Toward a bacterial genome technology: integration of theEscherichia coli prophage lambda genome into theBacillus subtilis 168 chromosome

A novel approach to the cloning large DNAs in theBacillus subtilis chromosome was examined. AnEscherichia coli prophage lambda DNA (48.5 kb) was assembled in the chromosome ofB. subtilis. The lambda DNA was first subcloned in four segments, having partially overlapping regions. Assembly of the complete prophage was achieved by successive transformation using three discrete DNA integration modes: overlap-elongation, Campbell-type integration, and gap-filling. In theB. subtilis chromosome, DNA was elongated, using contiguous DNA segments, via overlap-elongation. Jumping from one end of a contiguous DNA stretch to another segment was achieved by Campbell-type integration. The remaining gap was sealed by gap-filling. The incorporated lambda DNA thus assembled was stably replicated as part of the 4188 kbB. subtilis chromosome under non-selective conditions. The present method can be used to accommodate larger DNAs in theB. subtilis chromosome and possible applications of this technique are discussed.     

Mutagenesis during transformation of Bacillus subtilis I. An increase in “selfing” resulting from hybrid donor DNAs

Reverse mutations increase when competent Baciilus subtilis cells are transformed with high concentrations of homologous “selfer” DNA. A high proportion of the mutants were also transformants of linked genes. A stimulation in the appearance of reversed mutations occurred when homoduplex and heteroduplex “selfer” DNAs were used as donors. Digestions of native and hybrid DNAs with nuclease S1 from Aspergillus oryzae resulted in the preferential decrease of mutations as compared to a much smaller inactivation of single marker tranformation. Among various repair-deficient strains of B. subtilis, only polyA mutants showed a preferential effect of either suppressing or stimulating the frequency of reverse mutation induced by “selfer” DNA. The results are consistent with mutagenic errors occurring during gap-filling steps in the process of either mismatch repair or recombinational strand exchanges.     

A method to maintain introduced DNA sequences stably and safely on the bacterial chromosome: application of prophage integration and subsequent designed excision

By application of prophage integration and subsequent intended excision, a method to maintain an introduced DNA sequence stably onto a bacterial chromosome has been proposed. Recently-constructed integration plasmids using Campbell-type prophage integration system in Lactobacillus casei strain Shirota and its temperate phage phi FSW was modified for this purpose and a chloramphenicol (Cm)-resistance gene was used as a model passenger DNA. On the integration plasmid having an erythromycin (Em)-resistance gene as a selection marker, N- and C-terminally-truncated Cm-resistance genes were inserted into both sides of the attP of phi FSW, within which the site-specific recombination took place with the attB of phi FSW on the recipient chromosome through the phi FSW integrase. Primary integrants of the modified plasmid (integration-excision vector) exhibiting Em-resistant and Cm-sensitive phenotype generated Em-sensitive and Cm-resistant derivatives under the nonselective conditions. Sequence analyses showed that one copy of the complete Cm-resistance gene resided at the attachment site on the host chromosome and the other vector-derived sequences were excised probably by endogenous homologous recombination in the host cells to derive final integrants. The Cm-resistant phenotype of the final integrants was stable for more than 50 generations under non-selective conditions. Frequency of the homologous recombination suggests that negative selection is also adoptable. Thus, this method using the integration-excision vector gives a stable and safe derivatives of the strain and is likely to be applicable to various bacteria, since Campbell-type prophage integration system and homologous recombination are prevalent among bacteria.     

Reconstitution of an operon from overlapping fragments: use of the lambda SV2 integrative cloning system

We have used the lambda SV2 system [Howard and Gottesman. In Gluzman (Ed.), Eukaryotic Viral Vectors. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1982, pp. 211-216; in Inouye, M. (Ed.) Experimental Manipulations of Gene Expression. Academic Press, New York, 1983, pp. 137-153] to reconstitute the Salmonella typhimurium his operon from overlapping fragments. lambda SV2 can be propagated as an autonomously replicating plasmid or as a prophage integrated in the Escherichia coli chromosome at the lambda attachment site; our reconstitution was accomplished in the integrated state. We first inserted a portion of the his operon into lambda SV2 and integrated the resulting plasmid by site-specific recombination into the E. coli chromosome. This was achieved by brief induction of a resident prophage. The lysogen was then transformed with DNA from a lambda SV2 clone carrying the remainder of the his operon on an overlapping DNA fragment. The second plasmid was forced to integrate into the first by homologous recombination. When this recombination occurs at the his overlap, a lysogen carrying two lambda SV2 prophages is produced. One prophage carries the entire his operon and the other carries the his overlap region. The latter is removed by site-specific recombination, permitting further contiguous sequences to be sequentially added to the remaining prophage. This method should be applicable for the reconstitution and maintenance of large genes or gene clusters in the E. coli genome.     

Conversion of sub-megasized DNA to desired structures using a novel Bacillus subtilis genome vector

A novel genome vector using the 4215 kb Bacillus subtilis genome provides for precise target cloning and processing of the cloned DNA to the desired structure. Each process highly dependent on homologous recombination in the host B.subtilis is distinguished from the other cloning systems. A 120 kb mouse jumonji (jmj) genomic gene was processed in the genome vector to give a series of truncated sub-megasized DNA. One of these truncated segments containing the first intron was copied in a plasmid by a recombinational transfer method developed for B.subtilis. DNA manipulation previously considered difficult is argued with respect to DNA size and accuracy.     

DNA-Mediated Prophage Induction in Bacillus subtilis Lysogenic for φ105c4

Prophage was induced when strains of Bacillus subtilis 168 lysogenic for 105c4 were grown to competence and exposed to specific bacterial DNAs. The time course of phage production was similar to that observed for mitomycin C induction of wild-type prophage. Induction was directly dependent upon DNA concentration up to levels which were saturating for the transformation of bacterial auxotrophic markers. The extent of induction varied with the source of DNA. The burst of phage induced by DNA isolated from a W23 strain of B. subtilis was fivefold less than that induced by DNA from B. subtilis 168 strains, while B. licheniformis DNA was completely inactive. This order of inducing activity was correlated with the ability of the respective DNAs to transform auxotrophic markers carried by one of the 105c4 lysogens. Differences in inducing activity also were observed for different forms of 105 DNA. The DNAs isolated from 105 phage particles and 105c4 lysogens were inactive, whereas DNA from cells lysogenized by wild-type 105 induced a burst of phage. When tested for transforming activity, however, both 105c4 and 105 lysogen DNAs were equally effective. An induction mechanism which involves recombination at the prophage insertion site is proposed to explain these differences.     

Genetic Transfer of Large DNA Inserts to Designated Loci of the Bacillus subtilis 168 Genome

It was found that contiguous DNA segments of up to 50 kb can be transferred between Bacillus subtilis genomes when a sufficient length of the flanking genomic region is provided for homologous recombination, although the efficiency of transfer was reduced as the insert size increased. Inserts were translocated to different loci, where appropriate integration sites were created.     

Integration of repeated sequences (pBR322) in the Bacillus subtilis 168 chromosome without affecting the genome structure

The Escherichia coli plasmid pBR322 sequence (4363 bp) was integrated at the met, pro, or leuB locus of the Bacillus subtilis chromosome without duplication of the flanking chromosomal regions. The integrated pBR322 was stably maintained as part of the chromosome regardless of its orientation or location. It was found that a DNA segment as large as 17 kb cloned in pBR322 can be readily transferred to the B. subtilis chromosome by transformation. It was demonstrated that a second pBR322 sequence could be effectively introduced at different regions of the chromosome by sequential transformation using chromosomal DNA isolated from a strain that had already acquired a pBR322 sequence at a different locus. Similarly, a third pBR322 sequence could be introduced. By this method, two or three pBR322 sequences can be incorporated at unlinked loci without affecting the overall structure of the B. subtilis genome.     

Mechanism of non-tandem integration of prophage phi 80 into the chromosome of the wild-type Escherichia coli

We studied the ability of lambda, phi 80 and their hybrid lambda att80 to lysogenize homoimmune monolysogens and examined the prophage locations on the chromosome of the resulting polylysogens. We observed an effective integration of phi 80 and lambda att80, in contrast to lambda, into the host chromosome, exclusively, at the attachment sites that were not occupied by the resident prophage (nontandem). Besides, the lambda att80 (int+) prophage was observed to ensure effective nontandem integration of a homoimmune int mutant DNA. Hence, we inferred that the expression of the int gene in the phi 80 prophage is constitutive, cI-independent and results in nontandem integration of the homoimmune prophage. The validity of this inference has been supported experimentally: (i) the only lysogen that was found to contain a phi 80 tandem was highly unstable (spontaneous segregation of monolysogens occurred 6-7 times more frequently than with the lambda tandem); (ii) an int inactivating mutation stabilized the phi 80 tandem; as a result, the int mutant has the frequency of tandem integration as high as that of lambda, while no nontandem integration was observed. A hypothesis is proposed which accounts for the instability of the phi 80 tandems and explains the relation between this phenomenon and the prophage ability to integrate into secondary attachment sites in the presence of the primary (normal) one.     

Members of the pogo superfamily of DNA-mediated transposons in the human genome

Bacillus subtilis, likeEscherichia coli, possesses several sets of genes involved in the utilization ofβ-glucosides. InE. coli, all these genes are cryptic, including the genes forming thebgl operon, thus leading to a Bgl^? phenotype. We screened forB. subtilis chromosomal DNA fragments capable of reverting the Bgl⁺ phenotype associated with anE. coli hns mutant to the Bgl^? wild-type phenotype. OneB. subtilis chromosomal fragment having this property was selected. It contained a putative Ribonucleic AntiTerminator binding site (RAT sequence) upstream from thebglP gene. Deletion studies as well as subcloning experiments allowed us to prove that the putativeB. subtilis bglP RAT sequence was responsible for the repression of theE. coli bgl operon. We propose that this repression results from the titration of the BglG antiterminator protein ofE. coli bgl operon by our putativeB. subtilis bglP RAT sequence. Thus, we report evidence for a new cross interaction between heterologous RAT-antiterminator protein pairs.     

Electron microscope study of the structures of the Bacillus subtilis prophages, SPO2 and phi105

Circular duplex structures of the correct length are observed in the electron microscope in hybridization mixtures of lysogen DNA and mature phage DNA for the case of the temperate Bacillus subtilis bacteriophage SPO2. This result shows that the sequence order of the prophage is a circular permutation of that of the mature phage. By making heteroduplexes of prophage DNA with that of the SPO2 deletion mutants, R90 and S25, the att site of the phage has been mapped at 61.2 ± 0.6% from one end of the mature phage DNA, which has a length of 38,600 base pairs. In the same co-ordinate system, the R90 deletion extends from 58.9 ± 0.7 to 66.8 ± 0.8% on the SPO2 chromosome, whereas the S25 deletion extends from 63.2 ± 0.6 to 66.9 ± 0.7%. In similar experiments with lysogen and mature phage DNA's of the temperate B. subtilis phage, φ105, no circular structures were seen. This result shows that the sequence order in the prophage and the phage are colinear, without circular permutation.     

Construction of recombinant plasmid carrying the lambda DNA fragment responsible for prophage integration.

The recombinant DNA molecules were constructed from plasmid RSF2124 and the EcoRI fragment of lambda DNA containing the genes responsible for prophage integration. The presence of these genes in recombinant plasmids was detected genetically. lambda int-gene was shown to be expressed in either orientation of insertion in the plasmid. We found that recombinant plasmid was able to integrate into chromosome of lambda lysogens. The integration of plasmid into host chromosome was demonstrated by contransduction of chromosome and plasmid markers using generalized transducer P1 and by specialized transduction with lambda phages.     

Two-dimensional display of lambda and Escherichia coli restriction fragments separated by Hg-Cs2SO4 centrifugation and gel electrophoresis

EcoRI restriction fragments derived from the DNA of bacteriophage lambda and Escherichia coli were fractionated by density gradient centrifugation of their mercury complexes in Cs2SO4 and subsequent electrophoresis on a horizontal agarose-gel slab. In this two-dimensional display, lambda fragments were resolved into six components and E coli fragments into more than 108 components. Bacterial chromosome regions contiguous to lambda prophage integrated at different sites were amplified by induction, and the EcoRI fragments were subjected to the two-dimensional analysis. As expected, the sets of amplified fragments were clearly different among the various lysogens. The approximate genome region affected by induction was estimated as one-tenth of the whole chromosome.     

Prophage lambda induces terminal recombination in Escherichia coli by inhibiting chromosome dimer resolution. An orientation-dependent cis-effect lending support to bipolarization of the terminus

A prophage lambda inserted by homologous recombination near dif, the chromosome dimer resolution site of Escherichia coli, is excised at a frequency that depends on its orientation with respect to dif. In wild-type cells, terminal hyper- (TH) recombination is prophage specific and undetectable by a test involving deletion of chromosomal segments between repeats identical to those used for prophage insertion. TH recombination is, however, detected in both excision and deletion assays when Deltadif, xerC, or ftsK mutations inhibit dimer resolution: lack of specialized resolution apparently results in recombinogenic lesions near dif. We also observed that the presence near dif of the prophage, in the orientation causing TH recombination, inhibits dif resolution activity. By its recombinogenic effect, this inhibition explains the enhanced prophage excision in wild-type cells. The primary effect of the prophage is probably an alteration of the dimer resolution regional control, which requires that dif is flanked by suitably oriented (polarized) stretches of DNA. Our model postulates that the prophage inserted near dif in the deleterious orientation disturbs chromosome polarization on the side of the site where it is integrated, because lambda DNA, like the chromosome, is polarized by sequence elements. Candidate sequences are oligomers that display skewed distributions on each oriC-dif chromosome arm and on lambda DNA.     

Mechanism of transformation in B. subtilis

Summary Transformation in B. subtilis is achieved by the uptake of donor DNA into recipient cells and the integration of part of this donor DNA into the host chromosome. The evidence presented in this report is interpreted to indicate that donor double helical DNA, on entry into host cells is rapidly membrane bound and can remain in this state for a consicerable time, perhaps even until integration. This bound DNA consists of molecules which have been reduced in size and degraded on uptake, and appear as partially single-stranded molecules. It is suggested that the donor DNA initially forms single strands which rapidly assume a partially single stranded nature by association with the host DNA or by reannealing.Host cells, by virtue of the competent state, possess temporarily, and prior to the addition of donor DNA, chromosomes with single-stranded gaps. It is likely that such gaps are larger than the single-stranded segments of donor DNA which are to be integrated. Results are described which are best explained if integration is achieved by an initial annealing between the single-stranded donor and host segments followed by their covalent linkage.     

Isolation of Plaque-Forming, Galactose-Transducing Strains of Phage Lambda

Plaque-forming, galactose-transducing lambda strains have been isolated from lysogens in which bacterial genes have been removed from between the galactose operon and the prophage by deletion mutation.—A second class has been isolated starting with a lysogenic strain which carries a deletion of the genes to the right of the galactose operon and part of the prophage. This strain was lysogenized with a second lambda phage to yield a lysogen from which galactose-transducing, plaque-forming phages were obtained. These plaque-forming phages were found to be genetically unstable, due to a duplication of part of the lambda chromosome. The genetic instability of these partial diploid strains is due to homologous genetic recombindation between the two identical copies of the phage DNA comprising the duplication. The galactose operon and the duplication of phage DNA carried by these strains is located between the phage lambda P and Q genes.     

DNA amplification occurs between the core region of replicationori + of the ts plasmid integrated in the chromosome and its analog in the bacterial genome

Integrated in theBacillus subtilis chromosome, hybrid plasmid pGG10 is capable of thermosensitive amplification. One amplification site corresponds to the core region of replicationori ⁺ of pE194, a component of pGG10; the other is a homologous region of theB. subtilis chromosome. A model of illegitimate amplification mediated by pE194 RepF is proposed.     

Electroporation is a feasible method to introduce circularized or linearized DNA into <Emphasis Type="Italic">B. subtilis</Emphasis> chromosome

Here, we present the electroporation as a feasible and efficient method for introducing circularized and linearized DNA into Bacillus subtilis chromosome. Two integration experiments were carried out and demonstrated the feasibility and efficiency of electroporation to introduce the target DNA into the B. subtilis chromosome. By using of electroporation, a multiple-cistron contained five genes from B. subtilis biotin biosynthetic pathway was introduced into the B. subtilis chromosome efficiently and created a repeated copy in chromosome via a single crossover event. Then an ectopic promoter was introduced conveniently into the upstream of one of the repeated multiple-cistron via a double crossover event. To further demonstrate the application of electroporation in genetic research, the early sporulation gene spo0A of B. subtilis was knocked out and, consequently, the null of sporulation and logged growth was observed in this study. Thus, the electroporation as an alternative method of integration in B. subtilis is feasible and practical.     

Lambda Xis Degradation In Vivo by Lon and FtsH

Lambda Xis, which is required for site-specific excision of phage lambda from the bacterial chromosome, has a much shorter functional half-life than Int, which is required for both integration and excision (R. A. Weisberg and M. E. Gottesman, p. 489–500, in A. D. Hershey, ed., The Bacteriophage Lambda, 1971). We found that Xis is degraded in vivo by two ATP-dependent proteases, Lon and FtsH (HflB). Xis was stabilized two- to threefold more than in the wild type in a lon mutant and as much as sixfold more in a lon ftsH double mutant at the nonpermissive temperature for the ftsH mutation. Integration of lambda into the bacterial chromosome was delayed in the lon ftsH background, suggesting that accumulation of Xis in vivo interferes with integration. Overexpression of Xis in wild-type cells from a multicopy plasmid inhibited integration of lambda and promoted curing of established lysogens, confirming that accumulation of Xis interferes with the ability of Int to establish and maintain an integrated prophage.