Orientation of prophage Mu

Transposable Bacteriophages as Genetic Tools

Phage Mu is the paradigm of a growing family of bacteriophages that infect a wide range of bacterial species and replicate their genome by replicative transposition. This molecular process, which is used by other mobile genetic elements to move within genomes, involves the profound rearrangement of the host genome [chromosome(s) and plasmid(s)] and can be exploited for the genetic analysis of the host bacteria and the in vivo cloning of host genes. In this chapter we review Mu-derived constructs that optimize the phage as a series of genetic tools that could inspire the development of similarly efficient tools from other transposable phages for a large spectrum of bacteria.

Chromosomal gene transfer during conjugation by Staphylococcus aureus is mediated by transposon-facilitated mobilization

A chromosomal copy of the transposon Tn551 and a copy coresident on a gentamicin-resistant conjugative plasmid of Staphylococcus aureus resulted in the mobilization of chromosomal genes during filter mating. Gene mobilization was recA dependent and was not restricted to any specific region of the chromosome. Both essential and nonessential genes were transferred.

Integration of the bacteriophage HP1c1 genome into the Haemophilus influenzae Rd chromosome in the lysogenic state

Restriction fragments hybridizing to phage HP1c1 DNA were identified in digests of DNA from lysogenic strains of Haemophilus influenzae. The results showed that the cohesive ends of the mature phage DNA were joined in lysogens and that the phage genome was covalently linked to the host DNA, indicating that lysogeny involves recombination between specific sites on the phage and host chromosomes. The site on the phage chromosome at which this recombination occurred was between 110 and 750 base pairs of the left end on the mature phage genome.

Orientation and sequence analysis of right ends and target sites of bacteriophage mu and D108 insertions in the plasmid pSC101

We have isolated four independent insertions of the entire 37-kb D108cts 10 genome in the low-copy-number plasmid pSC101 in vivo. They were all formed by replicative transposition during the D108 lytic cycle. The orientation of these four insertions was found to be the same, with the left ends facing towards pSC101 replication, and the right end facing in the direction of all pSC101 transcription, as was previously found for a Mucts62 insertion in pSC101, pMC321. The exact sites of insertion of two of the D108 prophages, as well as the Mu prophage, have been determined by sequence analysis. All three insertions caused a 5-bp duplication of pSC101 sequences at the target site, as has been found for insertions formed by conservative integration upon lysogeny. Moreover, we have determined the nucleotide sequence of the first 75 bp of the right end of D108 and, though this end is interchangeable with the right end of Mu as a substrate for either phage's transposition functions, there are a number of nucleotide differences between them.

Chromosomal mapping in Erwinia carotovora subsp. carotovora with the IncP plasmid R68::Mu

Conjugational gene transfer was established in Erwinia carotovora subsp. carotovora SCRI193 by using plasmid R68::Mu c+ to mobilize the chromosome into multiply mutant recipients. It was observed that although the plasmid alone mobilized markers randomly at a frequency of ca. 10(-5) chromosomal recombinants per donor, the presence of a Mu prophage on the chromosome of the donor increased the frequency of mobilization of markers adjacent to the prophage by up to 10-fold. Using this system it was possible to order 17 chromosomal mutations. The behavior of Mu in E. carotovora subsp. carotovora was also studied.

glnF-lacZ fusions in Escherichia coli: studies on glnF expression and its chromosomal orientation

The regulatory gene, glnF, of Escherichia coli was fused to the structural genes of the lac operon by use of the hybrid Mu phage derivative Mudl (Ap lac). Analysis of two of these fusions showed that the glnF gene is expressed constitutively, i.e., independent of either the nitrogen source in the growth medium or the availability of the glnA, glnL, glnG or glnF functional gene products. The orientation of the Mud1 (Ap lac) insertions was determined by chromosome mobilization in F-merogenotes carrying either of the two glnF::Mud1 chromosomal insertions isolated, and either one of a pair of F'lacZ::Mucts62 episomes; the two episomes differing in that their Mucts62 insertions are located in opposite orientations with regard to lacZ. The direction of chromosome mobilization by the Hfrs that were probably formed via Mu homology demonstrated that orientation of the glnF gene is clockwise relative to that of the chromosome.

Determination of the transcription direction of the exuT gene in Escherichia coli K-12: divergent transcription of the exuT-uxaCA operons

The exuT gene of Escherichia coli, coding for the hexuronate transport system, was fused to lac genes by the use of Mu d(Apr lac) insertions (M. J. Casadaban and S. Cohen, Proc. Natl. Acad. Sci. U.S.A. 76:4530-4533, 1979). The method of chromosome mobilization with F' lac::Mu episomes (J. B. Zeldis, A. I. Bukhari, and D. Zipser, Virology 55:289-294, 1974) made it possible to determine the transcription direction of the exuT gene from the orientation of the Mu d(Apr lac) insertion in the fusion strains. Our results for a exuT-lac fusion strain suggest that the direction of transcription of other single gene operon exuT is clockwise on the standard E. coli map and confirm that the direction of transcription of uxaC is counterclockwise. The two close operons exuT and uxaCA are thus transcribed in opposite directions.

rho Mutations restore lamB expression in E. coli K12 strains with an inactive malB region

lamB, the structural gene for lambda receptor, is the second gene of the malK-lamB operon in the malB region of the Escherichia coli K12 chromosome. lamB is essentially not expressed in the absence of an active malT gene product, the activator of the maltose regulon. A malT strain is resistant to phage lambda. We show that: (i) Introduction of rho mutations in malT mutants restores lamB expression to a level sufficient to render the strain sensitive to phage lambda; (ii) This restoration is not dependent on the main promoter of the malK lamB operon. It depends on the distal part of the malK gene. We propose that rho inactivation unmasks the activity of a promoter located near the distal end of malK. Experiments with Mu insertions in gene malK suggest that in the (-) orientation a Mu promoter is also able to allow lamB expression in a rho background.

Vibrio cholerae conjugative plasmid pSJ15 contains transposable prophage dVcA1

Evidence is presented that defective prophage dVcA1 in Vibrio cholerae strain 162 was transposed to the hybrid P::Tn1 plasmid pSJ5. Properties of the resulting conjugative plasmid, pSJ15, indicated that bacteriophage VcA1, like coliphage Mu, can insert at many sites. By analogy with other Hfr-like donors, the high-frequency, polarized chromosomal transfer mediated by plasmid pSJ15 in strain 162 appeared to depend on plasmid integration through the homologous dVcA1 sequences in both replicons. When strain 162(pSJ15) donors were mated to the nonlysogenic El Tor strain RJ1, many potential ampicillin-resistant transconjugants were zygotically induced. However, surviving transconjugants (i) were immune to phage VcA1, (ii) cotransferred immunity and ampicillin resistance to nonlysogenic recipients, and (iii) did not preferentially transfer any chromosomal markers. Recombinant plasmids that transferred wild-type VcA1 prophages were readily isolated from strain RJ1 (VcA1+) lysogens that contained plasmid pSJ15. Physical measurements revealed that plasmid pSJ15 and the recombinant plasmids were about one VcA1 genome (22 to 24 megadaltons) larger than the 51-megadalton pSJ5 plasmid. Similar Hfr-like donors were constructed by introducing plasmid pSJ15 into different strain RJ1 (VcA1+) lysogens. Transfer properties of these donors indicated that the VcA1 prophage was integrated at several sites in the strain RJ1 chromosome.

Fusion of the lac genes to the promotor for the cytidine deaminase gene of Escherichia coli K-12

Phage Mu has been inserted into the structural gene for cytidine deaminase (cdd). By the use of phage lambda (lac, Mu) the promoter for the cdd gene has been fused to lacZ. In these strains lacZ expression is regulated by the cytR repressor protein and is therefore induced by cytidine. The fusion strains were used for the isolation of cddo mutants. Plaque forming lambda phages carrying the different cdd-lacZ fusions were isolated. Studies of the cdd-Mu strains showed that the cdd gene is transcribed clockwise with respect to the Escherichia coli map.

Introduction of bacteriophage Mu into bacteria of various genera and intergeneric gene transfer by RP4::Mu

The host range of coliphage Mu was greatly expanded to various genera of gram-negative bacteria by using the hybrid plasmic RP4::Mu cts, which is temperature sensitive and which confers resistance to ampicillin, kanamycin, and tetracycline. These drug resistance genes were transferred from Escherichia coli to members of the general Klebsiella, Enterobacter, Citrobacter, Salmonella, Proteus, Erwinia, Serratia, Alcaligenes, Agrobacterium, Rhizobium, Pseudomonas, Acetobacter, and Bacillus. Mu phage was produced by thermal induction from the lysogens of all these drug-resistant bacteria except Bacillus. Mu phage and RP4 or the RP4::Mu plasmid were used to create intergeneric recombinant strains by transfer of some genes, including the arylsulfatase gene, between Klebsiella aerogenes and E. coli. Thus, genetic analysis and intergeneric gene transfer are possible in these RP4::Mu-sensitive bacteria.

Transposition of Tn 1 to the Rhizobium meliloti genome

A derivative of the IncP1 plasmid RP4, carrying the thermoinducible prophage Mucts62, was obtained in Escherichia coli K12 J53 (RP4). It was impossible to maintain the hybrid plasmid RP4::Mucts62 in Rhizobium meliloti GR4. Thus, it was used as a vehicle for introducing the ampicillin-resistant transposon Tn1 into the R. meliloti genome. Transposition of Tn1 did not generate auxotrophic strains, suggesting that the insertion of Tn1 into the R. meliloti genome was relatively specific. Two chromosomal hot spots for Tn1 insertion were identified by cotransductional analysis, after general transduction by phage DF2. Plasmid-curing experiments, carried out by heat treatment, revealed that symbiotic plasmid(s) also contain at least one site for Tn1 insertion.

Use of lambda pMu bacteriophages to isolate lambda specialized transducing bacteriophages carrying genes for bacterial chemotaxis

A general method for constructing lambda specialized transducing phages is described. The method, which is potentially applicable to any gene of Escherichia coli, is based on using Mu DNA homology to direct the integration of a lambda pMu phage near the genes whose transduction is desired. With this method we isolated a lambda transducing phage carrying all 10 genes in the che gene cluster (map location, 41.5 to 42.5 min). The products of the cheA and tar genes were identified by using transducing phages with amber mutations in these genes. It was established that tar codes for methyl-accepting chemotaxis protein II (molecular weight, 62,000) and that cheA codes for two polypeptides (molecular weights, 76,000 and 66,000). Possible origins of the two cheA polypeptides are discussed.

Inversion induced by temperature bacteriophage mu-1 in the chromosome of Escherichia coli K-12

Induction of the Mu prophage of a lysogenic HfrP4X strongly stimulates the early transfer of the purE gene, which is located far from the origin of transfer. By using a rec- Mu cts62 X lysogenic donor, it was established that this process reflects the inversion of the origin of transfer in part of the Hfr population. Hfr's with inverted polarity of gene transfer were isolated; their analysis suggests that two Mu genomes in opposite orientation surround the inverted DNA fragment. Due to the presence of the Mu genome of the invertible G segment, homologous regions in the same orientation can appear in Mu genomes in opposite orientation. In a Rec+ background, Hfr's with inverted polarity (i) return to their original polarity of transfer by recomination between the two inverted Mu and (ii) produce new F' strains by recombination between the two similarly oriented G segments.

Transposon-facilitated recombination in Vibrio cholerae

Improved Vibrio cholerae donors were constructed by introducing the ampicillin transposon, Tn1, into both the conjugative plasmid, P, and the bacterial chromosome to provide "portable regions of homology." The resulting Tfr (Transposon-facilitated recombination) donors transferred genes at high frequency from origins specified by the chromosomally inserted Tn1 copies. Tn1 was transposed into the chromosome from a deleted P::Tn1 vector, which was eliminated from the cells by superinfection with a thermosensitive P::Tn9 (chloramphenicol) mutant plasmid. After eliminating the thermosensitive plasmid, the chromosomally resistant isolates were converted into donors with a P::Tn1 conjugative plasmid. Tfr donors were also obtained by isolating Tn1 insertion mutations in a gene for thymine biosynthesis. Chromosomal sites of Tn1 relative to bacterial genes were determined by measuring gene transfer frequencies and genetic linkage. In one case, linkage of the amp gene to the chromosomal genes that defined its location was demonstrated. Chromosomal transfer by Tfr donors was reversed by isolating P::Tn1 plasmids that contained Tn1 inserted in the opposite orientation.

Use of argA-lac fusions to generate lambda argA-lac bacteriophages and to determine the direction of argA transcription in Escherichia coli

Fusions of lac genes to the argA operator were constructed, and lambda phages carrying these fusions were isolated and characterized. With the aid of a lambda phage carrying an argA-lac fusion, the direction of argA transcription on the Escherichia coli chromosome was determined to be clockwise.

Mutational alteration of a nitrogen-fixing bacterium to sensitivity to infection by bacteriophage Mu: isolation of nif mutations of Klebsiella pneumoniae M5al induced by Mu

The nitrogen-fixing bacterium Klebsiella pneumoniae M5al is not sensitive to infection by bacteriophage Mu. A mutant of K. pneumoniae that is sensitive to Mu infection was isolated. Several Mu-induced auxotrophic mutations of K. pneumoniae including nif, trp, and rtl were isolated and genetically characterized. Evidence is presented that the Mu-induced mutations of nif arise as the result of insertion of Mu within (or near) the nif operon(s). The rtl locus, which determines the ability to utilize ribitol as a carbon source, was found to be linked to nif loci.

Conversion of beta-galactosidase to a membrane-bound state by gene fusion

We have isolated a series of strains in which the lacZ gene has been fused to one of the maltose operons, such that the synthesis of beta-galactosidase (beta-D-galactoside galactohydrolase; EC 3.2.1.23) is inducible by maltose. The most frequent event that generates such fusions results in strains in which an intact lacZ gene has become a part of the malE,F operon. By using a special selection procedure, we have detected much rarer fusion events resulting in an altered beta-galactosidase molecule. In these strains, we presume that there is a hybrid protein molecule produced, comprised of an NH2-terminal amino acid sequence from a maltose transport protein (malF) and a COOH-terminal amino acid sequence from beta-galactosidase. The hybrid protein, which still retains some beta-galactosidase activity, is found in the cytoplasmic membrane. These results provide information on the component of the malF gene essential for incorporation of its product into the membrane.

Model for the enchancement of lambde-gal integration into partially induced Mu-1 lysogens

Temperate phage Mu-1, which is able to integrate at random in its host chromosome, is also able to mediate integration of other circular deoxyribonucleic acid, as a lambda-gal mutant unable to integrate by itself. After mixed infection with lambda-gal and Mucplus, galplus transductants are recovered that have the lambda-gal integrated in any circular permutation, sandwiched between two complete Mu genomes in the same orientation, the whole Mu-lambda-gal-Mu structure being found at any location in the bacterial chromosome. Here we show that such a lambda-gal can integrate in an induced Mu lysogen. In this case the lambda-gal is again in any circular permutation, between two Mu in the same orientation, but it is always located at the site of the original Mu prophage, and the two surrounding Mu have always the same genotype as the original Mu prophage. Active Mu replication functions are not essential for that process to occur. This suggests that bacterial replication may generate two Mu copies that in some way can regenerate a Mu attachment site that recombines with the lambda-gal. A model is presented that accounts for these observations, may be helpful for understanding some complex features of Mu development, and may possibly offer a basis for explaining spontaneous duplications.