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PubMed1983

Yeast plasmid requires a cis-acting locus and two plasmid proteins for its stable maintenance.

Unstable ars1 (autonomously replicating sequence)-containing plasmids can be stabilized by connecting particular DNA segments of yeast 2 mu-plasmid. A cis-acting locus for the plasmid's stability (the STB locus) was found in the large unique region and separated from the replication origin of 2 mu-plasmid. Several direct repeats found in this region were essential for its function. Two proteins encoded by the plasmid (B and C) were required as trans-acting factors. The average copy number of the plasmid was not affected whether the plasmid carried the stability system or not, suggesting that the system was not directly associated with the replication function but was involved in partitioning at cell division.

Base Sequence↗

PubMed1985

Expression of a Rhizobium phaseoli Sym plasmid in R. trifolii and Agrobacterium tumefaciens: incompatibility with a R. trifolii Sym plasmid.

Identification of the Sym plasmid in Rhizobium phaseoli strain RCC3622 is described. Introduction of this plasmid into R. trifolii or Agrobacterium tumefaciens strains resulted in bacteria capable of forming characteristic spherical root nodules on beans. This Sym plasmid, designated pSym9, was characterized as 275 MDa and nonconjugative. pSym9 was incompatible with the R. trifolii Sym plasmid pSym5, and carries genes determining a melanin-like black pigment. A second plasmid of 135 MDa, pRph3622a, was also transferred from R. phaseoli to R. trifolii and A. tumefaciens. Transconjugants carrying this plasmid did not form root nodules on beans. In contrast to other Rhizobium plasmids, pRph3622a was unstable in A. tumefaciens.

Conjugation, Genetic↗

PubMed1985

The development of plasmid-free strains of Agrobacterium tumefaciens by using incompatibility with a Rhizobium meliloti plasmid to eliminate pAtC58.

Agrobacterium tumefaciens strains LBA275 and LBA290 were cured of their cryptic plasmid pAtC58 by the introduction of the Rhizobium meliloti plasmid pRme41a, which is incompatible with pAtC58. pRme41a and pTiC58, the resident Ti plasmid of LBA275, were subsequently eliminated by growth at supraoptimal temperature (40 degrees C). The resulting plasmid-free Agrobacterium strains, UBAPF1 and UBAPF2, have proved extremely useful for the study of Rhizobium plasmids. The loss of the cryptic plasmid pAtC58 has no effect on the tumor-forming ability of the Agrobacterium strains; when the Ti plasmid is present, normal tumors are formed on Kalanchoe daigremontiana.

DNA, Bacterial↗

PubMed1988

Characterization of a plasmid isolated from Branhamella catarrhalis and detection of plasmid sequences within the genome of a B. catarrhalis strain.

We isolated a 12.2-kb plasmid from two clinical strains of Branhamella catarrhalis and evaluated its distribution among other B. catarrhalis strains by colony hybridization experiments using the whole plasmid as a probe. Homology was detected with the two plasmid-bearing strains and also with a third B. catarrhalis strain named E7, which is plasmidless. Southern transfer analysis of total digested E7 DNA using the purified plasmid as a probe revealed a single band of hybridization, different from those observed in plasmid-bearing strains, for each restriction enzyme used. The region of the plasmid hybridizing with DNA of strain E7 was located within a 4.5-kb SstI-EcoRV fragment. No homology was noted between our B. catarrhalis plasmid and about 20 other strains of different genera tested by colony hybridization.

Blotting, Southern↗

PubMed1988

Enhanced transforming activity of pSV2 plasmids in human cells depends upon the type of damage introduced into the plasmid.

When pSV2-gpt or pSV2-neo plasmids are introduced into human cells by calcium phosphate coprecipitation, the yield of stable transformants (Gpt+ or Neo+) is increased by irradiating the respective plasmid DNA in vitro with UV (254 nm). To identify specific lesions that can increase the transforming activity of plasmids in human cells we examined pSV2 plasmids containing different types of damage. Of the lesions tested, cyclobutane pyrimidine dimers produced the greatest increase, and can nearly fully account for the effect of 254 nm UV on transformation. The enhancement of transformation produced by UV was not altered by the additional treatment of the plasmid DNA with T4 endonuclease V, an enzyme that nicks DNA specifically at pyrimidine dimers. Treatment of plasmid DNA with osmium tetroxide to produce thymine glycols, or with acid and heat to produce apurinic sites did not affect transformation frequency. The enhancement occurred in all the human cell lines tested, whether they contained or not sequences homologous to those in the plasmids, and was independent of the repair capacity of the recipient cells.

Cell Line↗

PubMed2004

What does "plasmid biology" currently mean? Summary of the Plasmid Biology 2004 Meeting.

Almost 200 scientists from America, Europe, Asia, Australia, and Africa participated in the Plasmid Biology 2004 meeting, which was organized between 15th and 21st September 2004 in Kanoni (Corfu island), Greece. Various aspects of biology of plasmids and other mobile genetic elements were discussed during the meeting, including problems of replication, transfer, stable inheritance, and evolution. Medical and veterinary aspects of plasmids were highlighted as well as other applications of these replicons. It appears that plasmids and other mobile genetic elements are still excellent models in studies of basic biological problems at the molecular level, and their role in medicine and genetic engineering can be enormous. Moreover, studies on ecology of plasmids provide extremely important data that can be used in environment protection as well as in biotechnology. Understanding the importance of studies on plasmids and other mobile genetic elements, participants of the meeting decided to establish the International Society for Plasmid Biology.

Biological Evolution↗

PubMed2006

Sequence and analysis of the 46.6-kb plasmid pA1 from Sphingomonas sp. A1 that corresponds to the typical IncP-1beta plasmid backbone without any accessory gene.

Sphingomonas sp. A1 (strain A1) is capable of directly incorporating macromolecules (e.g., alginate) through the specialized import system--"super-channel." Here, we report the complete DNA sequence and genetic organization of plasmid pA1 from strain A1. Nucleotide sequence analysis revealed that pA1 comprises 46,557 bp encoding 49 open reading frames (ORFs) with 65% G+C content and abundant GCCG/CGGC motifs. Many predicted pA1 ORFs showed high similarity to pA81 ORFs; pA81 is supposedly a self-transmissible promiscuous incompatibility (Inc) group P-1beta plasmid. Unlike any reported IncP-1 plasmids, pA1 contains no inserted mobile genetic elements. The genetic organization and predicted pA1 ORFs showed greater similarity to the IncP-1beta plasmid backbone than to the IncP-1alpha plasmid backbone. pA1 contains restriction site-associated repeat sequences typical of the IncP-1beta but absent in the IncP-1alpha and delta subgroups. Thus, the overall pA1 structure corresponds to that of the typical IncP-1beta plasmids. Phylogenetic analysis of the replication-associated proteins suggested that pA1 may have diverged later along with the two IncP-1beta plasmids--pA81 and pB4. The 2.4-kb duplicates of stable inheritance genes klcAB and korC in pA1 possibly resulted from insertion and/or recombination events via the repeat sequences flanking these duplicates.

Base Sequence↗

PubMed2003

Co-transformation with autonomous replicating and integrative plasmids in Penicillium chrysogenum is highly efficient and leads in some cases to rescue of the intact integrative plasmid.

The efficiency of co-transformation in Penicillium chrysogenum Wisconsin 54-1255 pyrG(-) and the fate of the transforming DNA were studied using an integrative (pEF43) and an autonomous replicating plasmid (pAM9L). The results showed a co-transformation frequency of nearly 70% of all transformants tested. The total efficiency of transformation was shown to be dependent on the plasmid marker used as transformant selection (i.e., markers in the integrative or autonomous replicating vector). Analysis of the plasmids re-isolated from several co-transformants showed that different populations of plasmids co-exist in the fungal host. Interestingly, in all co-transformants studied, the integrative plasmid was found to be replicating autonomously without integrating into the host genome. In some cases, co-integrates were formed by recombination between autonomous replicating (pAM9L) and integrative (pEF43) plasmids. However, unexpectedly in some cases, the non-reorganised pEF43 integrative plasmid used in the co-transformation assays was rescued from some co-transformants.

Blotting, Southern↗

PubMedDate not supplied

Novel method for covalent fluorescent labeling of plasmid DNA that maintains structural integrity of the plasmid.

We have developed a chemical strategy for covalent coupling of fluorophores to plasmid DNA. A p-azido-tetrafluoro-benzyl-lissamine conjugate was synthesized and purified. This conjugate was used to covalently associate fluorescent molecules to plasmid DNA by photoactivation. In contrast to nick-translated plasmid DNA, plasmid-lissamine conjugates appeared on gel as supercoiled DNA. Reporter gene was expressed after transfection of the plasmid-lissamine conjugates in NIH 3T3 cells, although gene transfer efficiency was decreased by 60% as compared with unlabeled DNA. Intracellular traffic of plasmid-lissamine conjugates was studied in transfected cells. After cytoplasmic microinjection, fluorescent plasmid did not diffuse from the site of injection and appeared to be progressively degraded in the cytoplasm.

3T3 Cells↗

PubMed1997

Altered ParA partition proteins of plasmid P1 act via the partition site to block plasmid propagation.

The partition system of the P1 plasmid, P1par, consists of the ParA and ParB proteins and a cis-acting site, parS. It is responsible for the orderly segregation of plasmid copies to daughter cells. Plasmids with null mutations in parA or parB replicate normally, but missegregate. ParB binds specifically to the parS site, but the role of ParA and its ATPase activity in partition is unclear. We describe a novel class of parA mutants that cannot be established or maintained as plasmids unless complemented by the wild-type gene. One, parAM314l, is conditional: it can be maintained in cells in minimal medium but cannot be established in cells growing in L broth. The lack of plasmid propagation in L broth-grown cells was shown to be caused by a ParB-dependent activity of the mutant ParA protein that blocks plasmid propagation by an interaction at the parS site. Thus, ParA acts to modify the ParB-parS complex, probably by binding to it. Partition is thought to involve selection of pairs of plasmids before segregation, either by physical pairing of copies or by binding of copies to paired host sites. We suggest that ParA is involved in this reaction and that the mutant ParA protein forms paired complexes that cannot unpair.

Bacterial Proteins↗

PubMed2005

VirA and VirG activate the Ti plasmid repABC operon, elevating plasmid copy number in response to wound-released chemical signals.

The vir genes of Agrobacterium tumefaciens tumor-inducing (Ti) plasmids direct the transfer of oncogenic portion of the Ti (tumor-inducing) plasmid that is transferred to plant cells (T-DNA) into plant cells and are coordinately induced by plant-released phenolic chemical signals. We have used DNA microarrays, representing all genes of the octopine- and nopaline-type Ti plasmids, to identify all Ti-plasmid-encoded genes in the vir regulons of both plasmids. Acetosyringone (AS) induced the expression of all known members of the vir regulons, as well as a small number of additional genes. Unexpectedly, AS also caused a modest induction of virtually every Ti plasmid gene. This suggested that the copy number of the Ti plasmid might increase in response to AS, a hypothesis confirmed by DNA dot blotting. VirA and VirG were the only Vir proteins required for this copy number increase. Promoter resections and primer extension analysis of the repABC promoter region showed that expression of the promoter closest to repA (promoter P4) was induced by AS. We also identified a sequence resembling a consensus VirG-binding motif approximately 70 nucleotides upstream from the P4 transcription start site. Mutating this sequence blocked the AS-induced copy number increase of a RepABC-dependent miniplasmid, indicating that phospho-VirG increases copy number solely by enhancing repABC expression.

Acetophenones↗

PubMed1978

Requirement of a plasmid-encoded protein for replication in vitro of plasmid R6K.

Conditions are described for the replication of exogeneous R6K DNA in an in vitro system prepared from Escherichia coli cells. Replication of plasmid DNA in this system is semiconservative and sensitive to actinomycin D, novobiocin, arabinofuranosyl-CTP,N-ethylmaleimide, and inhibitors of DNA-dependent RNA polymerase. An ammonium sulfate fraction prepared from cells carrying the R6K plasmid is required for replication. A direct role in replication for a plasmid-encoded protein, designated pi, in this fraction is indicated by the inactivity of this fraction when prepared from cells carrying a temperature-sensitive mutant plasmid and the thermolability of this fraction when prepared from cells carrying a partial revertant of the mutant plasmid. This plasmid-encoded protein is necessary for the initiation of R6K DNA replication and functions before or during the formation of nascent RNA in the initiation process. The results of titration assays of this protein using various template DNAs suggest that the protein interacts with the plasmid DNA at the region essential for DNA replication.

Anti-Bacterial Agents↗

PubMed1979

Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans.

pRK212.2, a derivative of the broad host range plasmid RK2, contains two EcoRI cleavage fragments, A and B, neither of which can replicate by itself in Escherichia coli. Fragment A (41.7 kilobases), but not fragment B (14.4 kilobases), can be cloned by insertion into the unrelated plasmids mini-F and ColE1. Fragment B contains the origin of replication and the ampicillin-resistance determinant of RK2. Transformation of E. coli cells containing the mini-F-fragment A hybrid plasmid with fragment B DNA results in the recircularization and replication of fragment B as a nonmobilizable plasmid (pRK2067) with the copy number and incompatibility properties of RK2. Fragment B cannot be cloned in the absence of fragment A because the latter fragment suppresses a function, specified by fragment B, that results in loss of host cell viability. A small segment (2.4 kilobases) of fragment B that contains the RK2 origin of replication but no longer affects host cell growth in the absence of fragment A had been cloned previously by insertion into a ColE1 plasmid. This hybrid plasmid, designated pRK256, will replicate in E. coli polA mutants only when a fragment A-bearing helper plasmid is present. These results demonstrate that the potentially lethal function specified by fragment B of RK2 is not necessary for replication and that at least one trans-acting function is directly involved in RK2 replication.

Coliphages↗

PubMed1984

Replication of the broad host range plasmid RSF1010: requirement for three plasmid-encoded proteins.

Cloning of specific regions of plasmid RSF1010, in conjunction with in vitro replication studies, has revealed three novel genes: repA, repB, and repC. They are clustered in one region of the plasmid, separated from the origin of replication by regions that are not essential for plasmid viability in an Escherichia coli host. In vivo, a 2.1-kilobase segment of the plasmid, bearing the replication origin, can establish itself as an autonomous replicon if the DNA region carrying the three rep genes is present in the same cell on an independent plasmid. In vitro, RSF1010 DNA is efficiently replicated by an ammonium sulfate fraction from the E. coli extract, provided the extracts are prepared from cells that can supply the required rep gene products. Using cells containing the cloned rep gene region as a source of elevated levels of the rep proteins, we have partially purified these proteins in functional form. When added to an enzyme fraction derived from plasmid-free cells, they specifically promote the replication of plasmid DNA bearing the RSF1010 origin.

Bacterial Proteins↗

PubMed2000

Critical energies for SSB and DSB induction in plasmid DNA by low-energy photons: action spectra for strand-break induction in plasmid DNA irradiated in vacuum.

PURPOSE: To measure action spectra for the induction of single-strand breaks (SSB) and double-strand breaks (DSB) in plasmid DNA by low-energy photons and provide estimates for the energy dependence of strand-break formation important for track-structure simulations of DNA damage. MATERIALS AND METHODS: Plasmid pMSG-CAT was irradiated as a monolayer, under vacuum, with 7 150eV photons produced by a synchrotron source. Yields of SSB and DSB were determined by the separation of the three plasmid forms by gel electrophoresis. RESULTS: The yields of SSB per incident photon increased from 1.4x 10(-15) SSB per plasmid per photon/cm2 at 7eV to 7.5 x 10(-14) SSB per plasmid per photon/cm2 at 150 eV. Direct induction of DSB was also detected increasing from 3.4 x 10(-17) DSB per plasmid per photon/cm2 at 7eV to 4.1 x 10(-15) DSB per plasmid per photon/cm2 at 150eV. When the absorption cross-section of the DNA was considered, the quantum efficiency for break formation increased over the energy range studied. Over the entire energy range, the ratio of SSB to DSB remained constant. CONCLUSIONS: These studies provide evidence for the ability of photons as low as 7 eV to induce both SSB and DSB. The common action spectrum for both lesions suggests that they derive from the same initial photoproducts under conditions where the DNA is irradiated in vacuum and a predominantly direct effect is being observed. The spectral and dose-effect behaviour indicates that DSB are induced predominantly by single-event processes in the energy range covered.

DNA↗

PubMed2002

The 2 micron plasmid purloins the yeast cohesin complex: a mechanism for coupling plasmid partitioning and chromosome segregation?

The yeast 2 micron plasmid achieves high fidelity segregation by coupling its partitioning pathway to that of the chromosomes. Mutations affecting distinct steps of chromosome segregation cause the plasmid to missegregate in tandem with the chromosomes. In the absence of the plasmid stability system, consisting of the Rep1 and Rep2 proteins and the STB DNA, plasmid and chromosome segregations are uncoupled. The Rep proteins, acting in concert, recruit the yeast cohesin complex to the STB locus. The periodicity of cohesin association and dissociation is nearly identical for the plasmid and the chromosomes. The timely disassembly of cohesin is a prerequisite for plasmid segregation. Cohesin-mediated pairing and unpairing likely provides a counting mechanism for evenly partitioning plasmids either in association with or independently of the chromosomes.

Bacterial Proteins↗

PubMed1987

Plasmidal maintenance of composite DNA derived from polyoma related plasmid, L factor.

Recently, we reported a multicopy mammalian plasmid with a structure related to polyoma. The plasmid, named L factor, was found at a high copy number (5,000 or more per cell) in a subclone derived from mouse L cells. We attempted to utilize L factor as a plasmid vector for mammalian cells. A series of composite DNA consisting of L factor and a foreign (herpes simplex virus tk) were constructed. These DNA could be established as plasmids after transfection to several mouse cell lines, although the copy number of the re-established plasmids was considerably less than that observed for the original subclone. The composite DNA maintained the structure of the original DNA after prolonged culture and the copy number remained constant even with no selective pressure. A composite DNA, with no DNA sequence corresponding to polyoma T antigen, could also be established as a plasmid in a mouse L cell line in which polyoma T antigen is expressed. The potential use of the plasmid is discussed.

Animals↗

PubMed1992

A survey of Col plasmids in natural isolates of Escherichia coli and an investigation into the stability of Col-plasmid lineages.

A survey of colicins in the ECOR reference collection of Escherichia coli is presented. Twenty-five of the 72 ECOR strains exhibited a phenotype consistent with colicin production and E. coli isolated from human hosts were more likely to be colicinogenic than those from animal hosts. Multiple representatives of two Col plasmids, low-molecular-mass ColE1 plasmids and high-molecular-mass, conjugative ColIa plasmids were isolated from the ECOR collection and were examined with a combination of restriction fragment and Southern analysis. These data suggested that ColE1 plasmids comprise a stable (cohesive) plasmid lineage, while ColIa plasmids represent a family of distinct plasmid lineages united by the presence of the colicin Ia operon.

Bacteriocin Plasmids↗