Single Crossover Event Research Articles

Creation of Markerless Genome Modifications in a Nonmodel Bacterium by Fluorescence-Aided Recombineering.

Metabolic engineering of nonmodel bacteria is often challenging because of the paucity of genetic tools for iterative genome modification necessary to equip bacteria with pathways to produce high-value products. Here, we outline a homologous recombination-based method developed to delete or add genes to the genome of a nonmodel bacterium, Zymomonas mobilis, at the desired locus using a suicide plasmid that contains gfp as a fluorescence marker to track its presence in cells. The suicide plasmid is engineered to contain two 500bp regions homologous to the DNA sequence immediately flanking the target locus. A single crossover event at one of the two homologous regions facilitates insertion of the plasmid into the genome and subsequent homologous recombination events excise the plasmid from the genome, leaving either the original genotype or the desired modified genotype. A key feature of this plasmid is that Green Fluorescent Protein (GFP) expressed from the suicide plasmid allows easy identification and sorting of cells that have lost the plasmid by use of a fluorescence activated cell sorter. Subsequent PCR amplification of genomic DNA from strains lacking GFP allows rapid identification of the desired genotype, which is confirmed by DNA sequencing. This method provides an efficient and flexible platform for improved genetic engineering of Z. mobilis, which can be easily adapted to other nonmodel bacteria.

Use of the counter selectable marker PheS* for genome engineering in Staphylococcus aureus.

The gold standard method for the creation of gene deletions in Staphylococcus aureus is homologous recombination using allelic exchange plasmids with a temperature-sensitive origin of replication. A knockout vector that contains regions of homology is first integrated into the chromosome of S. aureus by a single crossover event selected for at high temperatures (non-permissive for plasmid replication) and antibiotic selection. Next, the second crossover event is encouraged by growth without antibiotic selection at low temperature, leading at a certain frequency to the excision of the plasmid and the deletion of the gene of interest. To detect or encourage plasmid loss, either a beta-galactosidase screening method or, more typically, a counterselection step is used. We present here the adaptation of the counter-selectable marker pheS*, coding for a mutated subunit of the phenylalanine tRNA synthetase, for use in S. aureus. The PheS* protein variant allows for the incorporation of the toxic phenylalanine amino acid analogue para-chlorophenylalanine (PCPA) into proteins and the addition of 20-40 mM PCPA to rich media leads to drastic growth reduction for S. aureus and supplementing chemically defined medium with 2.5-5 mM PCPA leads to complete growth inhibition. Using the new allelic exchange plasmid pIMAY*, we delete the magnesium transporter gene mgtE in S. aureus USA300 LAC* (SAUSA300_0910/SAUSA300_RS04895) and RN4220 (SAOUHSC_00945) and demonstrate that cobalt toxicity in S. aureus is mainly mediated by the presence of MgtE. This new plasmid will aid the efficient and easy creation of gene knockouts in S. aureus.

The Molecular and Genetic Characterization of Second Chromosome Balancers in Drosophila melanogaster.

Balancer chromosomes are multiply inverted and rearranged chromosomes used in Drosophila melanogaster for many tasks, such as maintaining mutant alleles in stock and complex stock construction. Balancers were created before molecular characterization of their breakpoints was possible, so the precise locations of many of these breakpoints are unknown. Here, we report or confirm the positions of the 14 euchromatic breakpoints on the 2nd chromosome balancers SM1, SM5, CyO, and SM6a. This total includes three breakpoints involved in a complex rearrangement on SM5 that is associated with the duplication of two genomic regions. Unbiased sequencing of several balancers allowed us to identify stocks with incorrectly identified balancers as well as single and double crossover events that had occurred between 2nd chromosome balancers and their homologs. The confirmed crossover events that we recovered were at least 2 Mb from the closest inversion breakpoint, consistent with observations from other balancer chromosomes. Balancer chromosomes differ from one another both by large tracts of sequence diversity generated by recombination and by small differences, such as single nucleotide polymorphisms (SNPs). Therefore, we also report loss-of-function mutations carried by these chromosomes and unique SNP and InDel polymorphisms present on only single balancers. These findings provide valuable information about the structure of commonly used 2nd chromosome balancers and extend recent work examining the structure of X and 3rd chromosome balancers. Finally, these observations provide new insights into how the sequences of individual balancers have diverged over time.

High-throughput system for quantifying and characterizing homologous recombination in Chlamydomonas reinhardtii

In the green alga Chlamydomonas reinhardtii, introduced DNA fragments predominantly insert randomly into the nuclear genome by non-homologous recombination (NHR), often resulting in highly variable phenotypes between transformants. Homologous recombination (HR) can occur in C. reinhardtii but at very low frequency, and is often accompanied by insertions, deletions, and/or rearrangements at the recombination site. To benchmark the frequency and characterize the nature of HR integrations in C. reinhardtii, we developed a system for detecting and characterizing HR events that includes three intact markers and one split marker as well a novel design element: utilizing a long intron as the homology region. In this study we demonstrate that this system meets the following criteria: accommodates high-throughput screening; provides a high-fidelity phenotype for detecting HR without false positives from reversion or locus heterogeneity; allows and captures both single- and double-crossover HR events; reports HR and NHR rates from a single transformation; and allows characterization of imprecise recombination or rearrangement at the integration site. Using this system we reproducibly determined the HR rate in our recipient strain of C. reinhardtii and characterized a number of recombinants by restriction digests and sequencing of PCR amplified recombination junctions to show that both double and single crossover events were recovered and that integration occurred both via perfect and imperfect (i.e. accompanied by insertions, deletions, and rearrangements) HR. This system is valuable for systematically testing approaches for increasing HR efficiency and accuracy.

Genetic transformation to integrate two expression cassettes into the genome of yeast Pichia pastoris

Background Pichia pastoris is a methylotrophic species of yeast, which means that it can grow on methanol as its sole carbon and energy source [1]. The Pichia expression system has several advantages: short length of the oligosaccharide chains added to proteins, correct folding and very high cell densities [2]. P. pastoris vectors are designed for homologous integration into either AOX I locus, one of the two homologous AOX I genes present in this species or his4 locus. Gene insertion events at the AOX I (GS115) loci arise from a single crossover events between the loci and any of the three AOX I regions in the vector, the AOX I promoter, the AOX I transcription termination region (TT), or sequences even further downstream of AOX I (3′ AOX I) [3]. In either GS115 gene insertion events at his4 locus arise from a single crossover event between his4 locus in the chromosome and His4 gene of the vector. This results in the insertion of one or more copies of the vector in his4 locus [3].

Gamete-Type Dependent Crossover Interference Levels in a Defined Region ofCaenorhabditis elegansChromosome V

In certain organisms, numbers of crossover events for any single chromosome are limited (“crossover interference”) so that double crossover events are obtained at much lower frequencies than would be expected from the simple product of independent single-crossover events. We present a number of observations during which we examined interference over a large region of Caenorhabditis elegans chromosome V. Examining this region for multiple crossover events in heteroallelic configurations with limited dimorphism, we observed high levels of crossover interference in oocytes with only partial interference in spermatocytes.

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA

Background454 sequencing technology is a promising approach for characterizing HIV-1 populations and for identifying low frequency mutations. The utility of 454 technology for determining allele frequencies and linkage associations in HIV infected individuals has not been extensively investigated. We evaluated the performance of 454 sequencing for characterizing HIV populations with defined allele frequencies.ResultsWe constructed two HIV-1 RT clones. Clone A was a wild type sequence. Clone B was identical to clone A except it contained 13 introduced drug resistant mutations. The clones were mixed at ratios ranging from 1% to 50% and were amplified by standard PCR conditions and by PCR conditions aimed at reducing PCR-based recombination. The products were sequenced using 454 pyrosequencing. Sequence analysis from standard PCR amplification revealed that 14% of all sequencing reads from a sample with a 50:50 mixture of wild type and mutant DNA were recombinants. The majority of the recombinants were the result of a single crossover event which can happen during PCR when the DNA polymerase terminates synthesis prematurely. The incompletely extended template then competes for primer sites in subsequent rounds of PCR. Although less often, a spectrum of other distinct crossover patterns was also detected. In addition, we observed point mutation errors ranging from 0.01% to 1.0% per base as well as indel (insertion and deletion) errors ranging from 0.02% to nearly 50%. The point errors (single nucleotide substitution errors) were mainly introduced during PCR while indels were the result of pyrosequencing. We then used new PCR conditions designed to reduce PCR-based recombination. Using these new conditions, the frequency of recombination was reduced 27-fold. The new conditions had no effect on point mutation errors. We found that 454 pyrosequencing was capable of identifying minority HIV-1 mutations at frequencies down to 0.1% at some nucleotide positions.ConclusionStandard PCR amplification results in a high frequency of PCR-introduced recombination precluding its use for linkage analysis of HIV populations using 454 pyrosequencing. We designed a new PCR protocol that resulted in a much lower recombination frequency and provided a powerful technique for linkage analysis and haplotype determination in HIV-1 populations. Our analyses of 454 sequencing results also demonstrated that at some specific HIV-1 drug resistant sites, mutations can reliably be detected at frequencies down to 0.1%.

Construction of Chromosomal In-Frame Deletion Mutants in Rhodobacter capsulatus

Markerless chromosomal in-frame deletion mutants are often used to avoid polar effects, conserve antibiotic resistance markers or make multiple mutations. This protocol capitalizes on the sacB gene (lethal in the presence of sucrose), for selection against a single cross-over event, on a suicide vector (contains no Rhodobacter capsulatus compatible origin of replication). The bacterial strains, media and suicide vectors in this protocol are specific for R. capsulatus, but the concepts can be applied to other species.

Assessment of intergenomic recombination through GISH analysis of F1, BC1 and BC2 progenies of Tulipa gesneriana and T. fosteriana

Using 23 F1 hybrids, 14 BC1 and 32 BC2 progenies, the genome composition of Darwin hybrid tulips was analysed through genomic in situ hybridisation (GISH) of somatic chromosomes. All plants were diploids (2n = 2x = 24) with the exception of one tetraploid BC1 (2n = 4x = 48) and one aneuploid BC2 (2n = 2x + 1 = 25) hybrid. Morphometric analysis in F1 hybrids revealed a difference in the total length of chromosomes representing genomes of T. gesneriana and T. fosteriana, where the percentage of each genome equaled 55.18 ± 0.8 and 44.92 ± 0.6% respectively. GISH distinguished chromosomes from both parent genomes although there was a lack of consistent chromosome labelling in some cases. In both T. gesneriana and T. fosteriana chromosomes some segments of heterochromatin in the telomeric and intercalary regions exhibited a higher intensity of fluorescence. In situ hybridisation with 5S rDNA and 45S rDNA probes to metaphase chromosomes of F1 hybrids showed that these regions are rich in rDNA. A notable feature was that, despite genome differences, there was a considerable amount of intergenomic recombination between the parental chromosomes of the two species as estimated in both BC1 and BC2 offspring. The number of recombinant chromosomes ranged from 3 to 8 in BC1 and from 1 to 7 in BC2 progenies. All recombinant chromosomes possessed mostly a single recombinant segment derived from either a single crossover event or in a few cases double crossover events. This explains the fact that, unlike the situation in most F1 hybrids of other plant species, certain genotypes of Darwin hybrid tulips behave like normal diploid plants producing haploid gametes and give rise to mostly diploid sporophytes.

Construction of recombinant Bacillus subtilis strains for efficient pimelic acid synthesis

As a precursor, pimelic acid plays an important role in biotin biosynthesis pathway of Bacillus subtilis . Fermentations supplemented with pimelic acid could improve the production of biotin, however, with a disadvantage-high cost. So it is necessary to improve the biosynthesis of pimelic acid via genetic engineering in B. subtilis . In this study, we constructed a recombinant B. subtilis strain for improving the synthesis of pimelic acid, in which a maltose-inducible P glv promoter was inserted into the upstream of the cistron bioI-orf2-orf3 and, meanwhile, flanked by the tandem cistrons via a single crossover event. The copy number of the integrant was amplified by high-concentration resistance screen and increased to 4-5 copies. The production of pimelic acid from multiple copies integrant was about 4 times higher than that from single copy (1017.13 μg/ml VS. 198.89 μg/ml). And when induced by maltose the production of pimelic acid was about 2 times of that under non-induction conditions (2360.73 μg/ml VS. 991.59 μg/ml). Thus, these results demonstrated that the production of pimelic acid was improved obviously through reconstructed B. subtilis . It also suggested that our expression system provided a convenient source of pimelic acid that would potentially lower the cost of production of biotin from engineered B. subtilis .

Analysis of the mating-type loci of co-occurring and phylogenetically related species of Ascochyta and Phoma.

Ascochyta and Phoma are fungal genera containing several important plant pathogenic species. These genera are morphologically similar, and recent molecular studies performed to unravel their phylogeny have resulted in the establishment of several new genera within the newly erected Didymellaceae family. An analysis of the structure of fungal mating-type genes can contribute to a better understanding of the taxonomic relationships of these plant pathogens, and may shed some light on their evolution and on differences in sexual strategy and pathogenicity. We analysed the mating-type loci of phylogenetically closely related Ascochyta and Phoma species (Phoma clematidina, Didymella vitalbina, Didymella clematidis, Peyronellaea pinodes and Peyronellaea pinodella) that co-occur on the same hosts, either on Clematis or Pisum. The results confirm that the mating-type genes provide the information to distinguish between the homothallic Pey. pinodes (formerly Ascochyta pinodes) and the heterothallic Pey. pinodella (formerly Phoma pinodella), and indicate the close phylogenetic relationship between these two species that are part of the disease complex responsible for Ascochyta blight on pea. Furthermore, our analysis of the mating-type genes of the fungal species responsible for causing wilt of Clematis sp. revealed that the heterothallic D. vitalbina (Phoma anamorph) is more closely related to the homothallic D. clematidis (Ascochyta anamorph) than to the heterothallic P. clematidina. Finally, our results indicate that homothallism in D. clematidis resulted from a single crossover between MAT1-1 and MAT1-2 sequences of heterothallic ancestors, whereas a single crossover event followed by an inversion of a fused MAT1/2 locus resulted in homothallism in Pey. pinodes.

Arrested Oocyst Maturation in Plasmodium Parasites Lacking Type II NADH:Ubiquinone Dehydrogenase

The Plasmodium mitochondrial electron transport chain has received considerable attention as a potential target for new antimalarial drugs. Atovaquone, a potent inhibitor of Plasmodium cytochrome bc(1), in combination with proguanil is recommended for chemoprophylaxis and treatment of malaria. The type II NADH:ubiquinone oxidoreductase (NDH2) is considered an attractive drug target, as its inhibition is thought to lead to the arrest of the mitochondrial electron transport chain and, as a consequence, pyrimidine biosynthesis, an essential pathway for the parasite. Using the rodent malaria parasite Plasmodium berghei as an in vivo infection model, we studied the role of NDH2 during Plasmodium life cycle progression. NDH2 can be deleted by targeted gene disruption and, thus, is dispensable for the pathogenic asexual blood stages, disproving the candidacy for an anti-malarial drug target. After transmission to the insect vector, NDH2-deficient ookinetes display an intact mitochondrial membrane potential. However, ndh2(-) parasites fail to develop into mature oocysts in the mosquito midgut. We propose that Plasmodium blood stage parasites rely on glycolysis as the main ATP generating process, whereas in the invertebrate vector, a glucose-deprived environment, the malaria parasite is dependent on an intact mitochondrial respiratory chain.

A Large-Deviation Analysis of the Maximum-Likelihood Learning of Markov Tree Structures

The problem of maximum-likelihood (ML) estimation of discrete tree-structured distributions is considered. Chow and Liu established that ML-estimation reduces to the construction of a maximum-weight spanning tree using the empirical mutual information quantities as the edge weights. Using the theory of large-deviations, we analyze the exponent associated with the error probability of the event that the ML-estimate of the Markov tree structure differs from the true tree structure, given a set of independently drawn samples. By exploiting the fact that the output of ML-estimation is a tree, we establish that the error exponent is equal to the exponential rate of decay of a single dominant crossover event. We prove that in this dominant crossover event, a non-neighbor node pair replaces a true edge of the distribution that is along the path of edges in the true tree graph connecting the nodes in the non-neighbor pair. Using ideas from Euclidean information theory, we then analyze the scenario of ML-estimation in the very noisy learning regime and show that the error exponent can be approximated as a ratio, which is interpreted as the signal-to-noise ratio (SNR) for learning tree distributions. We show via numerical experiments that in this regime, our SNR approximation is accurate.

How and Why Chromosome Inversions Evolve

Alfred Sturtevant, who invented genetic mapping while still an undergraduate, published the first evidence of a chromosomal inversion in 1921 [1]. He suggested then, and later proved, that they have a dramatic effect on transmission: when heterozygous, inversions suppress recombination. Over the next half century, inspired largely by Dobzhansky and his coworkers, much of empirical population genetics devoted itself to studying the abundant polymorphisms within and fixed differences of inversions between species of Drosophila [2]. Starting in the 1970s, this rich literature largely sank from view with the rise of biochemical and then molecular genetics. But inversions are ascendant again. Comparative genomics is now revealing that chromosomes are far more structurally fluid than even Dobzhansky dared to suppose. Where classic cytogenetics identified only nine inversions that distinguish humans and chimpanzees, comparison of their genomic sequences reveals on the order of 1,500 [3] (Figure 1). Despite the importance of inversions as a major mechanism for reorganizing the genome, we are still struggling to understand how and why they evolve almost a century after Sturtevant's discovery. Figure 1 Chromosome inversions that distinguish humans and chimpanzees inferred from a comparison of their genomic sequences [3]. An inversion occurs when a chromosome breaks at two points and the segment bounded by the breakpoints is reinserted in the reversed orientation. Several molecular mechanisms can mediate this event [4]. Box 1 gives an overview of some basic properties of inversions and the ways that they are detected. Box 1. What are chromosome inversions? Inversions are a diverse class of chromsomal mutation. The majority are small (<1KB) [3]. Others, for example the famous 3RP inversion of Drosophila melanogaster, are several megabases in size, include several percent of the entire genome and span hundreds or thousands of genes [10]. Inversions fall into two classes: pericentric inversions include a centromere, while paracentric inversions do not. With pericentric inversions, a single crossover event that occurs between the breakpoints of a heterozygote produces unbalanced gametes that carry deletions, insertions, and either zero or two centromeres. This can reduce fertility, making the inversions underdominant (lowered heterozygote fitness). Some pericentric inversions apparently escape fitness costs when heterozygous, however, perhaps because they somehow suppress recombination [33]. Although these may represent but a small fraction of all pericentric inversions that arise by mutation, they are likely to be greatly enriched among those that spread to fixation. There are large systematic differences between taxa in the frequency and severity of fitness effects. For example, heterozygotes for inversions seem to show decreased fertility in plants much more commonly than in animals [10]. By contrast, many of the paracentric inversions segregating in nature may not suffer from underdominance. This is likely a major reason why they are orders of magnitude more common than pericentric inversions, both as polymorphisms within and fixed differences between species [33]. Inversions were first seen in the giant salivary chromosomes of larval flies, and Diptera remains the group in which large inversions can be most easily detected. Chromosome staining techniques are able to visualize inversions in some other groups, including mammals, but with much lower resolution (and greater effort). The presence of an inversion is suggested when a certain cross consistently shows blocked recombination in part of the genome, but this observation requires genetic markers that have been mapped. Sequencing is a third way in which inversions are detected. The short reads that are characteristic of current high-throughput sequencing methods are well-suited to determine if an individual carries an inversion that has already been characterized by its breakpoints, but this technology is poor at prospecting for new inversions. In many cases, there is virtually no difference in the genetic content of inverted and uninverted chromosomes—only the linear order of DNA bases is changed. This situation presents evolutionary biologists with an intriguing question: if an inverted chromosome has (almost) the same genetic information as an uninverted one, what could cause it to spread through a population? This primer begins with an overview of the evolutionary forces that act on inversions. It then discusses the importance of inversions to the evolution of sex chromosomes, speciation, and local adaptation. Finally, we will see how several of these themes are illuminated by an exciting study on an inversion in a plant that appears in this issue of PLoS Biology.

IS6100-mediated genetic rearrangement within the complex class 1 integron In104 of the Salmonella genomic island 1

IS6100-mediated genetic rearrangement within the complex class 1 integron In104 of the Salmonella genomic island 1

Cre- lox -Based Method for Generation of Large Deletions within the Genomic Magnetosome Island of Magnetospirillum gryphiswaldense

Magnetosome biomineralization and magnetotaxis in magnetotactic bacteria are controlled by numerous, mostly unknown gene functions that are predominantly encoded by several operons located within the genomic magnetosome island (MAI). Genetic analysis of magnetotactic bacteria has remained difficult and requires the development of novel tools. We established a Cre-lox-based deletion method which allows the excision of large genomic fragments in Magnetospirillum gryphiswaldense. Two conjugative suicide plasmids harboring lox sites that flanked the target region were subsequently inserted into the chromosome by homologous recombination, requiring only one single-crossover event, respectively, and resulting in a double cointegrate. Excision of the targeted chromosomal segment that included the inserted plasmids and their resistance markers was induced by trans expression of Cre recombinase, which leaves behind a scar of only a single loxP site. The Cre helper plasmid was then cured from the deletant strain by relief of antibiotic selection. We have used this method for the deletion of 16.3-kb, 61-kb, and 67.3-kb fragments from the genomic MAI, either in a single round or in subsequent rounds of deletion, covering a region of approximately 87 kb that comprises the mamAB, mms6, and mamGFDC operons. As expected, all mutants were Mag(-) and some were Mot(-); otherwise, they showed normal growth patterns, which indicates that the deleted region is not essential for viability in the laboratory. The method will facilitate future functional analysis of magnetosome genes and also can be utilized for large-scale genome engineering in magnetotactic bacteria.

Efficient and precise construction of markerless manipulations in the Bacillus subtilis genome

We have developed an efficient and precise method for genome manipulations in Bacillus subtilis that allows rapid alteration of gene sequence or multiple gene sequences without altering the chromosome in any other way. In our approach, the Escherichia coli toxin gene mazF, which was used as a counter-selectable marker, was placed under the control of a xylose-inducible expression system and associated with an antibiotic-resistance gene to create a mazF-cassette'. A polymerase chain reaction (PCR)-generated fragment, consisting of two homology regions joined to the mazF-cassette, was integrated into the chromosome at the target locus by homologous recombination, using positive selection for antibiotic resistance. Then, the excision of the mazF-cassette from the chromosome by a single-crossover event between two short directly-repeated (DR) sequences, included in the design of the PCR products, was achieved by counter-selection of mazF. We used this method efficiently and precisely to deliver a point mutation, to inactivate a specific gene, to delete a large genomic region, and to generate the in-frame deletion with minimal polar effects in the same background.

Transformation of Anaplasma marginale

The tick-borne pathogen, Anaplasma marginale, has a complex life cycle involving ruminants and ixodid ticks. It causes bovine anaplasmosis, a disease with significant economic impact on cattle farming worldwide. The obligate intracellular growth requirement of the bacteria poses a challenging obstacle to their genetic manipulation, a problem shared with other prokaryotes in the genera Anaplasma, Ehrlichia, and Rickettsia. Following our successful transformation of the human anaplasmosis agent, A. phagocytophilum, we produced plasmid constructs (a transposon bearing plasmid, pHimarAm-trTurboGFP-SS, and a transposase expression plasmid, pET28Am-trA7) designed to mediate random insertion of the TurboGFP and spectinomycin/streptomycin resistance genes by the Himar1 allele A7 into the A. marginale chromosome. In these trans constructs, expression of the fluorescent and the selectable markers on the transposon, and expression of the transposase are under control of the A. marginale tr promoter. Constructs were co-electroporated into A. marginale St. Maries purified from tick cell culture, and bacteria incubated for 2 months under selection with a combination of spectinomycin and streptomycin. At that time, ≤1% of tick cells contained colonies of brightly fluorescent Anaplasma, which eventually increased to infect about 80–90% of the cells. Cloning of the insertion site in E. coli and DNA sequence analyses demonstrated insertion of the entire plasmid pHimarAm-trTurboGFP-SS encoding the transposon in frame into the native tr region of A. marginale in an apparent single homologous crossover event not mediated by the transposase. Transformants are fastidious and require longer subculture intervals than wild type A. marginale. This result suggests that A. marginale, as well as possibly other species of Anaplasma and Ehrlichia, can be transformed using a strategy of homologous recombination.

Electroporation is a feasible method to introduce circularized or linearized DNA into B. subtilis 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.

Directed Mutagenesis of the Rickettsia prowazekii pld Gene Encoding Phospholipase D

Rickettsia prowazekii, the causative agent of epidemic typhus, is an obligately intracytoplasmic bacterium, a lifestyle that imposes significant barriers to genetic manipulation. The key to understanding how this unique bacterium evades host immunity is the mutagenesis of selected genes hypothesized to be involved in virulence. The R. prowazekii pld gene, encoding a protein with phospholipase D activity, has been associated with phagosomal escape. To demonstrate the feasibility of site-directed knockout mutagenesis of rickettsial genes and to generate a nonrevertible vaccine strain, we utilized homologous recombination to generate a pld mutant of the virulent R. prowazekii strain Madrid Evir. Using linear DNA for transformation, a double-crossover event resulted in the replacement of the rickettsial wild-type gene with a partially deleted pld gene. Linear DNA was used to prevent potentially revertible single-crossover events resulting in plasmid insertion. Southern blot and PCR analyses were used to confirm the presence of the desired mutation and to demonstrate clonality. While no phenotypic differences were observed between the mutant and wild-type strains when grown in tissue culture, the pld mutant exhibited attenuated virulence in the guinea pig model. In addition, animals immunized with the mutant strain were protected against subsequent challenge with the virulent Breinl strain, suggesting that this transformant could serve as a nonrevertible, attenuated vaccine strain. This study demonstrates the feasibility of generating site-directed rickettsial gene mutants, providing a new tool for understanding rickettsial biology and furthering advances in the prevention of epidemic typhus.