Genetic study of plasmid integration into yeast chromosomes. V. Mapping of integration sites for the plasmid pYF91

The data on mapping the episomal plasmid integration sites in yeast chromosomes I, III, IV, V, VII, XV are presented. In addition to the integration site at leu2 of chromosome III localized earlier, 6 more loci containing apparently the homologous yeast transposons, with a copy in a plasmid, were defined. The fact of plasmid integration was proved by colony hybridization technique with the pBR322 probe. The plasmid DNA segregation (the ratio 2:2) and its linkage to pLEU2 plasmid marker gene were observed in hybrids of all integrants studied.     

Genetic study of plasmid integration into yeast chromosomes. III. Selection for a phenotype of Saccharomyces cerevisiae (Meyen ex Hansen) clones which lost the 2-micron DNA and their genetic testing

We used the coloured adeI (cir+) haploid strain containing an episomal plasmid integrated into the chromosome I for visual detection and genetic testing of Saccharomyces cerevisiae clones having lost 2 microns DNA. During incubation, colonies of this strain were covered with numerous papillae of the same genotype. Stable clones which did not generate such papillae were isolated. Hybrids of these clones with (cir0) partner were not shown to exhibit destabilization of the chimeric chromosome. The stable clones isolated proved to lack 2 microns DNA, as shown by colony hybridization technique. We conclude therefore that the loss of the cryptic yeast plasmid may be phenotypically detected.     

Genetic study of plasmid integration into yeast chromosomes. IV. Integration of the plasmid pYF91 into different yeast chromosomes

Integration of the episomic chimeric plasmid pYF91 into yeast chromosomes has been studied. Plasmid insertion into the chromosomes was observed to occur with the frequency of 4 X 10(-8). 379 integrants were selected from the highly unstable (cir0) transformants. The fact of plasmid integration into particular chromosomes was confirmed for 318 integrants. Genetic analysis showed that the plasmid can integrate into the region of LEU2 gene or into another arm of chromosome III (227 integrants), and also into other chromosomes: I, II, IV, V, VI, VII, VIII, IX, XII, XV (91 integrants). It is suggested that integration is the result of recombination between yeast chromosomes and homologous plasmid regions carrying LEU2 gene or Ty element and "delta" sequence.     

Improvement of S-adenosylmethionine production by integration of the ethionine-resistance gene into chromosomes of the yeast Saccharomyces cerevisiae

An ethionine-resistance gene cloned from Saccharomyces cerevisiae DKD-5D-H was able to enhance S-adenosyl-l-methionine (AdoMet) accumulation when it was introduced into the yeast cells on multi-copy plasmid YEp13. In order to increase the AdoMet accumulation, the gene was integrated into the yeast chromosome by using a yeast transposon Ty element. When the YEp plasmid was used for the integration, the ethionine-resistance gene was efficiently inserted into the yeast chromosomes with a substantial increase in AdoMet productivity (about twofold) in comparison with that by the yeast cells carrying the gene on an extrachromosomal multi-copy plasmid.     

Transposon-mediated integration of the RP1 plasmid into chromosomes of methylotrophic bacteria

The homology region between the DNA of plasmid RP1ts::Tn601 and chromosome of the thermotolerant methylotrophic bacterium Methylobacterium sp. SKF240 has been constructed by transposon Tn601 translocation into the chromosome. The clones of Methylobacterium sp. SKF240 having integrated the plasmid RP1 into the chromosome have been obtained by conjugation on the basis of above mentioned genetic technique. The integration of plasmid RP1 into the chromosomal DNA of the methylotroph has been confirmed by the genetic and electrophoretic methods. Clones harbouring the integrated plasmid are able to transfer the chromosomal genes for methionine and isoleucine-valine synthesis to the recipient cells of P. aeruginosa PAO ML4262 by conjugation.     

人工染色体研究进展

人工染色体是人工构建的含有天然染色体基本功能单位的载体系统总称。人工染色体是非常优良的载体,具有超大的接受外源片段能力。由于不用整合到宿主基因组中,因此不会引起宿主基因的插入失活,及抑制转基因表达的位置效应。人工染色体已经从最初的酵母人工染色体(Yeast artificial chromosome,YAC)发展到细菌人工染色体(Bacterial artificial chromosome,BAC),再扩展到人类人工染色体(Human artificial chromosome,HAC)和植物人工染色体(Plant artificial chromosome,PAC)。文章就这4种人工染色体,尤其是植物人工染色体的研究进展和应用局限进行综述。目前,YAC和BAC已经广泛应用于基因组图谱制作、序列测定和基因克隆;HAC和PAC在基因治疗、外源医用蛋白的生产、新型优质高产高抗转基因作物构建中显现出广阔的应用前景。随着合成生物学的高速发展,美国科学家报道合成了一个"人造生命"。但是,和人工染色体一样,所谓的"人造生命",都是应用最新的基因工程技术,将不同的生命基础元件拼接组装而成,脱离了细胞环境并不能够自由存在。     

Sequential cloning by a vector walking along the chromosome.

A procedure was devised for sequential cloning of chromosomal DNA by cyclical integration and excision of a plasmid vector so that slightly overlapping chromosomal segments are successively cloned. The method depends on circular integration of the vector into the chromosome of a host nonpermissive for its replication, and on excision and reduction of a recombinant plasmid by use of an appropriately designed set of restriction enzyme sites in the vector. A vector suitable for cloning in Escherichia coli was constructed by combining a segment of pBR322 with a gene encoding chloramphenicol resistance expressible in many species. Sequential cloning was demonstrated in Streptococcus pneumoniae by extending a previously cloned segment of the region of the chromosome encoding maltosaccharide utilization by 8 kb in three cycles of cloning. Accuracy of the method was confirmed by hybridization of cloned DNA with chromosomal restriction fragments. It is pointed out that the similarity of the requisite genetic processes in bacteria and yeasts should allow use of the method for sequential cloning of yeast chromosomal DNA and of human or other mammalian DNA in artificial chromosomes of yeast.     

A Rapid Chromosome-Mapping Method for Cloned Fragments of Yeast DNA

A rapid and generally applicable method is described for mapping a cloned yeast DNA segment to the chromosome(s) from which it originated. The method is based upon the recent finding that the integration into a yeast chromosome of a segment of the 2 mu plasmid DNA results, in heterozygous diploids, in the specific loss of genetic information from the chromosome into which the 2 mu DNA was integrated (Falco et al. 1982). After verification of the accuracy of the method using several genes whose position was known in advance, the method was used to locate the yeast actin gene, which lies on the left arm of chromosome VI, about 50 cM distal to CDC4.     

Rearrangements of yeast chromosomes revealed by pulsed field gel electrophoresis

Electrophoretic karyotypes of yeast Saccharomyces cerevisiae integrant strains containing the pYF91 plasmid integrated into the chromosomes I, III, VI, IX, XI were studied. A possibility was demonstrated of visual identification of the chimaeric chromosomes via the molecular weight increase by 13200 bp (the plasmid size) determined by pulsed field gel electrophoresis. Several gamma-rays induced rearrangements of the yeast chimaeric chromosome I causing instability in hybrids were also studied. The deletions induced in the I chromosome were analysed and their size estimated. The technique of pulsed field gel electrophoresis is recommended for determination of insertions and deletions in the chromosomes of yeast Saccharomyces cerevisiae.     

FLP-mediated DNA mobilization to specific target sites in Drosophila chromosomes.

The ability to place a series of gene constructs at a specific site in the genome opens new possibilities for the experimental examination of gene expression and chromosomal position effects. We report that the FLP- FRT site-specific recombination system of the yeast 2mu plasmid can be used to integrate DNA at a chromosomal FRT target site in Drosophila. The technique we used was to first integrate an FRT- flanked gene by standard P element-mediated transformation. FLP was then used to excise the FRT- flanked donor DNA and screen for FLP-mediated re-integration at an FRT target at a different chromosome location. Such events were recovered from up to 5% of the crosses used to screen for mobilization and are easily detectable by altered linkage of a white reporter gene or by the generation of a white + gene upon integration.     

Chromosome-scale genetic mapping using a set of 16 conditionally stable Saccharomyces cerevisiae chromosomes

We have created a resource to rapidly map genetic traits to specific chromosomes in yeast. This mapping is done using a set of 16 yeast strains each containing a different chromosome with a conditionally functional centromere. Conditional centromere function is achieved by integration of a GAL1 promoter in cis to centromere sequences. We show that the 16 yeast chromosomes can be individually lost in diploid strains, which become hemizygous for the destabilized chromosome. Interestingly, most 2n - 1 strains endoduplicate and become 2n. We also demonstrate how chromosome loss in this set of strains can be used to map both recessive and dominant markers to specific chromosomes. In addition, we show that this method can be used to rapidly validate gene assignments from screens of strain libraries such as the yeast gene disruption collection.     

Suppression of initiation defects of chromosome replication in Bacillus subtilis dnaA and oriC-deleted mutants by integration of a plasmid replicon into the chromosomes.

We constructed Bacillus subtilis strains in which chromosome replication initiates from the minimal replicon of a plasmid isolated from Bacillus natto, independently of oriC. Integration of the replicon in either orientation at the proA locus (115 degrees on the genetic map) suppressed the temperature-sensitive phenotype caused by a mutation in dnaA, a gene required for initiation of replication from oriC. In addition, in a strain with the plasmid replicon integrated into the chromosome, we were able to delete sequences required for oriC function. These strains were viable but had a slower growth rate than the oriC+ strains. Marker frequency analysis revealed that both pyrD and metD, genes close to proA, showed the highest values among the markers (genes) measured, and those of other markers decreased symmetrically with distance from the site of the integration (proA). These results indicated that the integrated plasmid replicon operated as a new and sole origin of chromosome replication in these strains and that the mode of replication was bidirectional. Interestingly, these mutants produced anucleate cells at a high frequency (about 40% in exponential culture), and the distribution of chromosomes in the cells was irregular. A change in the site and mechanism (from oriC to a plasmid system) of initiation appears to have resulted in a drastic alteration in coordination between chromosome replication and chromosome partition or cell division.     

Host-vector system for integration of recombinant DNA into chromosomes of transformable and nontransformable streptococci.

We describe a genetic system in which transformation of Streptococcus pneumoniae and Streptococcus sanguis was used to insert recombinant DNA into the conjugative chromosomal element omega (cat tetM) 6001 (omega 6001). The element containing the recombinant DNA was then transferred by conjugation to the chromosome of transformable and nontransformable streptococci. When Escherichia coli plasmid pDP36 was used as donor in transformation, it was capable of inserting 5.9 kilobases of heterologous DNA into the chromosome of competent streptococcal strains carrying omega 6001; the transformants were scored for erythromycin resistance. Genetic analysis showed that in a fraction of the erythromycin-resistant transformants the integration via flanking homology of the heterologous DNA caused inactivation of the tetM gene of omega 6001. By analyzing the stability of the resistance markers, we found that stable integration of heterologous DNA was achieved only in the erythromycin-resistant, tetracycline-sensitive transformants. It was possible to detect conjugal transfer of the heterologous sequences from stable transformants to strains of S. pneumoniae, S. sanguis, Streptococcus pyogenes, and Streptococcus faecalis. The omega 6001-pDP36 host-vector system opens new possibilities for gene transfer in streptococci. By this method cloned streptococcal DNA (possibly mutagenized in vitro) can be returned to the original host, greatly facilitating complementation tests and fine physiological studies.     

Trans-kingdom T-DNA transfer from Agrobacterium tumefaciens to Saccharomyces cerevisiae.

Agrobacterium tumefaciens transfers part of its tumour-inducing (Ti) plasmid, the transferred or T-DNA, to plants during tumourigenesis. This represents the only example of naturally occurring trans-kingdom transfer of genetic material. Here we report that A.tumefaciens can transfer its T-DNA not only to plant cells, but also to another eukaryote, namely the yeast Saccharomyces cerevisiae. The Ti plasmid virulence (vir) genes that mediate T-DNA transfer to plants were found to be essential for transfer to yeast as well. Transgenic S.cerevisiae strains were analysed for their T-DNA content. Results showed that T-DNA circles were formed in yeast with precise fusions between the left and right borders. Such T-DNA circles were stably maintained by the yeast if the replicator from the yeast 2 mu plasmid was present in the T-DNA. Integration of T-DNA in the S.cerevisiae genome was found to occur via homologous recombination. This contrasts with integration in the plant genome, where T-DNA integrates preferentially via illegitimate recombination. Our results thus suggest that the process of T-DNA integration is predominantly determined by host factors.     

Structural organization and functional analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe.

Centromeric DNA in the fission yeast Schizosaccharomyces pombe was isolated by chromosome walking and by field inversion gel electrophoretic fractionation of large genomic DNA restriction fragments. The centromere regions of the three chromosomes were contained on three SalI fragments (120 kilobases [kb], chromosome III; 90 kb, chromosome II; and 50 kb, chromosome I). Each fragment contained several repetitive DNA sequences, including repeat K (6.4 kb), repeat L (6.0 kb), and repeat B, that occurred only in the three centromere regions. On chromosome II, these repeats were organized into a 35-kb inverted repeat that included one copy of K and L in each arm of the repeat. Site-directed integration of a plasmid containing the yeast LEU2 gene into K repeats at each of the centromeres or integration of an intact K repeat into a chromosome arm had no effect on mitotic or meiotic centromere function. The centromeric repeat sequences were not transcribed and possessed many of the properties of constitutive heterochromatin. Thus, S. pombe is an excellent model system for studies on the role of repetitive sequence elements in centromere function.     

Functions antagonistic to plasmid formation by lambda N- chromosomes

It was concluded in the preceding paper that lambda N- cI- genomes probably failed to form plasmids within infected Escherichia coli cells because they leakily express functions that act to destabilize the plasmid state. This prediction was investigated by examining the effect upon plasmid-forming ability of the loss of possible anti-plasmid functions. The loss of Ter function was found to allow long-term plasmid formation, although the efficiency of initial plasmid formation and the heritable stability without selection were low. The combined loss of the int, red and gam gene functions also promoted plasmid growth, although the absence of Ter lambda was necessary. In contrast, the presence of Ter80 (due to an h80 substitution) did not prevent plasmid formation when the int, red and gam genes were absent, indicating that Ter80 does not attack the closed-circular form of the lambda chromosome. The combined loss of the ter, int, red and gam gene functions facilitated fully efficient inheritance of the lambda N- cI- plasmids in the absence of selection, although the efficiency of initial plasmid formation remained low. However, cells harbouring such plasmids suffered a decline in viability, indicating that the plasmids expressed a function (or more than one) that acts to debilitate the host cells--presumably an effect that is increased with this genotype because the modified lambda N- cI- plasmids are inherently more stable. The possible involvement of the lambda S and kil functions in destabilization is discussed.     

New tools for the physical and genetic mapping of Lactococcus strains.

Tools for the genetic and physical analysis of the Lactococcus lactis subsp. lactis genome were developed. Plasmid pRC1 does not replicate in Gram+ bacteria; it contains unique ApaI, NotI and SmaI restriction sites and an erythromycin-resistance (ErR) encoding gene, ermAM, functional in L. lactis subsp. lactis. When a chromosomal L. lactis subsp. lactis DNA fragment was cloned into this vector, the resulting plasmid became integrated, after transformation, into the bacterial chromosome by homologous recombination in a Campbell-like manner. The integration lead to the generation of new rare restriction sites near to the host fragment. This procedure allows precise mapping of cloned genes onto the chromosomal restriction map. The mapping of the his operon of L. lactis subsp. lactis provides an illustration. The cloning into pRC1 of an IS element able to transpose into the chromosome of the target cell, gave rise to an integration plasmid able to insert randomly rare restriction sites onto the bacterial chromosome. The L. lactis IS element, ISS1RS, was cloned into pRC1, yielding pRL1. Pulsed-field gel electrophoresis analysis of ErR clones obtained after transformation with pRL1, showed that this plasmid was stably integrated at a number of different sites in the L. lactis subsp. lactis chromosome, via transposition. Plasmids pRC1 and pRL1 can greatly facilitate the construction of the physical and genetic map of the chromosome of lactococcal strains.     

Radiation-induced instability of yeast chimeric chromosomes

Instability of the I chimeric chromosome of the yeast Saccharomyces induced by gamma-irradiation has been studied. The chimeric chromosome analysed contained an integrated pYF91 plasmid. Cells of the integrant were irradiated and then mated with non-irradiated cells of the proper tester strain marked by ade1 mutation (red colour of colonies). We isolated 10 hybrids with pink colonies on selective medium. They displayed high degree of mitotic instability during growth on nonselective medium, segregating red colonies (15 to 90% of the total). Tetrad analysis showed that some of the unstable chromosomes exhibited lethal effect in haploids, while others were viable and could pass through meiosis retaining their instability.     

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

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

Topoisomerase IV is required for partitioning of circular chromosomes but not linear chromosomes in Streptomyces

Filamentous bacteria of the genus Streptomyces possess linear chromosomes and linear plasmids. Theoretically, linear replicons may not need a decatenase for post-replicational separation of daughter molecules. Yet, Streptomyces contain parC and parE that encode the subunits for the decatenase topoisomerase IV. The linear replicons of Streptomyces adopt a circular configuration in vivo through telomere–telomere interaction, which would require decatenation, if the circular configuration persists through replication. We investigated whether topoisomerase IV is required for separation of the linear replicons in Streptomyces. Deletion of parE from the Streptomyces coelicolor chromosome was achieved, when parE was provided on a plasmid. Subsequently, the plasmid was eliminated at high temperature, and ΔparE mutants were obtained. These results indicated that topoisomerase IV was not essential for Streptomyces. Presumably, the telomere–telomere association may be resolved during or after replication to separate the daughter chromosomes. Nevertheless, the mutants exhibited retarded growth, defective sporulation and temperature sensitivity. In the mutants, circular plasmids could not replicate, and spontaneous circularization of the chromosome was not observed, indicating that topoisomerase IV was required for decatenation of circular replicons. Moreover, site-specific integration of a plasmid is impaired in the mutants, suggesting the formation of DNA knots during integration, which must be resolved by topoisomerase IV.