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PubMed1980

Cyanobacterial plasmids: their widespread occurrence, and the existence of regions of homology between plasmids in the same and different species.

The results of screening of 29 diverse cyanobacterial (blue-green algal) strains for plasmid (CCC DNA) content are reported. Approximately one-half of the strains were shown to contain one or more CCC DNAs. CCC DNAs from four unicellular marine cyanobacteria were characterized in more detail. These strains contained multiple plasmids. Two kinds of Southern hybridization experiments allowed us to show that different plasmids within the same strain, and different plasmids within different strains, can ( but do not always) contain restricted regions of sequence homology. We suggest that these regions of homology may be analogous to the transposable genetic elements of bacterial plasmids. This, together with indirect but compelling evidence for interspecific (or intergeneric) plasmid transfer, indicates that CCC DNAs (although as yet genetically cryptic) may play a role in the ecology and evolution of obligately autotrophic prokaryotes, as they do in the ecology and evolution of the better-known heterotrophic bacteria.

Base Sequence↗

PubMed1981

Plasmid replication functions. VII. Electron microscopic localization of RNA polymerase binding sites in the replication control region of plasmid R6-5.

RNA polymerase binding sites on the R6-5 miniplasmid derivative, plasmid pKT401, were mapped by electron microscopy of DNA:RNA polymerase complexes formed with both circular-supercoiled and restriction endonuclease-linearized plasmid DNA molecules. Of eight specific binding sites on pKT401 that were identified, three were found to be in the P-6 fragment of the plasmid replication region, three in the Tn3 element, and two in other parts of the plasmid molecule. Binding sites 1 and 3 in the P-6 fragment are most probably the promoters of the copB and copA/incA plasmid replication control genes, respectively, whereas site 2 in this fragment appears to be the promoter of the essential replication gene, repA. The location of these promoters in relation to the site of action of the plasmid replication control elements, copT, and the origin of replication, oriV, suggests that replication control may be effected by regulation of transcription events initiated at site 2, or of the activity of transcripts initiated from this site, i.e., by regulation of the expression of the repA gene or another function dependent upon these events.

Binding Sites↗

PubMed1981

Cointegrates between bacteriophage P1 DNA and plasmid pBR322 derivatives suggest molecular mechanisms for P1-mediated transduction of small plasmids.

We characterized cointegrates formed in an Escherichia coli rec+ strain between bacteriophage P1 genomes and small plasmids related to pBR322. The partners were, on the one hand, either phage P1 DNA, which carries one copy of IS1, or phage P1-15 DNA, a derivative which lacks the IS1, and, on the other hand, plasmids containing either a split IS1 or no. In the presence of IS1 sequences on both partners, cointegrates were usually formed by reciprocal recombination between SI1 sequences. Cointegrates between P1 and a plasmid carrying no IS1 sequence were formed by transpositional cointegration mediated by IS1 of P1. Cointegrates between P1-15 and small plasmid containing a split IS1 were formed by one of three ways: (a) acquisition of an IS1 by P1-15 followed by reciprocal recombination between IS1 sequences, (b) transpositional cointegration mediated by the split IS1 element, Tn2657, or (c) involvement of the invertible segment carried on P1-15 DNA. Most cointegrates segregated into the small plasmids and phage P1 derivatives. A comparison of the phenomenon studied and of their frequencies allowed us to conclude that cointegrate formation is a molecular mechanism involved in the transduction of plasmids smaller than those packageable into P1 virions, although it does not seem to be the only process used.

Bacteriophages↗

PubMed1995

Isolation of cryptic plasmids from moderately halophilic eubacteria of the genus Halomonas. Characterization of a small plasmid from H. elongata and its use for shuttle vector construction.

Three cryptic plasmids have been isolated from moderately halophilic eubacteria belonging to three species of the genus Halomonas. These three plasmids were designated pHE1 (4.2 kb, isolated from H. elongata ATCC 33174), pHI1 (48 kb, isolated from "H. israelensis" ATCC 43985), and pHS1 (ca. 70 kb, isolated from H. subglaciescola UQM 2927). Because of its small size, the plasmid pHE1 was selected for further characterization and construction of a shuttle vector for Halomonas strains. pHE1 was cloned into pBluescript KS and a detailed restriction map was constructed. Hybridization experiments excluded the existence of sequences homologous to pHE1 in total DNA from other strains of the genus Halomonas. Moreover, no DNA homology with pMH1, the only plasmid described so far from moderate halophiles, was found. Since pHE1 appeared to be unable to replicate in Escherichia coli cells, a number of mobilizable pHE1-derived hybrid plasmids were constructed that could be selected and maintained both in E. coli and in H. elongata. Finally, an improved shuttle vector, pHS15, was generated. The vector pHS15 contains an origin of replication from E. coli as well as one from H. elongata, a streptomycin resistance gene for positive selection in moderate halophiles, a number of unique restriction sites commonly used for cloning, and the mobilization functions of the broad host range IncP plasmid RK2. The vector pHS15 was readily mobilized by the RK2 derivative pRK2013 to all Halomonas strains tested so far. This is the first report on the development of a cloning vector useful for moderately halophilic eubacteria.

Genetic Vectors↗

PubMed1995

A novel family of linear plasmids with homology to plasmid pAL2-1 of Podospora anserina.

Three recently isolated wild-type strains of the ascomycete Podospora anserina were analyzed for the presence of linear mitochondrial plasmids. In one of these strains, designated Wat, at least 12 distinct plasmid-like elements were identified. From molecular analyses a minimum number of 78 individual linear molecules with proteins bound to their 5' ends was estimated. In addition, the different members of this family of typical linear plasmids were shown to possess a common central region and terminal sequences which differ from one plasmid to another due to the presence of different numbers of a 2.4 kb sequence module. Finally, the pWa6 plasmids share a high degree of sequence similarity with pAL2-1, a linear plasmid previously identified in mitochondria of a long-lived mutant of P.anserina. A mechanism is proposed which explains the generation of these distinct, closely related extra-chromosomal genetic traits.

Ascomycota↗

PubMed1994

Agrobacterium vitis nopaline Ti plasmid pTiAB4: relationship to other Ti plasmids and T-DNA structure.

The Ti plasmid of the Agrobacterium vitis nopaline-type strain AB4 was subcloned and mapped. Several regions of the 157 kb Ti plasmid are similar or identical to parts of the A. vitis octopine/cucumopine (o/c)-type Ti plasmids, and other regions are homologous to the nopaline-type Ti plasmid pTiC58. The T-DNA of pTiAB4 is a chimaeric structure of recent origin: the left part is 99.2% homologous to the left part of the TA-DNA of the o/c-type Ti plasmids, while the right part is 97.1% homologous to the right part of an unusual nopaline T-DNA recently identified in strain 82.139, a biotype II strain from wild cherry. The 3' noncoding regions of the ipt genes from pTiAB4 and pTi82.139 are different from those of other ipt genes and contain a 62 bp fragment derived from the coding sequence of an ipt gene of unknown origin. A comparison of different ipt gene sequences indicates that the corresponding 62 bp sequence within the coding region of the AB4 ipt gene has been modified during the course of its evolution, apparently by sequence transfer from the 62 bp sequence in the 3' non-coding region. In pTi82.139 the original coding region of the ipt gene has remained largely unmodified. The pTiAB4 6b gene differs from its pTi82.139 counterpart by the lack of a 12 bp repeat in the 3' part of the coding sequence. This leads to the loss of four glutamic acid residues from a series of ten. In spite of these differences, the ipt and 6b genes of pTiAB4 are functional. Our results provide new insight into the evolution of Agrobacterium Ti plasmids and confirm the remarkable plasticity of these genetic elements. Possible implications for the study of bacterial phylogeny are discussed.

Amino Acid Sequence↗

PubMed1990

When a glycolytic gene on a yeast 2 mu ORI-STB plasmid is made essential for growth its expression level is a major determinant of plasmid copy number.

This study demonstrates how varying the promoter strength of an essential gene on a yeast 2 mu ORI-STB YEp multicopy vector can influence vector copy levels. A phosphoglycerate kinase gene (PGK) on this plasmid was made essential for fermentative growth by transformation into a pgk- yeast strain. When in these PGK+ transformants the requirement for PGK expression was the sole selective criterion for plasmid maintenance, PGK promoter activity was inversely related to vector copy levels. Plasmids with an efficiently-transcribed PGK gene were maintained at approximately one copy per cell, whereas those lacking the UAS that normally directs high basal PGK transcription levels were present at up to 10-15 copies. All cultures of these PGK+ transformants contained only a low proportion of pgk- cells. Since mitotic loss of the plasmid arrests growth through loss of a functional PGK allele, PGK confers high stability to the YEp vector in such a pgk- genetic background. In this system YEp vector levels are probably influenced by PGK transcription because high expression of PGK is needed in rapid fermentative growth. Remarkably, low plasmid PGK promoter activity caused PGK mRNA levels slightly higher than those found in yeast with normal PGK regulation. A higher plasmid copy number is therefore not the only factor counteracting the effects of low PGK transcription, and it is possible that PGK mRNA becomes more stable in response to inefficient PGK transcription.

Fermentation↗

PubMed1976

Mutagenesis of plasmid DNA with hydroxylamine: isolation of mutants of multi-copy plasmids.

An investigation of in vitro mutagenesis of plasmid DNA with hydroxylamine is described. The treated plasmid DNA was used to transform Escherichia coli K12. Mutants of the plasmid NTP3, which codes for resistance to ampicillin and sulphonamides, were isolated and characterised. They were classified according to the reduction in level of their beta-lactamase activity. Hydroxylamine-induced mutants of NTP14 were also isolated. This plasmid codes for ampicillin resistance, synthesis of colicin E1, and the EcoRI restriction and modification enzymes. One class of mutants is lethal to the host strain at temperatures above 33 degrees C, but carrier strains grow well at 28 degrees C. There is evidence that these mutants code for a temperature-sensitive EcoRI modification activity: the lethal effect probably results from the cleavage of the host-cell DNA by the restriction enzyme at non-permissive temperatures. The possible genetic uses of the mutant plasmids for the production of hybrid plasmids in the bacterial cell are discussed.

Ampicillin↗

PubMed1983

Isolation of a DNA sequence related to several plasmids from Bacillus thuringiensis after a mating involving the Streptococcus faecalis plasmid pAM beta 1.

The transmissible plasmid pAM beta 1, which codes for resistance to erythromycin and lincomycin, was transferred from Streptococcus faecalis to several strains of Bacillus thuringiensis by a filter-mating process. Introduction of pAM beta 1 into the Emr transconjugant strains of B. thuringiensis was confirmed by Southern hybridisation using the 32P-labelled pAM beta 1 as a probe. In the B. thuringiensis transconjugant strains, used as donors, the beta plasmid conserved its ability to be transferred during intraspecific mating, with a frequency of 10(-4) per recipient cell. In addition, the transconjugant clones acted as donors of the erythromycin resistance marker and permitted the transfer of cryptic plasmids present in the B. thuringiensis (beta) strains used as donors. From a transconjugant clone of B. thuringiensis a hybrid plasmid resulting from an in vivo insertion into pAM beta 1 of a 3 Md DNA sequence was isolated. This 3 Md DNA molecule originated from a 54 Md plasmid of a kurstaki strain and is related to several plasmids found in different serotypes of B. thuringiensis.

Bacillus thuringiensis↗

PubMed1981

Plasmid transformation in Bacillus subtilis. The significance of partial homology between plasmid and recipient cell DNAs.

A series of hybrid plasmids consisting of pC194 or pUB112 and B. subtilis DNA were constructed. In contrast to plasmid pC194, purified monomeric forms of such plasmids were active in transformation, provided the recipient cells were recombination proficient. Similarly the monomers of pC194 derived plasmids, containing bacteriophage phi 105 DNA were able to transform phi 105 lysogenic but not nonlysogenic cells. From the results it is concluded that the presence of DNA/DNA homology between chromosomal DNA of the recipient cell and part of the hybrid plasmids used is a sufficient condition to endow monomeric plasmids with transforming activity.

Bacillus subtilis↗

PubMed2004

A highly selectable and highly transferable Ti plasmid to study conjugal host range and Ti plasmid dissemination in complex ecosystems.

A conjugal donor system, ST2, was constructed to study the conjugal dissemination of a Ti plasmid to wild-type recipient bacteria in vitro and in situ. The system consisted of a polyauxotrophic derivative of C58 harboring a hyperconjugative and highly selectable Ti plasmid, pSTiEGK, which was constructed by inserting a multiple antibiotic resistance cassette in the traM- mcpA region of pTiC58Delta accR. ST2 transfers pSTiEGK constitutively at frequencies up to 10(-1) to plasmidless Agrobacterium recipients. The host range of pSTiEGK includes all the known genomic species of Agrobacterium, indigenous soil agrobacteria and some Rhizobium and Phyllobacterium spp. All transconjugants became pathogenic upon acquisition of the Ti plasmid and were also able to transfer pSTiEGK by conjugation. This host range was indistinguishable from that of its wild-type parent pTiC58, and therefore pSTiEGK constitute a valid proxy to study the dissemination of Ti plasmids directly in the environment. Transconjugants can be selected on a combination of four antibiotics, which efficiently prevents the growth of the indigenous microbiota present in complex environments. The transfer of pSTiEGK to members of the genus Agrobacterium was affected primarily by the plasmid content of the recipient strain (10(3)- to 10(5)-fold reduction), e.g., the presence of incompatible plasmids. As a consequence, a species should be considered permissive to Ti transfer whenever one permissive isolate is found.

Chromosome Mapping↗

PubMed1986

Regulation of lambda dv plasmid DNA replication. A quantitative model for control of plasmid lambda dv replication in the bacterial cell division cycle.

A quantitative model for the regulation of replication of plasmid lambda dv in the Escherichia coli cell division cycle has been developed. The regulatory processes include the interactions of cro repressor proteins with the rightward operator DNA sites, the transcriptional activation of the lambda dv replication origin, and the interaction of initiation proteins with activated origins to form functional replication initiation complexes. A statistical thermodynamic model was used to predict probable configurations of the regulatory processes in a single growing cell. These probabilities were coupled by a kinetic model to the events of the cell cycle such as initiation of mRNA transcription and protein translation and the initiation of plasmid DNA replication. Parameter values were chosen so that the simulated values for plasmid copy number and repressor and initiator protein concentrations of the model agreed with experimentally determined estimates. Simulated deviations from regular segregation of the various components at cell division, such as plasmid copies and free and bound repressor proteins, suggest that lambda dv replication control responds only slowly to these perturbations. The consequence of this slow response to perturbations, which are expected at a random frequency, was simulated for a population of lambda dv-containing cells in a growing culture. This simulation predicts instability of inheritance of lambda dv plasmids in the population, despite the very high plasmid copy number, in agreement with experimental observation.

Bacteriophage lambda↗

PubMed1984

RepFIC, a basic replicon of IncFI plasmids that has homology with a basic replicon of IncFII plasmids.

It was found that a DNA segment containing genes for autonomous replication and its control (basic replicon) present in the IncFI plasmid P307 has homology with RepA, a basic replicon present in IncFII plasmids. The basic replicon in P307 is referred to as RepFIC and the homologous basic replicon in IncFII plasmids is referred to as RepFIIA. In 11 other IncFI plasmids studied a region that has homology with RepFIC and RepFIIA was demonstrated. Thus, of the several basic replicons present in IncFI plasmids, RepFIC is evolutionarily related to a basic replicon of IncFII plasmids.

Base Sequence↗

PubMed1986

Evidence for the involvement of the incC locus of broad host range plasmid RK2 in plasmid maintenance.

Plasmid pRK2501 is a deletion derivative of broad host range plasmid RK2 and encodes two trfB-regulated operons: the trfA operon which codes for both kilD, which interferes with plasmid maintenance if unregulated, and trfA whose protein product(s) is essential for replication from oriVRK2; and part of the trfB operon, containing both trfB/korA/korD, whose product negatively regulates transcription of both trfA and trfB operons, and incC, the product of which interferes in trans with inheritance of RK2 and certain of its derivatives. Plasmid pRK2501ts3 is a derivative with a point mutation in trfB, rendering plasmid maintenance temperature sensitive. Transcriptional fusions of the trfB operon and the galK gene demonstrate that this mutation derepresses trfB operon transcription at both 30 and 42 degrees C. The trfA operon is also derepressed by this mutation. Since the trfB gene product appears to be defective at both permissive and non-permissive temperatures the temperature sensitivity of pRK2501ts3 must be due to a secondary effect. In fact, it appears to arise from the inhibitory behavior of derepressed incC at the non-permissive temperature since a major class of "revertant" of pRK2501ts3 contains deletions inactivating incC and a reconstruction experiment demonstrates that such a deletion is sufficient for "reversion." Maxicell experiments show that at the non-permissive temperature the trfA operon polypeptide products are produced at much lower levels, an effect partly reversed by a deletion affecting incC. It is proposed that incC normally plays a role in maintenance of IncP plasmids by modulation of trfA operon expression.

Bacterial Proteins↗

PubMed1992

Amplification of plasmid (L factor) DNA and increased production of a plasmid gene product (gamma-interferon) in mouse L cells.

It has previously been reported that composite DNAs derived from L factor, a polyoma-related mammalian plasmid, can be established in several mouse cell lines after transfection. Here, we report that the copy number of a plasmid composite DNA consisting of L factor, pBR DNA, dihydrofolate reductase (dhfr) gene, and gamma-interferon (gamma-IFN) gene was increased more than 10-fold after two successive adaptations of the plasmid-bearing mouse L cells to increasing concentrations of methotrexate (MTX), an inhibitor of dhfr. The structure of the amplified L factor plasmid remained intact during prolonged cell culture, but the copy number remained to be amplified only when the selective pressure (presence of MTX in the medium) has been exerted during the culture. Cells bearing the amplified plasmid produced a higher level of gamma-IFN compared with the original clone, which was likely to be derived from the plasmid gamma-IFN gene amplified along with L factor and the dhfr gene.

Animals↗

PubMed1979

High frequency of yeast transformation by plasmids carrying part or entire 2-micron yeast plasmid.

By using two chimeric plasmids containing yeast ura3 gene and 2-micron yeast DNA linked to the bacterial plasmid pCR1, yeast transformation of a high frequency has been achieved. The first plasmid is such that the 2-micron DNA part, in which the ura3 gene is incorporated, can be removed in one step and thus the 2-micron-ura3 sequence can be considered as a "transposable" block. In contrast, the second one bears the entire 2-micron plasmid and the ura3 gene is inserted in the bacterial plasmid part. As shown through hybridization experiments and genetic studies, the ura3 gene was maintained as a cytoplasmic element. Plasmids recovered from the yeast transformants were used to transform Escherichia coli. Their analysis by EcoRI showed that in many cases the vector had recombined with the endogenous 2-micron DNA of the recipient strain. The specific activity of orotidine 5'-monophosphate decarboxylase (coded by ura3) in yeast transformants was 10- to 30-fold higher than in the wild type.

Chimera↗

PubMed1996

Mobilization of vancomycin resistance by transposon-mediated fusion of a VanA plasmid with an Enterococcus faecium sex pheromone-response plasmid.

A striking feature of recent outbreaks of vancomycin-resistant (VmR) enterococci is the apparent horizontal dissemination of resistance determinants. The plasmids pHKK702 and pHKK703 from Enterococcus faecium clinical isolate R7 have been implicated in the conjugal transfer of VmR. pHKK702 is a 41-kb plasmid that contains an element indistinguishable from the glycopeptide-resistance transposon Tn1546. pHKK703 is an approx. 55-kb putative sex pheromone-response plasmid that is required for conjugative mobilization of pHKK702. During experiments in which strain R7 was used as a donor, a highly conjugative VmR transconjugant was isolated that formed constitutive cellular aggregates. Restriction analyses and DNA hybridizations revealed that the transconjugant harbored a single plasmid of approx. 92 kb and this plasmid (pHKK701) was composed of DNA from both pHKK702 and pHKK703. Results from DNA sequence analyses showed that a 39-kb composite transposon (Tn5506) from pHKK702 had inserted into pHKK703. The left end of Tn5506 contained a single insertion sequence (IS) element, IS1216V2, whereas the right end was composed of a tandem IS structure consisting of the novel 1065-bp IS1252 nested within an IS1216V1 element. Transposition of Tn5506 from pHKK702 to pHKK703 created an 8-bp target sequence duplication at the site of insertion and interrupted an ORF (ORFX) that was 91% identical to that of prgX, a gene proposed to negatively regulate sex pheromone response of the E.faecalis plasmid, pCF10. We propose that the interruption of ORFX by Tn5506 led to the constitutive cellular aggregation phenotype and thereby enhanced the efficiency with which VmR was transferred. Similar IS1216V-mediated transposition events may contribute to the horizontal spread of glycopeptide resistance among enterococci in nature.

Amino Acid Sequence↗

PubMed2004

Effect on antibody and T-cell responses of mixing five GMP-produced DNA plasmids and administration with plasmid expressing GM-CSF.

One potential benefit of DNA vaccines is the capacity to elicit antibody and T-cell responses against multiple antigens at the same time by mixing plasmids expressing different proteins. A possible negative effect of such mixing is interference among plasmids regarding immunogenicity. In preparation for a clinical trial, we assessed the immunogenicity of GMP-produced plasmids encoding five Plasmodium falciparum proteins, PfCSP, PfSSP2, PfEXP1, PfLSA1, and PfLSA3, given as a mixture, or alone. The mixture induced higher levels of antibodies against whole parasites than did the individual plasmids, but was associated with a decrease in antibodies to individual P. falciparum proteins. T-cell responses were in general decreased by administration of the mixture. Immune responses to individual plasmids and mixtures were generally higher in inbred mice than in outbreds. In inbred BALB/c and C57BL/6 mice, coadministration of a plasmid expressing murine granulocyte-macrophage colony-stimulating factor (mGM-CSF), increased antibody and T-cell responses, but in outbred CD-1 mice, coadministration of mGM-CSF was associated with a decrease in antibody responses. Such variability in data from studies in different strains of mice underscores the importance of genetic background on immune response and carefully considering the goals of any preclinical studies of vaccine mixtures planned for human trials.

Animals↗