Intergenotic transformation of the Bacillus subtilis genospecies

GENETIC EXCHANGE BETWEEN BACILLUS SUBTILIS AND BACILLUS LICHENIFORMIS: VARIABLE HYBRID STABILITY AND THE NATURE OF BACTERIAL SPECIES

Experiments employing both broth and soil cultures demonstrated the capacity for bidirectional genetic exchange between the eubacterial species Bacillus subtilis and Bacillus licheniformis. The process was studied using standard laboratory strains and wild isolates of these species. The genetic exchange in soil occurs spontaneously. The interspecific recombination involved markers for antibiotic resistance and for the use of specific carbon sources (API characters). Hybrids frequently had unstable phenotypes, i.e., lacked a consistent expression of foreign genes over repeated transfer and growth. This instability often involved a "correction" back toward the phenotype of one or the other of the parental species for many differentiating characters; the final phenotype was always that of the more probable or actually known recipient species. This "correction" process is reminiscent of phenomena associated with the instability of artificial fusion protoplasts or noncomplementing diploids of B. subtilis, as well as the merodiploids formed by intergeneric crosses with enteric bacteria. The hybrids observed here must also be diploid, in some manner, because they sequentially express traits of both parental species at rates well above the frequency of mutation. Among the unstable changes in hybrids of the wild strains there was a 3:1 bias in favor of "correction." The dynamics of the hybridization process in soil are described. It appears that the hybrids are formed most rapidly following outgrowth from spores and during the early growth of parental vegetative cell populations. Later on, the hybrids are much less frequent in the soil cultures, suggesting that they are competitively inferior to the parental species. It is argued that the capacity for recombination found between B. subtilis and B. licheniformis could locally erase their distinctness, even though they possess only about 15% DNA sequence homology. Yet they remain distinct in the wild. The methods and results of these experiments prepare the way for detailed studies of the nature of species and species boundaries throughout the genus Bacillus.

Chromosomal transformation in Bacillus subtilis is a non-polar recombination reaction

Natural chromosomal transformation is one of the primary driving forces of bacterial evolution. This reaction involves the recombination of the internalized linear single-stranded (ss) DNA with the homologous resident duplex via RecA-mediated integration in concert with SsbA and DprA or RecO. We show that sequence divergence prevents Bacillus subtilis chromosomal transformation in a log-linear fashion, but it exerts a minor effect when the divergence is localized at a discrete end. In the nucleotide bound form, RecA shows no apparent preference to initiate recombination at the 3′- or 5′-complementary end of the linear duplex with circular ssDNA, but nucleotide hydrolysis is required when heterology is present at both ends. RecA·dATP initiates pairing of the linear 5′ and 3′ complementary ends, but only initiation at the 5′-end remains stably paired in the absence of SsbA. Our results suggest that during gene transfer RecA·ATP, in concert with SsbA and DprA or RecO, shows a moderate preference for the 3′-end of the duplex. We show that RecA-mediated recombination initiated at the 3′- or 5′-complementary end might have significant implication on the ecological diversification of bacterial species with natural transformation.

Mosquitocidal Bacillus amyloliquefaciens: dynamics of growth & production of novel pupicidal biosurfactant

BACKGROUND & OBJECTIVES

A strain of Bacillus amyloliquefaciens (VCRC B483) producing mosquito larvicidal and pupicidal biosurfactant was isolated from mangrove forest soil. The present study was aimed at studying the kinetics of growth and production of the mosquitocidal biosurfactant by this bacterium.

METHODS

Dynamics of growth, sporulation and production of mosquitocidal biosurfactant were studied by standard microbiological methods. The mosquitocidal biosurfactant was precipitated from the culture supernatant and bioassayed against immature stages of mosquito vectors to determine lethal dose and lethal time. The activity, biological and biochemical properties of the biosurfactant have also been studied.

RESULTS

The pupal stages of mosquitoes were found to be more vulnerable to the biosurfactant produced by this bacterium with Anopheles stephensi being the most vulnerable species. The median lethal time (LT 50 ) was found to be 1.23 h when the pupal stages of the above species were exposed to lethal concentration LC 90 (9 µg/ml) dosage of the biosurfactant. Production of biosurfactant was found to increase with incubation time and maximum biomass, maximum quantity of biosurfactant (7.9 mg/ml), maximum biosurfactant activity (6 kBS unit/mg) and maximum mosquitocidal activity (5 µg/ml) were attained by 72 h of growth. The lipopeptide nature of the biosurfactant was confirmed by β-haemolysis, lipase activity, biofilm forming capacity, thermostability and biochemical analysis.

INTERPRETATION & CONCLUSIONS

The mosquitocidal biosurfactant produced by B. amyloliquefaciens (VCRC B483) may be a prospective alternative molecule for use in mosquito control programmes involving bacterial biopesticides.

Role of ComEA in DNA uptake during transformation of competent Bacillus subtilis

The role of the competence protein ComEA in DNA uptake during transformation of competent Bacillus subtilis was analyzed by lysed-protoplast transformation (LP transformation). A comEA deletion mutant was constructed by a fusion polymerase chain reaction. Transformants of the mutant were obtained by LP transformation at a frequency of 1.1 × 10(2) transformants per μg DNA, representing a low relative efficiency of transformation [RET (mutant/wild type)] of 2.7 × 10(-6). This implied an important role of the protein during DNA uptake. When analyzing LP transformation of comEA with a plasmid (5.7 kb), a similar RET (mutant/wild type) of 5.6 × 10(-5) was obtained. Following addition of DNA into the comEA mutant culture, the number of transformants increased at a rate of 0.5 transformants/min, which was very low compared with the wild-type (6.9×10(4) transformants/min). However, even in the comEA mutant, DNA uptake began immediately after addition of DNA. Using co-transformation analysis of the comEA mutant, short linkages at distances of 2-156 kb could be detected, but not long linkages at distances of 671-1662 kb. Taken together, the results indicate that ComEA plays an important role in the transfer of transforming DNA into the DNA channel and in controlling the rate of DNA uptake.

Role of ComFA in controlling the DNA uptake rate during transformation of competent Bacillus subtilis

The roles of ComFA and ComEC in DNA uptake by competent Bacillus subtilis were analyzed by transformation with DNA in protoplast lysates (LP transformation). Deletion mutants of comFA and comEC and putative Walker A mutants (K152N, K152Q, K152E) of comFA were constructed by fusion polymerase chain reaction. Transformants of comEC mutant with purified DNA and DNA in protoplast lysate were not obtained, which shows a lack of transformation ability and backwards recombination of the mutant. Transformants of the comFA mutant were obtained by LP transformation (1.8 × 10(4) transformants/μg DNA). Low relative efficiency of transformation (RET) of comFA compared to wild type (4.3 × 10(-4)) showed an important role for comFA in DNA uptake. Walker A mutants showed 1.8-19 × 10(-4) RET, suggesting a dependence on ATPase activity for transformation. Co-transformation between short linkages was only detected in comFA mutants. The results demonstrated that ComFA controlled the DNA uptake rate. The interpretation was further supported by analyzing the plasmid used in LP transformation of the comFA mutant. The RET of comFA compared to the wild type was 2.7 × 10(-2), 60-fold higher than that with chromosomal DNA (4.3 × 10(-4)). Following addition of DNA into comFA culture, transformants were obtained after 15 min, with the number of transformants increasing over time. The kinetics strongly suggested that in comFA mutants, formation of another DNA uptake complex without ComFA would be a lengthy process.

Sexual isolation in Acinetobacter baylyi is locus-specific and varies 10,000-fold over the genome

Naturally transformable bacteria acquire chromosomal DNA from related species at lower frequencies than from cognate DNA sources. To determine how genome location affects heterogamic transformation in bacteria, we inserted an nptI marker into random chromosome locations in 19 different strains of the Acinetobacter genus (>24% divergent at the mutS/trpE loci). DNA from a total of 95 nptI-tagged isolates was used to transform the recipient Acinetobacter baylyi strain ADP1. A total of >1300 transformation assays revealed that at least one nptI-tagged isolate for each of the strains/species tested resulted in detectable integration of the nptI marker into the ADP1 genome. Transformation frequencies varied up to approximately 10,000-fold among independent nptI insertions within a strain. The location and local sequence divergence of the nptI flanking regions were determined in the transformants. Heterogamic transformation depended on RecA and was hampered by DNA mismatch repair. Our studies suggest that single-locus-based studies, and inference of transfer frequencies from general estimates of genomic sequence divergence, is insufficient to predict the recombination potential of chromosomal DNA fragments between more divergent genomes. Interspecies differences in overall gene content, and conflicts in local gene organization and synteny are likely important determinants of the genomewide variation in recombination rates between bacterial species.

DNA taken into Bacillus subtilis competent cells by lysed-protoplast transformation is not ssDNA but dsDNA

Competent Bacillus subtilis incorporates whole-genome DNA (4215 kb) from the protoplast lysate of B. subtilis subtilis [Akamatsu, T. and Taguchi, H., Biosci. Biotechnol. Biochem., 65, 823-829 (2001)]. A continuous incorporated DNA is longer than 1500 kb [J. Biosci. Bioeng., 101, 257-262 (2006)]. Whether the incorporated DNA is single-stranded (ssDNA) or double-stranded DNA (dsDNA) has been studied by examining the transforming activity of the incorporated DNA. B. subtilis BEST7027 was used as the donor strain, which has a heterologous region consisting of the 145 kb region of the Synechocystis sp. PCC6803 genome and erm gene. The donor DNA was transferred to a wild-type or a recA recipient strain (AYG2 or SYN9), and protoplast lysate was prepared from the transformants and used as the donor DNA source for the second recipient strain (AU1 or AV1). The intergenote region showed a significant transforming activity. When DNase I was added to both cells collected from the first transformation mixture and the following protoplastization, the result was similar to that obtained without DNase I. All of the observations strongly suggest that the incorporated DNA is dsDNA, and the transformation of competent B. subtilis by DNA in protoplast lysate is different from that by purified DNA taken up conventionally.

Fate of transforming bacterial genome following incorporation into competent cells of Bacillus subtilis: a continuous length of incorporated DNA

In contrast to the conventional transformation of Bacillus subtilis using purified DNA, those using DNA in lysed protoplasts have a high transformation efficiency and enable whole-genome transfer into competent B. subtilis [Akamatsu, T. and Taguchi, H., Biosci. Biotechnol. Biochem., 65, 823-829 (2001)]. Here, we examined the length of incorporated continuous DNA by analyzing the cotransfer ratio with selected and unselected markers, on the basis of a new experimental design. The cotransfer ratio of a selected marker with an unselected marker on the opposite side of the genetic map of the B. subtilis chromosome was about 5.6% and could be interpreted as congression (double transformation) ratio. In the wild-type strain, the cotransfer ratio of cysA (113 kb position on 4215 kb of B. subtilis chromosome) with metC (1384 kb) and leuB (2891 kb) was 0.77%, twice the value (5.6% x 5.6%=0.31%) calculated from the congression ratio. Moreover, in a genetic background, the cotransfer ratios of metC with cysA and leuB, and metC with cysA and arg1 (3012 kb) were 2.7% and 7.2%, respectively. These results strongly suggest that the length of continuous DNA incorporated into B. subtilis is most probably greater than 1271 kb. When the DNA from the protoplast lysate was fragmented by mixing, the cotransfer ratios of arg1 with metC, and arg1 with metC and trpC (2374 kb) were 2.8% and 0.16%, respectively. A high cotransfer ratio (2.7-7.2%) could not, therefore, be obtained using the fragmented DNA. Based on these observations, we propose a working hypothesis on the mechanism of the transformation of competent B. subtilis by DNA in protoplast lysates (LP transformation).

Barriers to recombination between closely related bacteria: MutS and RecBCD inhibit recombination between Salmonella typhimurium and Salmonella typhi

Previous studies have shown that inactivation of the MutS or MutL mismatch repair enzymes increases the efficiency of homeologous recombination between Escherichia coli and Salmonella typhimurium and between S. typhimurium and Salmonella typhi. However, even in mutants defective for mismatch repair the recombination frequencies are 10(2)- to 10(3)-fold less than observed during homologous recombination between a donor and recipient of the same species. In addition, the length of DNA exchanged during transduction between S. typhimurium and S. typhi is less than in transductions between strains of S. typhimurium. In homeologous transductions, mutations in the recD gene increased the frequency of transduction and the length of DNA exchanged. Furthermore, in mutS recD double mutants the frequency of homeologous recombination was nearly as high as that seen during homologous recombination. The phenotypes of the mutants indicate that the gene products of mutS and recD act independently. Because S. typhimurium and S. typhi are approximately 98-99% identical at the DNA sequence level, the inhibition of recombination is probably not due to a failure of RecA to initiate strand exchange. Instead, these results suggest that mismatches act at a subsequent step, possibly by slowing the rate of branch migration. Slowing the rate of branch migration may stimulate helicase proteins to unwind rather than extend the heteroduplex and leave uncomplexed donor DNA susceptible to further degradation by RecBCD exonuclease.

The effect of DNA sequence divergence on sexual isolation in Bacillus

We have investigated the relationship between sexual isolation and DNA sequence divergence in the transformation (at locus rpoB) of a naturally competent strain of Bacillus subtilis. Using both genomic DNA and a PCR-amplified segment of gene rpoB as donor, we found that the extent of sexual isolation at locus rpoB was closely predicted, over three orders of magnitude, as a log-linear function of sequence divergence at that locus. Because sexual isolation between a recipient and any potential donor may be determined as a general mathematical function of sequence divergence, transformation is perhaps the only sexual system, in either the prokaryotic or the eukaryotic world, in which sexual isolation can be predicted for a pair of species without having to perform the cross. These observations suggest the possibility of a general approach to the indirect prediction of sexual isolation in bacteria recombining principally by natural transformation.

Physical maps of the six smallest chromosomes of Saccharomyces cerevisiae at a resolution of 2.6 kilobase pairs

Physical maps of the six smallest chromosomes of Saccharomyces cerevisiae are presented. In order of increasing size, they are chromosomes I, VI, III, IX, V and VIII, comprising 2.49 megabase pairs of DNA. The maps are based on the analysis of an overlapping set of lambda and cosmid clones. Overlaps between adjacent clones were recognized by shared restriction fragments produced by the combined action of EcoRI and HindIII. The average spacing between mapped cleavage sites is 2.6 kb. Five of the six chromosomes were mapped from end to end without discontinuities; a single internal gap remains in the map of chromosome IX. The reported maps span an estimated 97% of the DNA on the six chromosomes; nearly all the missing segments are telomeric. The maps are fully cross-correlated with the previously published SfiI/NotI map of the yeast genome by A. J. Link and M. V. Olson. They have also been cross-correlated with the yeast genetic map at 51 loci.

The structure of the trpE, trpD and 5' trpC genes of Bacillus pumilus

The nucleotide (nt) sequences of the Bacillus pumilus trpE, trpD and 5' portions of trpC genes have been determined. Genetic analysis suggested the presence of an internal promoter upstream from the trpC gene, yet no typical consensus sequences were found. The nt and amino acid sequence homologies between the B. pumilus, Bacillus subtilis and Escherichia coli trp genes are presented.

Expression of heterologous genes for wall teichoic acid in Bacillus subtilis 168

A localized region of low DNA sequence homology was revealed in two strains of Bacillus subtilis by a specific 100-fold reduction in transformation by W23 DNA of the tag1 locus, a teichoic acid marker of strain 168. Fifty nine rare recombinants, hybrid at this locus, had all acquired donor-specific phage resistance characters, while losing those specific to the 168 recipient. Chemical analysis of isolated cell walls showed that these modifications are associated with major changes in the wall teichoic acids. Genetic analysis demonstrated that determinants for the ribitol phosphate polymer of strain W23 had been transferred to 168, replacing those for the glycerol phosphate polymer in the recipient. All W23 genes coding for poly(ribitol phosphate) in the hybrids and those specifying anionic wall polymers in strain 168 are clustered near hisA. In addition to tag1, the region exchanged extends just beyond gtaA in some hybrids, whereas in others it may include the more distant gtaB marker, encompassing a region sufficient to contain at least 20 average-sized genes. Surface growth, flagellation, transformability and sporulation all appeared normal in hybrids examined. Recombinants without a major wall teichoic acid from either strain were not found, suggesting that an integral transfer of genes for poly(ribitol phosphate) from W23 had occurred in all hybrids isolated. We interpret these results as indicating an essential role for anionic wall polymers in the growth of B. subtilis.

Characterization of interspecific plasmid transfer mediated by Bacillus subtilis temperate bacteriophage SP02

Plasmid pPL1010 is a 7.0-kilobase derivative of plasmid pUB110 that harbors the cohesive end site of the bacteriophage SP02 genome. Plasmid pPL1017 is a 6.8-kilobase derivative of plasmid pC194 that contains the immunity region of bacteriophage phi 105 and the cohesive end site of bacteriophage SP02. These plasmids are transducible by bacteriophage SP02 at a frequency of 10(-2) transductants per PFU among mutant derivatives of Bacillus subtilis 168 and have been transferred to other strains of B. subtilis and B. amyloliquefaciens by means of bacteriophage SP02-mediated transduction, with frequencies ranging from 10(-5) to 10(-7) transductants per PFU. The introduced plasmids were stably maintained in nearly all new hosts in the absence of selective pressure. An exception was found in B. subtilis DSM704, which also harbored three cryptic plasmids. Plasmids pPL1010 and pPL1017 were incompatible with a 7.9-kilobase replicon native to strain DSM704. Furthermore, plasmid pPL1017 was processed by strain DSM704 into a approximately 5.3-kilobase replicon that was compatible with the resident plasmid content of strain DSM704. The use of bacteriophage SP02-mediated plasmid transduction has allowed the identification of Bacillus strains that are susceptible to bacteriophage SP02-mediated genetic transfer but cannot support bacteriophage SP02 lytic infection.

Characterization of Bacillus subtilis DSM704 and its production of 1-deoxynojirimycin

A Bacillus subtilis strain, DSM704, was characterized by genetic means, and its production of a human intestinal sucrase inhibitor, 1-deoxynojirimycin, was described. Synthesis of this compound is detected concomitant with the detection of heat-resistant spores. The amount of 1-deoxynojirimycin produced is highly dependent on the carbon source, with growth on substrates metabolized via glycolysis giving the greatest amount of production (up to 1 mg/ml). 1-Deoxynojirimycin appears to be nonmetabolizable by the producing strain in that it cannot serve as a sole carbon or nitrogen source.

Addition, deletion, and substitution of long nonhomologous deoxyribonucleic acid segments by genetic transformation of Haemophilus influenzae

A complete EcoRI digest of Haemophilus influenzae phage HP1 deoxyribonucleic acid (DNA) was mixed with incomplete digests of various H. influenzae R plasmids, sealed with T4 ligase, and transformed into an HP1 lysogen. Most of the chloramphenicol- and tetracycline-resistant transformants did not produce phage although they possessed all the phage genes examined. They also did not transfer antibiotic resistance by conjugation. DNA lysates from them transformed other lysogens to resistance and to loss of phage production at different but quite high frequencies (addition of long DNA segments). They themselves could be transformed efficiently to strains with a wild prophage (deletion of long DNA segments). It was concluded that lysogenic cultures had been constructed with various DNA inserts in their prophages carrying antibiotic resistance genes from the R plasmids. The site of insertion was determined by genetic crosses. DNAs with inserts that transferred with lower efficiency were more sensitive to ultraviolet radiation. This supports the view that insert transfer efficiencies reflect the sizes of the insert.

Integration of the bacteriophage phi 3T-coded thymidylate synthetase gene into the Bacillus subtilis chromosome

Transformation of Bacillus subtilis 168 Thy- auxotrophs with phi 3T deoxyribonucleic acid (DNA) to thymine independence was found to involve site-specific recombination of phi 3T DNA sequences with their homologous counterparts in the bacterial chromosome. During the transformation, the phage phi 3T-encoded thymidylate synthetase gene, thyP3, was shown to integrate at two genetically distinct sites in the B. Subtilis 168 chromosome. The first site was identified to be in the bacterial thymidylate synthetase gene, thyA. The second site was in a prophage (SPB) known to be carried in the host genome. The frequency of the integration of the thyP3 gene at each of the two loci and some of the parameters affecting this frequency were studied. The common origin of the thyP3 and thyA genes and their molecular evolution are also reported.

Genetic and nucleotide sequence homologies in bacillus genomes

The extent of divergence in the organization of the aromatic amino acid cluster among the heterogenetic strains of Bacillus subtilis has been examined by hybridizations to a trp homolog from B. pumilus and by marker survivals after restriction. The trp operon in the W23, 3610 and 168M genomes exhibit variations in the location of the ECoRI and HindIII cleavage sites consistent with the relative transforming activity of the surviving genes and the history of the strains.

Mechanism of additive genetic transformation in Haemophilus influenzae

Transforming deoxyribonucleic acid (DNA) preparations from Haemophilus influenzae Rd strains carrying a chromosomally integrated, conjugative, antibiotic resistance transfer (R) plasmid were exposed to ultraviolet radiation and then assayed for antibiotic resistance transfer on sensitive wild-type Rd competent suspensions and on similar suspensions of a uvr-1 mutant unable to excise pyrimidine dimers. No host cell reactivation of resistance transfer (DNA repair) was observed. Parallel experiments with ethanol-precipitated, heated, free R plasmid DNA preparations gave much higher survival when assayed on the wild-type strain compared to the survival on the uvr-1 strain. These observations indicate that additive genetic transformation (in this case, the addition of the integrated R plasmid to the recipient genome) involves single-strand insertion.

DNA cloning in Bacillus subtilis. III. Efficiency of random-segment cloning and insertional inactivation vectors

Random segments of Bacillus amyloliquefaciens and yeast Saccharomyces cerevisiae DNA were used to determine two parameters pertinent to cloning in Bacillus subtilis, the yield of hybrids and the mean size of cloned segments. 10(3) to 10(4) hybrids/micrograms of DNA segments were obtained. Hybrids represented 11--18% of transformants. Mean m. wt. of cloned DNA segments was about 1 x 10(6), substantially lower than 3 x 10(6) found for donor DNAs after digestion with restriction endonucleases. We have cloned a B. amyloliquefaciens DNA segment which complemented a deficiency in B. subtilis hisH and E. coli hisC genes, which encode imidazolylacetolphosphate aminotransferase. The cloning efficiency for this gene was 10 transformed hosts/micrograms of donor DNA. Several B. subtilis insertional-inactivation cloning vectors were examined. One, pHV41, allows inactivation of the kanamycin-resistance (KmR) gene by insertion into its unique Bg/II site. In two other vectors, pHV11 and pHV23, insertion in their unique Kpn site inactivates the tetracycline-resistance (TcR) gene. pHV23 replicates both in E. coli and B. subtilis, and carries unique sites for seven restriction endonucleases (BamHI, EcoRI, HpaI, KpnI, PstI, SalI, XbaI). This makes it one of the most versatile B. subtilis cloning vectors yet described.

Expression of thymidylate synthetase activity in Bacillus subtilis upon integration of a cloned gene from Escherichia coli

The gene from Escherichia coli encoding thymidylate synthetase was cloned in the plasmid pBR322. The resulting chimeric plasmid, pER2, was effective in transforming both E. coli and Bacillus subtilis to thymine prototrophy. Uncloned linear E. coli chromosomal DNA was unable to transform thymine-requiring strains of B. subtilis to thymine independence. Linearization of the chimeric plasmid, pER2, with restriction enzymes markedly diminished its ability to transform B. subtilis auxotrophs. The Thy+ transformants derived from the transformation of B. subtilis with pER2 DNA did not contain detectable extrachromosomal DNA as demonstrated by Southern hybridization patterns and centrifugation in CsCl gradients of DNA isolated from B. subtilis colonies transformed with the chimeric plasmid. We conclude that the DNA from the chimeric plasmid was integrated into the chromosome of B. subtilis, demonstrating that extensive homology is not required for the integration of foreign DNA. This is the first reported case of a gene from a Gram-negative bacterium functioning in a Gram-positive organism.

Exclusion of bacteriophage T1 by bacteriophage lambda. II. Synthesis of T1-specific macromolecules under N-mediated excluding conditions

The results of experiments investigating T1 macromolecular synthesis under N-mediated excluding conditions failed to demonstrate a substantial alteration in the T1 mRNA production in excluding cultures at any stage in the T1 infectious cycle. The number of T1 DNA sequences in the excluding culture was found to be one-third to one-half that found in T1-infected cultures. The most severe reduction in T1-specific macromolecules was seen in protein synthesis. Total incorporation of labeled amino acids was reduced sixfold, and gel experiments confirmed that the T1-specific proteins capable of detection are reduced in excluding cells.

Molecular cloning of heterologous chromosomal DNA by recombination between a plasmid vector and a homologous resident plasmid in Bacillus subtilis

The difficulty experienced in the shotgun cloning of chromosomal DNA on plasmid vectors in Bacillus subtilis is analyzed and an explanation for this difficulty is offered based on an inherent property of competent cells which imposes a requirement of plasmid multimers in transformation of plasmid-free recipients (Canosi et al., 1978). A stratagem which uses cloning by recombination between the vector and a resident homologous plasmid is tested and shown to be successful. Several recombinant plasmids are obtained containing Bacillus licheniformis DNA fragments which complement aromatic amino acid mutants of Bacillus subtilis. The yield of recombinant clones ranges from 6.7 to 210 per microgram of chromosomal DNA, depending on the selection and the restriction endonuclease. The various trp clones obtained after cutting chromosomal DNA with BglII and BclI do not complement trpE and exhibit both orientations with respect to the vector. The location of several restriction endonuclease cleavage sites in the cloned trp fragments is presented, and their relationship to the genetic map of Bacillus licheniformis is described.

Insertional inactivation of trpC in cloned Bacillus trp segments: evidence for a polar effect on trpF

Plasmid pUB110 was previously used as a vector to clone fragments of deoxyribonucleic acid that complement the trpC2 mutation in Bacillus subtilis from endonuclease EcoRI digested B. licheniformis, B. pumilus, and B. subtilis cellular deoxyribonucleic acid. Each of several such trp plasmids was subsequently shown to contain a segment of the trp gene cluster on the basis of genetic complementing activity. In the present study, analysis of the Trp enzyme levels in B. subtilis harboring the constructed trp plasmids confirms the genetic constitution of the plasmids. Thus, plasmids that complement mutations in specific trp genes specify the corresponding enzyme activities. The levels of the plasmid-specified Trp enzymes in B. subtilis were generally above the repressed level of the chromosomally specified Trp enzymes and equal to or below the derepressed levels of the chromosomally specified Trp enzymes. Certain cloned trp segments contain a single HindIII-sensitive site. Insertion of HindIII-generated deoxyribonucleic acid fragments into these trp plasmids resulted in inactivation of trpC complementing activity, loss of the trpC-specified enzyme activity, and a 10-fold reduction in the specific activity of the plasmid-specified trpF product. The HindIII insertions had no detectable effect on the level of the trpD product, nor did the insertions detectably alter plasmid-specified complementing activity other than to abolish trpC complementation. Removal of the HindIII insertions was accompanied by recovery of trpC complementing activity and restoration of the trpC-and trpF-determined enzymes to the levels specified by the parent plasmids.

Biochemical and genetic properties of site-specific restriction endonucleases in Bacillus globigii

Bacillus globigii contains two site-specific endonucleases, BPGLI AND BglI. A rapid technique for selection of mutants deficient in each of these enzymes was developed using sensitivity to infection by bacteriophage SP50 as an indication of the levels of enzyme. Mutants defective in BglI, BglII, and both BglI and BglII retained the wild-type modification phenotype. Genetic and biochemical studies have established that these enzymes are involved in restriction in vivo. Simplified purification procedures for BglI and BglII using these mutants are described.

Interspecies transformation in Bacillus: mechanism of heterologous intergenote transformation

Bacillus subtilis-Bacillus globigii hybrids were made by integration of the B. globigii aromatic region (aroB to aroE) as an intergenote in the B. subtillis chromosome. Transformation of the heterologous intergenote by B. subtillis DNA (or vice versa) occurred at about 10% of the frequency of homologous transformation by hybrid donors into the same region. Heterologous intergenote crosses were unusually sensitive to shear fragmentations of donor DNA to sizes less than 30 X 10(6) to 40 X 10(6) daltons. In all cases, the entire intergenote was transferred en bloc. Homologous transformation of intergenote markers by B. globigii DNA was not unusually shear sensitive, and linkage was normal for markers in the intergenote. A model is proposed in which efficient heterologous intergenote transformation occurs by recognition and base pairing of homologous DNA sequences of both flanks of the intergenote.

Interspecies transformation in Bacillus: sequence heterology as the major barrier

The relative contribution of DNA restriction and of sequence heterology as barriers to interspecies transfer of DNA was studied in the heterologous transformation of Bacillus subtilis recipients by DNA was studied in the heterologous transformation of Bacillus subtilis recipients by DNA isolated from B. globigii. Transformants were obtained at very low frequencies in the evolutionarily nonconserved aromatic region; high cotransfer of linked markers was observed. New mutations were introduced into the B. globigii intergenote sequence in the resulting hybrids; these markers could be transformed with high efficiency by both B. globigii and B. subtilis DNA, representing a 10(5)-fold increase in heterologous transforming efficiency. A restriction activity in B. globigii crude extracts inactivated the biological activity of B. subtilis and hybrid DNA but not B. globigii DNA in vitro, demonstrating different sites for restriction and modification between these species. In vivo, however, B. globigii and hybrid DNA transformed the B. globigii sequence in a hybrid recipient with the same efficiency. These results show that sequence heterology is the major barrier to interspecies transformation and that, in this system, enzymatic restriction does not prevent interspecies transformation.

Molecular cloning of genetically active fragments of Bacillus DNA in Bacillus subtilis and properties of the vector plasmid pUB110

Plasmid pUB110 (approximately 2.8 x 10(6) daltons), originally detected in Staphylococcus aureus, specifies resistance to neomycin and has been transformed into Bacillus subtilis 168, In B. subtilis, pUB110 is stably maintained at about 50 copies per chromosome and renders the host resistant to neomycin sulfate at 5 microgram/ml. pUB110 isolated from B. subtilis transforms Rec+ and recE4-containing strains of B. subtilis at frequencies greater than or equal to 10(3) transformants per microgram of plasmid. pUB110 was transferred by PBS1 or SP10 transduction from B. subtilis to strains of B. pumilus and B. licheniformis. pUB110 is compatible with each of four previously described Bacillus plasmids, including pPL576, pPL10, pPL7065, and pPL2. pUB110 contains a single EcoR1-sensitive site and was used as vector to clone DNA fragments that complement the trpC2 mutation in B. subtilis 168 from EcoR1 digests of the chromosome DNA isolated from B. pumilus strains NRRL B-3275 and NRS576, B. licheniformis strains 9945A and 749C, and B. subtilis 168. Genetic and physical properties of each of the constructed Trp derivatives of pUB110 are described.

Restriction and modification in Bacillus species: genetic transformation of bacteria with DNA from different species, part I

Host specific restriction was detected in 13 Bacillus strains, when 63 strains of Bacillus subtilis and 15 other Bacillus strains were tested with phage phi 105C. These 13 strains were classified into 8 groups (M,H,C,N,E,F,G,P) by the type of restriction. M-type strains (B. subtilis Marburg 168, its derivatives, and two other strains) showed relatively weak restriction, restricting phi 105C from other groups of Bacillus by ratios of 10(-1) to 10(-3). Strains of groups H,C,N,E,F,G, and P restricted phi 105C from other groups by ratios of 10(-2) to 10(-8). It was confirmed with some of the strains that type-specific modification was endowed only by the last host. Furthermore, we isolated one restriction deficient mutant of B. subtilis Marburg 168-YS11, which had also lost its modification phenotype.

Transformation of Bacillus subtilis and Escherichia coli by a hybrid plasmid pCD1

The gene thyP3 from Bacillus subtilis bacteriophage phi 3T was cloned in the plasmid pMB9. The resulting chimeric plasmid, pCD1, is effective in transforming both Escherichia coli and Bacillus subtilis to thymine prototrophy. The activity of the thyP3 gene product, thymidylate synthetase, was assayed and found to be 9 times greater in a transformed strain of Escherichia coli than in a phi 3T lysogen of Bacillus subtilis. The physical location of restriction sites has been determined for two related plasmids pCD1 and pCD2. Hybridization studies clearly indicate that the plasmid gene responsible for Thy+ transformation is the gene from the bacteriophage phi 3T. The lack of restriction in this transformation process is consistent with our previous studies using bacterial DNA in heterospecific exchanges indicating that the nucleotide sequence surrounding the gene is the dominant factor in determining interspecific transformation.

Temperate Bacillus subtilis bacteriophage phi 3T: chromosomal attachment site and comparison with temperate bacteriophages phi 105 and SPO2

The temperate Bacillus subtilis bacteriophage phi 3T contains within its genome a locus, designated thyP3, that encodes for a protein with thymidylate synthetase activity. Bacteriophage phi 3T is different from the two previously characterized temperate phages, phi 105 and SPO2, in: heteroimmunity, response to bacteriophage antisera, endonuclease digestion pattern, induction in the presence of 6-(p-hydroxyphenylazo)-uracil, and effect on the lytic cycle of bacteriophage phi 1. The mean burst size of phi 3T is 56. The dose response curve with bacteriophage phi 3T DNA is linear for transfection and transformation to the Thy+ phenotype. The inserted prophage has been mapped by PBS1 transduction; it is between chromosomal markers ilvA8 and gltA in the terminus of the chromosome. Thus thyP3 maps at a site separate from, but between, the bacterial markers thyA and thyB when thyP3 is in the prophage state.

Restriction and modification in B. subtilis. Purification and general properties of a restriction endonuclease from strain R

All Bacillus subtilis R-type strains showing the phenomena of restriction and modification contain an endonuclease that inactivates in vitro the biological activity of a variety of DNAs lacking R-specific modification, such as transfecting SPPI, SPO2 and phi105 DNA, and transforming B. subtilis 168-type DNA. The corresponding DNAs carrying R-specific modification are resistant to the enzyme. The enzyme has been purified approximately 400-fold and is essentially free from contaminating double strand-directed unspecific exo- or endonuclease activity. Only Mg2+ is required as cofactor. The substrate DNAs are cleaved at specific sites. The double-stranded fragments produced from SPP1 DNA (molecular weight 2.5 x 10(7)) have an average molecular weight of about 3 x 10(5).

Intrageneric transformation of neisseria gonorrhoeae and neisseria perflava to streptomycin resistance and nutritional independence

Auxotrophic mutants of Neisseria gonorrhoeae and Neisseria perflava were transformed to prototrophy using homologous and heterologous deoxyribonucleic acid (DNA). Within either species the efficiencies of transformation for nutritional markers were found to be very similar to the values obtained for transformation to streptomycin resistance. The number of transformants in the interspecific N. perflava (donor) - - leads to N. gonorrhoeae (recipient) cross was 100-fold lower than the number obtained in the intraspecific N. gonorrhoeae - - leads to N. gonorrhoeae cross for streptomycin resistance, as well as for several nutritional markers. In the reciprocal experiment the difference in the number of transformants in the interspecific N. gonorrhoeae - - leads to N. perflava cross and the number obtained in the intraspecific N. perflava - - leads to N. perflava cross varied from 600 to 1,000-fold for the streptomycin resistance marker. Of greater interest was the finding that N. perflava auxotrophs, although transformable to prototrophy with wild-type N. perflava DNA, were not transformed to nutritional independence by gnoncoccal DNA. These same mutants were transformable to streptomycin resistance using the heterologous gonococcal DNA. When the DNAs of N. meningitidis, N. flava, and N. lactamicus were used to transform N. gonorrhoeae to prototrophy or streptomycin resistance, the transformation frequencies obtained fell along a gradient that in general reflected taxonomic relationships. On the other hand, with N. perflava as the recipient for these same DNAs, only N. flava DNA could transform auxotrophs to prototrophy, although transformation to streptomycin resistance occurred in all cases. DNA from N. perflava - - leads to N. gonorrheae streptomycin-resistant or Ade+ intergenotic transformants transformed N. gonorrhoeae cells at a 100-fold-higher efficiency than did DNA from N. perflava. Our findings suggest that (i) N. gonorrhoeae and N. perflava are more closely related than hitherto suspected and (ii) N. perflava is more selective with respect to heterologous DNA than is N. gonorrhoeae.

Genetic hybridization at the unlinked thy and str loci of Streptococcus

The sanguis and pneumoniae species of Streptococcus were used as recipients in transformations from str+ to str-r and from thy- to thy+. The str-r mutations in the two species had been previously shown to be allelic. Homology of the thy- mutations in the two species was demonstrated in the similar phenotypic properties they conferred (death in the absence of thymidine, lack of thymidylate synthetase). The str and thy loci are unlinked in each species.--- When the two species are transformed by both homospecific and heterospecific DNA, the efficiency is always lower in the heterospecific cross. The efficiency of heterospecific transformation is considerably lower at the thy than at the str locus. DNA was extracted from recipients that had integrated markers of heterospecific origin. When such hybrid DNA is tested on the original recipient species, the heterospecific markers are usually as efficient as homospecific markers. When tested on the original donor species, however, the hybrid DNA is usually more efficient than heterospecific DNA. This is true for both thy and str transformation. -- -- Forty independent thy+ hybrids were obtained in the cross of sanguis thy- recipients with pneumoniae thy+ DNA. These hybrids fall into a number of classes based upon the relative efficiency with which their extracted DNA's are able to transfer the thy+ marker into pneumoniae thy- cells. The most efficient of these DNA's exhibits about 20% of the efficiency of homospecific pneumoniae thy+ DNA and three orders of magnitude greater efficiency than heterospecific sanguis thy+ DNA. Thus, very little of the inefficiency of heterospecific transformation of the thy locus is ascribable to a classic restriction mechanism. Rather, the wild-type thy+ loci in the two species appear to differ at multiple sites, and independent heterospecific transfers result in differential extents of integration of these sites. On this basis, the thy+ loci of the two species differ at a greater number of sites than do the respective str+ loci.

Biochemical studies of two Bacillus pumilus plasmids

Bacillus pumilus NRS 576 harbored an estimated two copies per chromosome of a covalently closed, circular (CCC) deoxyribonucleic acid (DNA) molecule, the 576 plasmid. The 576 plasmid has a buoyant density of 1.698 g/cm(3) and a molecular weight of about 28 x 10(6). Plasmid copy number remained about the same in both exponentially growing and stationary-phase cells. Spontaneous variants of NRS 576 that formed spores at an elevated frequency were designated as W mutants. W mutants appeared to have lost the 576 plasmid on the basis of the following: W mutants (38 tested) lacked detectable CCC DNA, and the majority of the plasmid homologous sequences in bulk NRS 576 DNA were absent from bulk W mutant DNA. B. pumilus ATCC 7065 harbored at least 10 copies per chromosome of a CCC DNA element, the 7065 plasmid. The 7065 plasmid has a buoyant density of 1.696 g/cm(3) and a molecular weight of about 6 x 10(6). Although the copy number of the plasmid appeared to remain the same in exponentially growing and stationary-phase cells, an additional CCC form of higher molecular weight was detected in stationary-phase cells.

Restriction and modification of bacteriophage in Bacillus stearothermophilus

Host-controlled restriction and modification of TP-1C phage and infectious phage DNA occurs in Bacillus stearothermophilus and is subject to control by TP-8 or TP-12 prophage.

On the conservation of aminoacyl-transfer ribonucleic acid synthetase genes in Bacillus

None of the heterologous deoxyribonucleic acid from various bacilli was capable of transforming lysyl- and tryptophanyl-transfer ribonucleic acid (tRNA) synthetase mutants of Bacillus subtilis to wild type. It was concluded that there is little conservation of the aminoacyl-tRNA synthetases even though the tRNA cistrons are conserved genetic functions.