phut

Tn1000-mediated insertion mutagenesis of the histidine utilization (hut) gene cluster from Klebsiella aerogenes: genetic analysis of hut and unusual target specificity of Tn1000

The histidine utilization (hut) genes from Klebsiella aerogenes were cloned in both orientations into the HindIII site of plasmid pBR325, and the two resulting plasmids, pCB120 and pCB121, were subjected to mutagenesis with Tn1000. The insertion sites of Tn1000 into pCB121 were evenly distributed throughout the plasmid, but the insertion sites into pCB120 were not. There was a large excess of Tn1000 insertions in the "plus" or gamma delta orientation in a small, ca. 3.5-kilobase region of the plasmid. Genetic analysis of the Tn1000 insertions in pCB120 and pCB121 showed that the hutUH genes form an operon transcribed from hutU and that the hutC gene (encoding the hut-specific repressor) is independently transcribed from its own promoter. The hutIG cluster appears not to form an operon. Curiously, insertions in hutI gave two different phenotypes in complementation tests against hutG504, suggesting either that hutI contains two functionally distinct domains or that there may be another undefined locus within the hut cluster. The set of Tn1000 insertions allowed an assignment of the gene boundaries within the hut cluster, and minicell analysis of the polypeptides expressed from plasmids carrying insertions in the hut genes showed that the hutI, hutG, hutU, and hutH genes encode polypeptides of 43, 33, 57, and 54 kilodaltons, respectively.

Cloning and nucleotide sequences of histidase and regulatory genes in the Bacillus subtilis hut operon and positive regulation of the operon

An 8-kilobase HindIII fragment carrying the histidase gene (hutH) and its regulatory region (hutP), from the Bacillus subtilis histidine utilization (hut) operon, was cloned in the temperate bacteriophage phi 105. Histidine utilization was restored in a hutH1 mutant by the specialized transducing phage (phi 105hutH11). The histidase gene in phi 105hutH11 was inducible and was shown to be under catabolite repression. The nucleotide sequence of 3,932 base pairs including the hutH and hutP loci revealed three open reading frames (ORFs). The molecular weights of ORF1 and ORF2 proteins were calculated to be 16,576 (151 amino acid residues) and 55,675 (508 amino acid residues), respectively. Reverse transcriptase mapping experiments showed that the putative promoter for the hut operon could be recognized by RNA polymerase sigma 43. The transcript starts at an adenosine residue 32 base pairs upstream from the initiation codon of ORF1. hutH+-transforming activity was found in ORF2, indicating that ORF2 encoded the histidase. A hutP1 mutation was determined as a substitution of an amino acid in ORF1. By using a specialized transducing phage containing the wild-type ORF1 gene, it was demonstrated that the presence of ORF1 protein in trans was absolutely required for the induction of the hut operon in a hutP1 mutant. These data strongly suggested that ORF1 encodes a positive regulator of the hut operon.

Role of Escherichia coli RecBC enzyme in SOS induction

Induction of the SOS genes is required for efficient repair of damaged DNA in Escherichia coli. SOS induction by nalidixic acid or oxolinic acid, two inhibitors of DNA gyrase, requires the RecBC enzyme of E. coli. We report here that the nuclease activity of RecBC enzyme is not needed for SOS induction by these agents. We suggest that the unwinding activity of RecBC enzyme produces single-stranded DNA which activates the RecA protein to stimulate LexA repressor cleavage and SOS induction.

Chi-dependent DNA strand cleavage by RecBC enzyme

Chi sites enhance in their vicinity homologous recombination by the E. coli RecBC pathway. We report here that RecBC enzyme catalyzes Chi-dependent cleavage of one DNA strand, that containing the Chi sequence 5'G-C-T-G-G-T-G-G3'. Chi-specific cleavage is greatly reduced by single base pair changes within the Chi sequence and by mutations within the E. coli recC gene, coding for a RecBC enzyme subunit. Although cleavage occurs preferentially with double-stranded DNA, the product of the reaction is single-stranded DNA. These results demonstrate the direct interaction of RecBC enzyme with Chi sites that was inferred from the genetic properties of Chi and recBC, and they support models of recombination in which Chi acts before the initiation of strand exchange.

A restriction enzyme cleavage map of the histidine utilization (hut) genes of Klebsiella aerogenes and deletions lacking regions of hut DNA

The histidine utilization (hut) operons of Klebsiella aerogenes were cloned into pBR322. The hut genes are wholly contained on a 7.9 kilobase pair fragment bounded by HindIII restriction sites and expression of hut is independent of the orientation of the fragment with respect to pBR322. A restriction map locating the 27 cleavage sites within hut for the enzymes, HindIII, PvuII, SalI, BglII, KpnI, PstI, SmaI, AvaI, and BamHI was deduced. Several of the cleavage sites for the enzymes HaeIII and HinfI were also mapped. A set of deletion plasmids was isolated by removing various restriction fragments from the original plasmid. These deletions were characterized and were used to assist in mapping restriction sites. This physical characterization of hut DNA opens the way for genetic and molecular analysis of the regulation of hut gene expression in vitro as well as in vivo.

Escherichia coli RecBC pseudorevertants lacking chi recombinational hotspot activity

Pseudorevertants of an Escherichia coli exonuclease V (RecBC enzyme)-negative mutant have been isolated after ethyl methane sulfonate mutagenesis of a recC73 (presumed missense) mutant. The remedial mutations in each of the four pseudorevertants studied in detail map and complement as recC mutations. By several criteria, such as recombination proficiency, support of phage growth, RecBC nuclease activity, and cell viability, the pseudorevertants appear to have regained partially or completely various aspects of RecBC activity. However, chi recombinational hotspots, which stimulate exclusively the RecBC pathway of recombination, have no detectable activity in lambda vegetative crosses in the pseudorevertants. The properties of these mutants, in which the RecBC pathway of recombination is active yet in which chi is not active, are consistent with the hypothesis that wild-type RecBC enzyme directly interacts with chi sites; alternatively, the mutants may block or bypass the productive interaction of another recombinational enzyme with chi.

Nucleotide sequence analysis of in vivo recombinants between bacteriophage lambda DNA and pBR322

The nucleotide sequences involved in the illegitimate recombination of four recombinants between bacteriophage lambda DNA and pBR322 in E. coli (lambda TA6, lambda KA3, lambda TA1R, and lambda KA7) were determined. Each resulted from recombination between regions of homology of 10 to 13 base pairs. The presence of a recA+ allele was found to stimulate recombination between lambda DNA and pBR322 approximately 10-fold. Lambda TA6, lambda KA3, and lambda KA7 were isolated in the presence of a recA+ allele and therefore, may have been generated by the recA recombination system. However, lambda TA1R was isolated in a recA mutant, and was presumably generated by a different recombination system. The possibility that it was generated by DNA gyrase is discussed. Two recombination events were required to form lambda KA7, which may indicate that it also was generated by DNA gyrase.

Physical maps of Klebsiella aerogenes and Salmonella typhimurium hut genes

The recognition sites for several restriction endonucleases were mapped within deoxyribonucleic acid coding for histidine utilization (hut) genes of Salmonella typhimurium and Klebsiella aerogenes. Deoxyribonucleic acid fragments containing the two hut promoters were identified by ribonucleic acid polymerase binding.

Introduction of bacteriophage lambda into cells of Klebsiella aerogenes

We have shown that a mutation in the cro gene of phage lambda greatly reduces zygotic induction. This observation has allowed us to move this phage on an episome into cells of Klebsiella aerogenes where it grows as well as in cells of Escherichia coli. This technique should allow the introduction of various derivatives of lambda into any organism which is able to receive deoxyribonucleic acid from E. coli.

Deletion analysis of the expression of rRNA genes and associated tRNA genes carried by a lambda transducing bacteriophage

Transducing phage lambdailv5 carries genes for rRNA's, spacer tRNA's (tRNA1 Ile and tRNA1B Ala), and two other tRNA's (TRNA1 Asp and tRNA Trp). We have isolated a mutant of lambdailv5, lambdailv5su7, which carries an amber suppressor mutation in the tRNA Trp gene. A series of deletion mutants were isolated from the lambdailv5su7 phage. Genetic and biochemical analyses of these deletion mutants have confirmed our previous conclusion (E. A. Morgan, T. Ikemura, L. Lindahl, A. M. Fallon, and M. Nomura, Cell 13:335--344, 1978) that the genes for tRNA1 Asp and tRNA Trp located at the distal end of the rRNA operon (rrnC) are cotranscribed with other rRNA genes in that operon. In addition, these deletions were used to define roughly the physical location of the promoter(s) of the rRNA operon carried by the lambdailv5su7 transducing phage.

Transcription of the hut operons of Salmonella typhimurium

We have measured, by ribonucleic acid-deoxyribonucleic acid hybrid formation, the amounts of hut-specific ribonucleic acid contained in extracts of various mutant strains of Salmonella typhimurium. Our data are consistent with a model in which regulation of Hut enzyme production occurs at the level of transcription and support earlier genetic evidence indicating that all of the hut genes are transcribed in the clockwise direction on the S. typhimurium chromosome. These results also suggest that promoter sites of the two hut operons may differ in their ability to initiate transcription.

Deoxyribonucleic acid-binding studies on the hut repressor and mutant forms of the hut repressor of Salmonella typhimurium

In Salmonella typhimurium the genes coding for the enzymes of histidine utilization (hut) are clustered in two adjacent operons, hutMIGC and hut(P,R,Q)UH. A single repressor, the product of the C gene, regulates both operons by binding at two operator sites, one near M and one in (P,R,Q). The deoxyribonucleic acid (DNA)-binding activity of the repressor was measured using DNA's containing separate operators. The repressor had greater activity when assayed using DNA containing the operator of the (P,R,Q)UH operon than when assayed using DNA containing the operator of the MIGC operon. The binding to either operator was absent in the presence of the inducer, urocanate. The DNA-binding activities were also determined for two super-repressors. The super-repressors had altered DNA-binding properties, although the self-regulated nature of the repressors complicated the analysis of the results. A purfication procedure for the wild-type repressor is presented. The purified repressor was somewhat unstable, and additional experiments using it were not performed.

Transduction of chromosomal genes between enteric bacteria by bacteriophage P1

We have used P1 transduction to create intergeneric hybrid strains of enteric bacteria by moving the genA and hut genes between Klebsiella aerogenes, Escherichia coli and Salmonella typhimurium. The use of E. coli as the recipient in such transductions permits the construction of episomes and specialized transducing phage containing non-E. coli material. The effect of host restriction modification and deoxyribonucleic acid homology on the frequency of intergeneric transduction of these loci has been examined.

Synthesis of ribosomal RNA in E. coli: analysis using deletion mutants of a lambda transducing phage carrying ribosomal RNA genes

Transducing phage lambdarifd18 carries on rRNA transcription unit containing genes for 5S, 16S, and 23S rNAs and also tRNAGlu/2. Mutants were isolated from this phage that carry deletions removing various amounts of the distal end of this transcription unit. These deletions were physically mapped on the lambdarifd18 phage genome. Synthesis of rRNAs and of tRNAGlu/2 was examined in ultraviolet-irradiated E. coli cells infected with lambdarifd18 or with various deletion mutants. It was observed that mutant phages in which the distal end (the 5S rRNA gene and a part of the 23S rRNA gene) of the rRNA transcription unit is deleted can still synthesize both 16S rRNA (or its precursor) and tRNAGlu/2. Apparently, the post-transcriptional cleavage that produces these RNA molecules does not require the presence of the entire transcription unit, that is, it can take place without the complete structure of the transcript ("30S pre-ribosomal RNA"). In addition, the experimental results support the gene order, 16S rRNAGlu/2, 23S rRNA, and 5S rRNA genes, in the rRNA transcription unit carried by lambdarifd18.

Identification of a gene for the alpha-subunit of RNA polymerase at the str-spc region of the Escherichia coli chromosome

A structural gene for the alpha-subunit of RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase; EC 2.7.7.6) has been identified and mapped between spcA and trkA, near 64 min on the E. coli chromosome. It appears to be coordinately expressed and possibly cotranscribed with the genes for ribosomal proteins S11, S4, and L17.

Transduction by phage P1CM clr-100 in Salmonella typhimurium

Phage P1 does not adsorb to S. typhinurium wild type cells. It does adsorb to rough derivatives including strains with mutations in the galE gene. Phage strain P1CM clr-100 can be efficiently propagated in S. typhimurium derivatives, either by induction of a lysogene, or by lytic infection. Phage P1 lysates are able to mobilize genetic markers in a generalized fashion. The transduction system is essentially identical to that in Escherichia coli, except that CaCl2 is not required for efficient adsorption. Two regions of the S. typhimurium chromosome were mapped by P1-mediated transduction. Several examples of genes linked by P1, and unlinked by P22, are presented. The relative efficiency of P1 over P22 in transduction was not determined, however. Data presented indicate unambigously that the gene order for the trp region is: his ... dad A-hem A-trp-pyrF ... pyrC but known markers in between were not used. The gene order for the cys A region was determined to be as follows: pheA ... purC-cys A-trz A-pts-dsd-aro D-purF ... his, and special mapping problems for this region are discussed.

Isolation of super-repressor mutants in the histidine utilization system of Salmonella typhimurium

Two super-repressor mutations in the histidine utilization (hut) operons of Salmonella typhimurium are described. Cells bearing either of these mutations have levels of hut enzymes that do not increase above the uninduced levels when growth is in the presence of either histidine or the gratuitous inducer imidazole propionate. Both mutations lie in the region of the gene for the hut repressor, hutC, and reverse mutations of both are to the constitutive (repressor-negative) rather than to the inducible (wild type) phenotype. In hybrid merodiploid strains the super-repressor mutations are dominant over either wild-type (hutC+) or repressor-negative (hutC-) alleles. Whereas both super-repressor mutations cause the uninducible synthesis of hut enzymes, the degree of repression is different. One mutation causes repression of enzyme synthesis in one of the two hut operons to a level below the basal, uninduced level of wild-type cells. The other mutation causes repression to a lesser degree than in wild-type cells, so that the hut enzymes are present at a level above the normal basal level; this partially constitutive synthesis is greater for the enzymes of one of the hut operons than for the enzymes of the other. Thus, both mutations apparently result in repressors with altered operator-binding properties, in addition to altered inducer-binding properties.

Isolation of a trans-dominant histidase-negative mutant of Salmonella typhimurium

A mutation of Salmonella typhimurium was obtained that results in the failure of cells to synthesize the enzyme l-histidine ammonia-lyase (histidase). The mutation mapped within the hutH gene and in merodiploid strains was dominant over the wild-type allele. Extracts from cells bearing the trans-dominant histidase-negative allele were shown to contain material that reacts immunologically with antiserum against purified wild-type histidase. It is proposed that the trans-dominant allele results in the synthesis of defective histidase subunits that can combine with, and partially inactivate, wild-type histidase subunits. This subunit mixing presumably does occur, as the enzyme synthesized in a hybrid merodiploid strain is abnormally heat sensitive.

Autogenous regulation of gene expression

A new term, autogenous regulation, is used to describe a phenomenon that is not a new discovery but rather is newly appreciated as a mechanism common to a number of systems in both prokaryotic and eukaryotic organisms. In this mechanism the product of a structural gene regulates expression of the operon in which that structural gene resides. In many (perhaps all) cases, the regulatory gene product has several functions, since it may act not only as a regulatory protein but also as an enzyme, structural protein, or antibody, for example. In a few cases, this protein is the multimeric allosteric enzyme that catalyzes the first step of a metabolic pathway, gearing together the two most important mechanisms for controlling the biosynthesis of metabolites in bacterial cells-feedback inhibition and repression. Autogenous regulation may provide a mechanism for amplification of gene expression (84); for severe and prolonged inactivation of gene expression (85); for buffering the response of structural genes to changes in the environment (45, 52); and for maintaining a constant intracellular concentration of a protein, independent of cell size or growth rate (86). Thus, autogenous regulation provides the cell with means for accomplishing a number of different regulatory tasks, each suited to better satisfying the needs of the organism for its survival.

Activation of transcription of hut DNA by glutamine synthetase

The correct transcription of the hut (histidine utilization) operon DNA of Salmonella typhimurium requires activation either by 3':5'-cyclic adenosine monophosphate and catabolite-activating protein or by nonadenylylated glutamine synthetase (EC 6.3.1.2.). Thus, glutamine synthetase plays a regulatory role distinct from its enzymatic function.

Isolation of the self-regulated repressor protein of the Hut operons of Salmonella typhimurium

In Salmonella typhimurium the structural genes of the enzymes responsible for histidine utilization (hut) are clustered in two adjacent operons. A single repressor regulates both operons. The repressor itself is a member of one of the hut operons and, thus, regulates its own synthesis. We have assayed the hut repressor by its ability to bind radioactive DNA to nitrocellulose filters. The binding is specific for DNA bearing the hut operons, and the binding is abolished by the inducer, urocanate. As a member of one of the hut operons, the repressor is inducible, subject to catabolite repression, and affected by a promoter mutation.

Lytic replication of coliphage lambda in Salmonella typhosa hybrids

Hybrids between Escherichia coli K-12 and Salmonella typhosa which conserved a continuous K-12 chromosomal diploid segment extending from pro through ara to the strA locus were sensitive to plaque formation by wild-type lambda. These partially diploid S. typhosa hybrids could be lysogenized with lambda and subsequently induced to produce infectious phage particles. When the K-12 genes were segregated from a lysogenic S. typhosa hybrid, phage-productive ability was no longer detectable due to loss of a genetic region necessary for vegetative replication of lambda. However, lambda prophage was shown to persist in a quiescent state in the S. typhosa hybrid segregant with phage-productive ability being reactivated after replacement of the essential K-12 lambda replication region. Low-frequency transduction and high-frequency transduction lysates containing the gal(+) genes of S. typhosa were prepared by induction of lambda-lysogenic S. typhosa hybrids indicating that the attlambda site is chromosomally located in S. typhosa in close proximity to the gal locus as in E. coli K-12. After propagation in S. typhosa hybrids, lambda was subject to restriction by E. coli K-12 recipients, thus establishing that S. typhosa does not perform the K-12 modification of lambda deoxyribonucleic acid. Hybrids of S. typhosa, however, did not restrict lambda grown previously on E. coli K-12. The K-12 genetic region required for lambda phage production in S. typhosa was located within min 66 to min 72 on the genetic map of the E. coli chromosome. Transfer of an F-merogenote encompassing the 66 to 72 min E. coli chromosomal region to lambda-insensitive S. typhosa hybrids enabled them to replicate wild-type lambda. The lambda-insensitive S. typhosa hybrid, WR4255, which blocks lambda replication, can be mutagenized to yield mutant strains sensitive to lambdavir and lambdaimm434. These WR4255 mutants remained insensitive to plaque formation by wild-type lambda.