Spontaneous transformation and its use for genetic mapping in Bacillus subtilis

Using a simple semi-synthetic competence and sporulation medium (CSM), we found evidence that Bacillus subtilis cells transformed in the competence phase can sporulate, indicating that genetic information acquired during the competence phase is inherited by the next generation after germination of the transformed spores. Moreover, the results from mixed cell culture experiments suggest that spontaneous genetic transformation can occur between competent cells and DNA released from lysed cells in the natural environment. We also found evidence that the spontaneous transformation system can be used for genetic mapping in B. subtilis.     

Natural genetic transformation of Pseudomonas stutzeri by sand-adsorbed DNA

In a soil/sediment model system we have shown recently that a gram-positive bacterium with natural competence (Bacillus subtilis) can take up transforming DNA adsorbed to sand minerals. Here we examined whether also a naturally transformable soil bacterium of the gramnegative pseudomonad (Pseudomonas stutzeri) can be transformed by mineral-associated DNA. for these studies the transformation protocol of this species was further improved and characterized. The peak of competence during growth of P. stutzeri was determined to occur at the beginning of the stationary phase. The competence state was conserved during shock freezing and thawing of cells in 10% glycerol. Kinetic experiments showed that transformant formation after addition of DNA to competent cells proceeded for more than 2 h with DNA adsorption to cells being the rate limiting step. By means of the defined protocol P. stutzeri was shown to be transformed by sand-adsorbed DNA. Transformation by adsorbed or dissolved DNA occurred between 16° and 44°C. Efficiency and DNaseI-sensitivity of transformation by DNA adsorbed to sand or in liquid were comparable. It is concluded that uptake of particle-bound DNA by P. stutzeri in soil is possible. This finding adds evidence to the view that transformation occurs in natural environments where DNA is assumed to be significantly associated with mineral/particulate material and thereby is protected against enzymatic degradation.     

An efficient transformation method for <Emphasis Type="Italic">Bacillus subtilis</Emphasis> DB104

Bacillus subtilis strains are used for extracellular expression of enzymes (i.e., proteases, lipases, and cellulases) which are often engineered by directed evolution for industrial applications. B. subtilis DB104 represents an attractive directed evolution host since it has a low proteolytic activity and efficient secretion. B. subtilis DB104 is hampered like many other Bacillus strains by insufficient transformation efficiencies (≤10³ transformants/μg DNA). After investigating five physical and chemical transformation protocols, a novel natural competent transformation protocol was established for B. subtilis DB104 by optimizing growth conditions and histidine concentration during competence development, implementing an additional incubation step in the competence development phase and a recovery step during the transformation procedure. In addition, the influence of the amount and size of the transformed plasmid DNA on transformation efficiency was investigated. The natural competence protocol is “easy” in handling and allows for the first time to generate large libraries (1.5 × 10⁵ transformants/μg plasmid DNA) in B. subtilis DB104 without requiring microgram amounts of DNA.     

Characterization of genetic transformation in Streptococcus oralis NCTC 11427: Expression of the pneumococcal amidase in S. oralis using a new shuttle vector

Summary We have worked out conditions for the study of competence development and genetic transformation in Streptococcus oralis NCTC 11427 (type strain), a species that contains choline in the cell wall. The peak of competence was found at the early exponential phase of growth and the optimal conditions for transformation were achieved with shuttle plasmids prepared from S. pneumoniae or from Escherichia coli serving as donor DNA. Transformation with dye-bouyant density gradient purified plasmid preparations followed first-order kinetics. The pneumococcal amidase can be expressed in S. oralis harbouring a plasmid carrying the lytA gene. This enzyme lysed the cell wall of the transformed cell in the presence of detergents.     

The causes of instability of linkage in transformation of Bacillus subtilis

Summary To explain the instability of linkage between distantly situated markers in transformation of B. subtilis, the following proposal, and experimental evidence to support it, are presented.When cells are transformed with low concentrations of DNA, any molecule can interact simultaneously with more than one recipient cell. This results in a fragmentation of the molecules, which can separate genetic markers initially coresident on the same molecule into different recipient cells. The frequency with which this occurs depends on the concentration of DNA, concentration of recipient cells, the competence of the culture and the distance between the markers. When markers are close together, only rarely does the break in the molecules occur between them and the linkage is stable at all concentrations of DNA; when markers are far apart, division often occurs between them and the major protion of the linkage is lost at all but saturating levels of DNA.     

DNA fixation and development of transformability and transfectability in Bacillus subtilis

Summary After pre-competent cells of Bacillus subtilis are placed in the medium in which competence develops, peak competence for transformation is found to occur earlier than competence for transfection by DNA from phages whose DNA is dissimilar to that of the cells. There is a nonlinear dependence of transfection on the concentration of DNA from phage SP 82 despite a linear dependence of DNA fixation on DNA concentration. Both results support the idea that fixation of DNA is a poor indicator of the actual competence of the cells for both transformation and transfection.     

Verlust der Kompetenz für genetische Transformation in Bacillus subtilis-Zellen während des Überganges in die stationäre Wachstumsphase

Zusammenfassung Im Gegensatz zu den Hinweisen, daß kompetente Bacillus subtilis-Zellen solche sind, die sich in frühen Sporulationsphasen befinden, stehen die genannten Befunde, wonach Zellen sporulieren, ohne dabei kompetent zu werden. Wenn die Sporulation durch den Übergang einer Kultur in die stationäre Wachstumsphase ausgelöst wurde, nahm sofort die Zahl der kompetenten Zellen ab. Bei einem Wechsel der Stickstoffquelle von Ammoniumsulfat zu Histidin, der bei einem Drittel der Population zur Ausbildung thermoresistenter Sporen führte, verminderte sich sofort die Anzahl transformierbarer Zellen von 4,5·10⁵ ml^-1 auf 2,0·10¹ ml^-1, ohne später wieder den zuvor gemessenen Wert zu erreichen.Der genannte Widerspruch läßt sich aufheben durch die Annahme, daß Zellen, die während des exponentiellen Wachstums der Kultur in den stationären Zustand übergehen und sporulieren, sich von denen unterscheiden, deren Sporulation durch Substratlimitation induziert wurde. Nur die ersteren sind transformierbar. Wahrscheinlich ist bei den letztgenannten die Synthese oder Funktion der zur Kompetenzausbildung und Erhaltung notwendigen Substanzen gehemmt.

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Loss of competence in the Bacillus subtilis transformation system during transition to the stationary growth phase

Summary Former experiments of several authors indicated that competence in the Bacillus subtilis transformation system is linked to an early phase of sporulation. The results presented here show that B. subtilis cells may sporulate without becoming competent. If mass sporulation was induced by transition of the culture to the stationary growth phase the number of competent cells decreased abruptly. Substitution of ammonium sulphate by histidine as the sole source of nitrogen induced a third of the population to form thermoresistant spores. Simultaneously, the number of cells which could be transformed was reduced from 4.5×10⁵ ml^-1 to 2.0×10¹ ml^-1. After prolonged incubation no total recovery of competence could be observed.The differing results concerning the connection of sporulation and transformability may be explained by the assumption that there exists a difference between single cells which sporulate after entering the stationary state during the exponential growth of the culture and such cells the sporulation of which is induced by limitation of substrate. Only the former ones may be subject to transformation while in the latter cells synthesis or function of substances necessary for establishing and maintaining competence may be inhibited.

     

The mechanism of competence in the transformation of streptococci of serological group H

Summary The production of a special competence factor (cpf) by the recipient cells is one of the key-elements of the complex mechanims of competence in transformation. The role of cpf and its interrelation with the other factors involved in competence remain obscure. The evidence regarding the genetic background of competence is also very scarce.The cpf production ability was demonstrated to be a genetic unit which could be transferred in transformation. The cpf marker was transformed in a heterospecific reaction, in which the S. challis (cpf ⁺) strain was the DNA donor, and S. wicky (cpf ^–) its recipient.As a result of the incorporation of this marker, S. wicky cells acquired the stable cpf production ability and, consequently, the transformation ability in a yield equal to that shown by the donor cells. DNA isolated from the S. wicky (cpf ⁺) transformants could be applied, in turn, as a donor of the cpf marker. The experiments were performed by a semiquantitative technique and the yield of the transfer of the cpf marker amounted to about 1%.     

Development of Competence in the Bacillus subtilis Transformation System

Competence in Bacillus subtilis, assayed by the ability of cells to be transformed with bacterial deoxyribonucleic acid (DNA) or transfected by phage DNA, has been shown to occur in a single semisynthetic medium with peak activity occurring 3 hr after the cessation of logarithmic growth. No step-down conditions or culture manipulations were necessary for routine transfection of 1% of the population. The results demonstrate that bacteriophage DNA is a valid assay for studying the development of competence in B. subtilis. Predictions of workers using transforming bacterial DNA, who have suggested that competence in B. subtilis is associated with a specific phase of growth, are substantiated. The peak of competence is not affected by marked differences in the rate of growth during the logarithmic phase. The effect on development of competence by this procedure of some components (including casein hydrolysate, tryptophan, and histidine) which were routinely included in the transformation medium by other investigators has been determined by use of infectious phage DNA as an assay. We have demonstrated that tryptophan, as well as histidine, increases the transformation frequency—even in strains which do not have auxotrophic demands for these components. Glutamic acid and alanine depress optimal levels of transfection.     

Spontaneously immortalized mouse mesothelial cells display characteristics of malignant transformation

Abstract. Objectives: Mesotheliomas occur in occult serous cavities after chronic exposure of mesothelial cells to asbestos fibres. Molecular events that contribute to the development of this cancer are therefore not readily accessible for study. We have used in vitro culture systems to study and compare induced and spontaneous transformation events in primary mouse mesothelial cells. Materials and methods: Mouse mesothelial cells were cultivated until small populations of proliferating cells emerged from senescing cultures. Spontaneously transformed cultures of cells were characterized and compared to malignantly transformed cells. Results: Human mesothelial cells had a finite lifespan of 10–15 population doublings when cultured in vitro; mouse mesothelial cells typically exhibit this same pattern. Here, we show that mouse mesothelial cells can be cultured for extended periods and that these cells can transform spontaneously. Lines of spontaneously transformed cells generated in this study are immortal and growth factor‐independent. They display the salient characteristic features of transformation, including increased proliferation rate, lack of contact inhibition, aneuploidy and ability to grow in anchorage‐independent conditions. A subset of these cell lines developed into tumours in syngeneic mice. Comparative gene expression analysis demonstrated that spontaneously transformed cell lines were more closely related to neoplastic cells than to primary cells. Conclusion: These findings have implications for interpretation of in vitro transformation studies, demonstrating broad similarity between spontaneous and induced genetic changes.     

<Emphasis Type="Italic">Bacillus subtilis</Emphasis> CinA is a stationary phase–induced protein that localizes to the nucleoid and plays a minor role in competent cells

CinA is a conserved bacterial protein that has been reported to play an important role during competence in Streptococcus pneumoniae by recruiting the RecA protein to the cell membrane. Here, we provide information on the homologous CinA in Bacillus subtilis. We found that the synthesis of CinA is upregulated during stationary phase in all cells. The loss of CinA has a mild effect during competence, but it has no influence on the localization of RecA. CinA was observed to be associated with the nucleoid in the cell, and not with the cell membrane, as shown for S. pneumoniae. Purified CinA is a soluble protein, probably forming trimers, like other homologues, which share a domain with CinA that has been reported to be involved in molybdopterine biosynthesis. Our results suggest that CinA plays a nucleoid-associated general role in cells entering stationary phase that is not specific to competence in B. subtilis and possibly in many other bacteria.     

Release of transforming plasmid and chromosomal DNA from two cultured soil bacteria

The release of chromosomal and plasmid DNA from Acinetobacter calcoaceticus and Bacillus subtilis cultivated in minimal medium and broth over a period of 50 h was monitored and related to growth phase, autolysis, DNase production and natural competence. The released DNAs were biologically active in natural transformation. In addition, the circular integrity of a released B. subtilis shuttle vector (pHV14) was demonstrated by artificial transformation of Escherichia coli. In cultures of both strains high molecular weight DNA accumulated, particularly during the stationary and death phase (up to 30 g ml^-1). Generally, despite the presence in culture fluids of DNase activity (and of an intracellular enzyme, catalase, indicating some cell lysis) there was high transforming activity of chromsomal and plasmid DNA even 40 h after the cultures reached the stationary phase. In cultures of B. subtilis in minimal medium a presumably active release of intact plasmids and chromsomal DNA occurred during the competence phase. The release of biologically functional DNA during essentially all growth phases of a gram-positive and a gram-negative member of soil bacteria might facilitate horizontal gene transfer by transformation in natural habitats.     

Molecular mechanism of genetic recombination in bacterial transformation

Summary B. subtilis cells auxotrophic for two linked markers (ind-his, ind-tyr, his-tyr) have been transformed by means of DNA preparations obtained by hybridization of wild type DNA with the DNA of a strain auxotrophic for one of the linked markers. It was established that hybridization does not increase the transforming activity of DNA for the heterozygous marker. A genetic analysis of the progeny of cells transformed by hybrid or wild type DNA was performed. On the basis of the data obtained a model of genetic recombination in transformation is proved. According to this model both strands of the donor DNA interact independently with the chromosome, and either strand can be incorporated into the cell genome with equal probability. According to the estimate made on the basis of this hypothesis, the probability of integration of a single DNA strand carrying a particular genetic marker is 8%.With 3 Figures in the Text     

Plasmid transformation in Bacillus subtilis: Fate of plasmid DNA

Summary Only multimeric, and not monomeric forms of B. subtilis plasmids can transform B. subtilis cells (Canosi et al. 1978). This finding prompted us to study the physico-chemical fate of plasmid DNA in transformation. Competent cells of B. subtilis were exposed to either unfractionated preparations or to preparations of multimeric plasmid DNA. Plasmid DNA was re-extracted from such cells and then analyzed by sedimentation and isopycnic centrifugation and also defined by its sensitivity to nuclease S1 degradation. No double-stranded plasmid DNA could be recovered from cells transformed with unfractionated plasmid preparations which contained predominantly monomeric covalently closed circular (CCC) DNA, Re-extracted plasmid DNA was single-stranded, had a molecular weight considerably smaller than monomer length DNA and had been subject to degradation to acid soluble products. However, when transformations were performed with multimeric DNA (constructed by in vitro ligation of linearized pC194 DNA), both double-stranded and partially double-stranded DNA could be recovered in addition to single-stranded DNA.We assume that plasmid DNA is converted to a single-stranded form in transformation, irrespective of its molecular structure. Double-stranded and partially double-stranded DNAs found in transformation with multimeric DNA would be the products of intramolecular annealing.Some of these results were presented at the 5th European Meeting on Bacterial Transformation and Transfection, September 1980, Florence     

Can Ca2+-dependent competence be repeatedly induced in the same Escherichia coli cells?

Summary With the help of devised multicycle consecutive transformation (MCT) it is shown that Ca²⁺-dependent competence can be repeatedly induced in the same population of Escherichia coli cells. The same fraction of cells is induced to competence and transformed during MCT. In contrast to the results on classical transformation with mixed DNA preparations, no double transformants are observed in MCT. The competent cells and transformants are found to be more fragile than nontransformed cells. The latter are represented presumably by the cells that have not absorbed exogenous plasmid DNA. The results suggest that there is strong interference between plasmid DNAs during MCT, and that the presence of exogenous DNA makes the cells more sensitive to the apparently harmful procedure of repeated competence induction.     

Transformation and transduction of a large deletion mutation in Bacillus subtilis

Summary Large arsenate sensitive deletion mutations of B. subtilis 168 are transformed to wild type at least 100 times less efficiently than they are transduced by PBS1 phage. The lower transformation efficiency is apparently due to the degradation of the donor DNA by competent cells to fragments ineffective for repair of long deletions. The efficiency of transduction of deletion mutations is also reduced when competent cells, rather than logarithmically growing cells are used as recipients. An endonuclease activity specifically associated with the physiological state of competence is proposed to explain these observation.     

THE POTENTIAL FOR GENETIC EXCHANGE BY TRANSFORMATION WITHIN A NATURAL POPULATION OF BACILLUS SUBTILIS

We have investigated the potential for genetic exchange by transformation within a Mojave Desert population of Bacillus subtilis. Almost all strains surveyed were competent for transformation, and the strains varied over almost three orders of magnitude in their levels of competence. This high degree of variation suggests that natural selection toward an optimal level of competence is, at most, very weak in this population. Six of 24 competent strains showed sexual isolation from laboratory strain 168 (i.e., heterogamic transformation was reduced). Direct crosses between selected pairs of Mojave strains indicated sexual isolation within the Mojave population. Levels of sexual isolation observed within this population of B. subtilis were much less than those previously observed for transformation between named Bacillus species. Sexual isolation between 168 and Mojave strains, and among Mojave strains, was due to differences in restriction-modification systems and to DNA sequence divergence.     

Optimum Conditions for Electric Pulse-mediated Gene Transfer to Bacillus subtilis Cells

It was found that plasmid DNA (pUB 110) can be introduced into not only protoplasts but also intact cells of Bacillus subtilis by electric field pulses. The transformation of, B. subtilis using protoplasts results in an efficiency of 2.5 × 10⁴ transformants per μg of DNA, with a single pulse of 50 jisec with an initial electric field strength of 7kV/cm. Even transformation of intact B. subtilis cells results in a maximum efficiency of 1.5 × 10³ transformants per μg DNA, with a single pulse of 400 μsec with an initial electric field strength of 16kV/cm. The cell survival of protoplasts and intact cells was approximately 100% and 30%, respectively, under the conditions found to be optimal for the transformation process. Plasmid DNA isolated from pUB 110 containing transformants was indistinguishable from authentic preparations of pBU 110 on gel electrophoretic analysis.     

Optimal Strategy for Competence Differentiation in Bacteria

A phylogenetically diverse subset of bacterial species are naturally competent for transformation by DNA. Transformation entails recombination of genes between different lineages, representing a form of bacterial sex that increases standing genetic variation. We first assess whether homologous recombination by transformation is favored by evolution. Using stochastic population genetic computer simulations in which beneficial and deleterious mutations occur at many loci throughout the whole genome, we find that transformation can increase both the rate of adaptive evolution and the equilibrium level of fitness. Secondly, motivated by experimental observations of Bacillus subtilis, we assume that competence additionally entails a weak persister phenotype, i.e., the rates of birth and death are reduced for these cells. Consequently, persisters evolve more slowly than non-persisters. We show via simulation that strains which stochastically switch into and out of the competent phenotype are evolutionarily favored over strains that express only a single phenotype. Our model''s simplicity enables us to derive and numerically solve a system of finite- deterministic equations that describe the evolutionary dynamics. The observed tradeoff between the benefit of recombination and the cost of persistence may explain the previously mysterious observation that only a fractional subpopulation of B. subtilis cells express competence. More generally, this work demonstrates that population genetic forces can give rise to phenotypic diversity even in an unchanging and homogeneous environment.