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PubMed1998

Closely related plasmid replicons coexisting in the phytopathogen pseudomonas syringae show a mosaic organization of the replication region and altered incompatibility behavior

Many Pseudomonas syringae strains contain native plasmids that are important for host-pathogen interactions, and most of them contain several coexisting plasmids (pPT23A-like plasmids) that cross-hybridize to replication sequences from pPT23A, which also carries a gene cluster coding for the phytotoxin coronatine in P. syringae pv. tomato PT23. In this study, three functional pPT23A-like replicons were cloned from P. syringae pv. glycinea race 6, suggesting that the compatibility of highly related replicons is a common feature of P. syringae strains. Hybridization experiments using three separate incompatibility determinants previously identified from pPT23A and the rulAB (UV radiation tolerance) genes showed that the organization of the replication region among pPT23A-like plasmids from several P. syringae pathovars is poorly conserved. The putative repA gene from four pPT23A-like replicons from P. syringae pv. glycinea race 6 was amplified by using specific primers. The restriction profiles of the resulting PCR products for the race 6 plasmids were more similar to each other than they were to that of pPT23A. These data, together with the existence of other cross-hybridizing DNA regions around the replicon among the race 6 pPT23A-like plasmids, suggest that some of these plasmids may have originated from duplication events. Our results also imply that modifications of the repA sequences and the poor conservation of putative maintenance determinants contribute to the suppression of incompatibility among members of the pPT23A-like family, thus enhancing the genomic plasticity of P. syringae.

Journal Article↗

PubMed1988

A novel replicon occurring naturally in Escherichia coli is a phage-plasmid hybrid.

A novel DNA replicon in Escherichia coli was identified. It is the smallest natural isolate (1282 bp) found so far. In the presence of phage M13 it grows as a filamentous single-stranded DNA phage. Contrary to previously identified mini-phages this replicon displays sequence homology only to parts of the M13 viral and complementary strand origin. In the absence of M13 this DNA replicates autonomously. The only gene (arp) of the replicon encodes a 32-kd protein, which is essential for autonomous replication. The host rep gene required for replication of single-stranded DNA phages is dispensable. Distinct replication mechanisms are thus involved during growth as defective phage or as autonomous plasmid.

Amino Acid Sequence↗

PubMed1995

Effect of increased ppGpp concentration on DNA replication of different replicons in Escherichia coli.

The plasmids harbouring the relA gene under an inducible promoter allowed us to increase the guanosine 5'-diphosphate-3'-diphosphate (ppGpp) concentration in Escherichia coli cells without any starvation and thus, to directly investigate the effect of ppGpp on DNA replication. We studied all types of replicons which were investigated previously in amino acid-starved bacteria and found that ColE1, oriC, lambda plasmid and pSC101 but not RK2 replicons are sensitive to high ppGpp level. To our knowledge, this paper presents the first direct evidence that replication of most, but not all, replicons is dependent on ppGpp concentration and thus, is under stringent control.

DNA Replication↗

PubMed1993

Characterization of the replicon from plasmid pAC1 from Acetobacter pasteurianus.

A panel of recombinant plasmids pACK5 and pACT7 was prepared by introducing kanamycin and tetracycline resistance into the partially split plasmid pAC1 which contained replicon isolated from Acetobacter pasteurianus. The replicon in plasmid pAC1 is compatible with the ColE1 replicon. Compared to pBR322, the plasmid had more than 30 copies per chromosome in Escherichia coli cells. Plasmids were transformed into E. coli DH1, Acetobacter pasteurianus 3614, Acetobacter aceti 3620, Shigella, Citrobacter, and Brevibacterium flavum cells, and the stability of plasmid DNA was tested after cultivation in nonselective conditions.

Acetobacter↗

PubMed1994

Nucleotide sequence and replication characteristics of RepHI1B: a replicon specific to the IncHI1 plasmids.

The IncHI1 plasmids are multireplicon plasmids. They contain at least three autoreplicative regions, one of which is closely related to the RepFIA replicon of F. Two other IncHI1-specific replicons, RepHI1A and RepHI1B, have been recently isolated and mapped on the R27 (IncHI1) genome (P. Gabant, P. Newnham, D. Taylor, and M. Couturier, J. Bacteriol. 175, 7697-7701, 1993). In the present work, the DNA sequence of RepHI1B was determined. It reveals DNA repeats of 17 base pairs located upstream and downstream from a gene coding for a 32 kilodalton protein (RepA) required for replication. Interestingly, RepA presents significant homology with other Rep proteins encoded by plasmids belonging to different incompatibility groups: P1 (IncY), Rts1 (IncT), RepFIB (IncFI) and RepHI1A (IncHI1). All these results provide strong evidence that the RepHI1B replicon of the IncHI1 subgroup belongs to the group of plasmids which control their copy number by an iteron mechanism.

Amino Acid Sequence↗

PubMed1996

Use of a DNA polymerase III bypass mutant of Escherichia coli, pcbA1, to isolate potentially useful mutations of a complex plasmid replicon.

The essential replicon region of plasmid pCU1 has, within 1.2 kb, two origins of replication that can function in the absence of Escherichia coli DNA polymerase I and one that requires this polymerase. To isolate mutants in the replicon pathway that uses the PolI-dependent origin in the presence of the two other origins, we examined the feasibility of exploiting E. coli strains carrying a polymerase c bypass mutation (pcbA) and which can survive and form colonies with the polymerase activity of polC inactivated at 42 degrees C. The selection scheme that is described was successful and resulted in the isolation of a mutant replicon that is not maintained at 42 degrees C in a PcbA-PolC+tsPolA+ strain. Nucleotide sequencing indentified the mutated region to be within the origin (OriV) that was known to be polA-dependent. Electron microscopy of mutant plasmid molecules replicating in a Pcb+ strain confirmed that OriV is inactivated.

Base Sequence↗

PubMed1996

Nucleotide sequence and analysis of pWC1, a pC194-type rolling circle replicon in Lactococcus lactis.

A 2.8-kb cryptic plasmid showing no homology to either pFX3 (rolling circle, pE194-type) or pCI305 (theta-type) lactococcal replicons was identified in Lactococcus lactis subsp. cremoris 2204. The plasmid, pWC1, was compatible with both pCI3340 (a pCI305 derivative) and pFX3 in L. lactis subsp. cremoris 2204. Sequence analysis of pWC1 showed one major ORF encoding a protein with a deduced size of 316 amino acids (aa). Database comparisons showed that the protein was distinct from the pFX- and pCI-type replication proteins (less than 21% aa identity), but shared significant homology (up to 57% aa identity) with the replication proteins from a different group of rolling circle plasmids (pC194-type) commonly found in gram-positive bacteria. A pC194-type rolling circle plasmid has not been previously described in L. lactis. Further sequence analysis showed a conserved double-stranded origin of replication in pWC1 preceded by a large (118-bp) direct repeat. The chloramphenicol-resistance gene from pC194 was inserted into a nonessential region of pWC1 to give pCP12. The host range of pCP12 included Streptococcus thermophilus, Enterococcus faecalis, and Staphylococcus aureus, but not Escherichia coli. Both pCP12 and to a lesser extent pWC1 generated single-stranded DNA (ssDNA) in L. lactis. A possible single-stranded origin of replication was identified by sequence analysis of pWC1 and by comparing levels of ssDNA produced by pCP12 deletion derivatives. The pWC1 replicon may be a useful addition to other replicons currently available for vector construction.

Amino Acid Sequence↗

PubMed1996

Molecular analysis of the replication elements of the broad-host-range RepA/C replicon.

RepA/C is a replicon specific to the IncA/C incompatibility group of plasmids and was isolated recently from plasmid RA1. The sequence of this autoreplicative region was established; it contains 13 repeats, suggesting that the replicon uses iterons to control its copy number. The sequence contains two ORFs, one potentially coding for a 33-kDa protein (ORF1) and a second potentially coding for a 14-kDa protein (ORF2) (Llanes et al., 1994b). In this work, using an in vitro transcription/translation system, we detected a polypeptide whose size corresponded well to that of the deduced product of ORF1. Deletion and insertion mutation analysis showed that ORF1 is essential for replication; it encodes an initiator protein (called RepA). ORF2 was not essential for replication in Escherichia coli and its function remains to be determined. Using complementation experiments, the replication origin (ori) of RepA/C was defined. The ori was located in a 600-bp fragment downstream from repA, containing 10 direct repeats. To study the control of repA expression, a transcriptional fusion PrepA::lacZ was constructed. Its analysis showed that repA is transcriptionally autoregulated as are most repA genes of replicons controlled by iterons.

Cloning, Molecular↗

PubMed1993

Plasmid pHH1 of Halobacterium salinarium: characterization of the replicon region, the gas vesicle gene cluster and insertion elements.

The DNA sequence of the 5.7 kb plasmid pHH9 containing the replicon region of the 150 kb plasmid pHH1 from Halobacterium salinarium was determined. The minimal region necessary for stable plasmid maintenance lies within a 2.9 kb fragment, as defined by transformation experiments. The DNA sequence contained two open reading frames arranged in opposite orientations, separated by an unusually high AT-rich (60-70% A+T) sequence of 350 bp. All H. salinarium strains (H. halobium, H. cutirubrum) investigated harbour endogenous plasmids containing the pHH1 replicon; however, these pHH1-type plasmids differ by insertions and deletions. Adjacent to the replicon, and separated by a copy of each of the insertion elements ISH27 and ISH26, is the 9 kb p-vac region required for gas vesicle synthesis. Analysis of these and other ISH element copies in pHH1 revealed that most of them lack the target DNA duplication usually found with recently transposed ISH elements. These results underline the plasticity of plasmid pHH1.

Base Sequence↗

PubMed1998

Use of the Sindbis replicon system for expression of LaCrosse virus envelope proteins in mosquito cells.

The Sindbis replicon expression system was used to express La Crosse (LAC) virus envelope glycoprotein genes in both mammalian and mosquito cell culture. Replicon expressed LAC proteins had correct molecular mass (Mr) and were antigenically similar to wild type LAC envelope proteins. In addition, LAC G1 and G2 proteins colocalized when expressed from separate constructs in both mammalian and mosquito cells suggesting that they were trafficked through the cell similarly to wild type LAC proteins. A truncated form of the G1 protein was secreted from mosquito cells when expressed alone. The truncated G1 protein was also secreted from mosquito cells when expressed with the G2 protein, but to a lesser extent than when expressed alone, suggesting that the G2 protein sequestered G1 protein intracellularly. The Sindbis replicon system is a powerful tool for the study of LAC virus protein maturation within mosquito cells and mosquitoes.

Aedes↗

PubMed1980

Ultraviolet radiation inhibits replicon initiation in S phase human cells.

DNA replication was examined in ultraviolet-irradiated human fibroblasts and HeLa cells. The principal effect of exposures to low radiation fluences (less than 1.3 J/m2) was a reduced synthesis of molecules about one-half replicon in size resulting from an inhibition of replicon initiation. As the fluence of radiation was increased, inhibitory effects on strand elongation and joining masked the effect on replicon initiations.

Cell Cycle↗

PubMed1981

Nascent replicons are synchronously joined at the end of S phase or during G2 phase in peas.

In synchronized meristematic cells of Pisum sativum replicon-size DNA-fragments ((14--27) . 10(6) daltons) are not joined until the cells achieve a 4C DNA content. The combined use of a pulse-chase labeling protocol, single-cell autoradiography, cytophotometry, and velocity sedimentation in alkaline sucrose gradients showed that, unlike low molecular weight DNA (i.e., Okazaki fragments) which is ligated soon after replication starts, the joining of nascent replicon-size DNA is delayed until G2. In addition, this observation argues for the existence of replicon termini, although the data are insufficient to determine the true nature of these termini, i.e., whether they are coded in the DNA itself or simply arise as a consequence of the convergence of two replicating forks.

Cell Cycle↗

PubMed1984

Theophylline does not reverse DNA replicon initiation inhibition in human cells resistant to alkylating agent-theophylline killing synergism.

The human Burkitt's lymphoma cell line BHM fails to show synergistic killing by alkylating agents in the presence of theophylline. Nitrosoureas (BCNU and CNU), a mustard agent (L-phenylalanine mustard), and a platinum coordination complex (cis-diamminedichloroplatinum-II) did not show increased cytotoxicity when cells were treated in the presence of theophylline. Despite varying abilities of the drugs to induce DNA damage in BHM cells (no DNA interstrand cross-linking with nitrosoureas or platinum and significant interstrand cross-linking following L-PAM treatment) theophylline did not alter the pattern of DNA damage. DNA interstrand cross-linking following treatment by L-PAM with theophylline was slightly decreased from that seen with L-PAM alone. All three drugs induced DNA replicon initiation inhibition in BHM cells as measured both by alkaline sucrose gradient sedimentation and pH step alkaline elution. As opposed to cell lines where methylxanthines increase alkylating agent cytotoxicity, theophylline and caffeine failed to reverse the drug-induced replicon initiation inhibition seen in BHM cells. These findings support the hypothesis that the synergistic killing seen in some cell lines with alkylating agents and methylxanthines is due to the reversal of replicon initiation inhibition by the methylxanthines.

Alkylating Agents↗

PubMed1985

Effects of psoralen on replicon size and mean rate of DNA synthesis in partially synchronized cells of Pisum sativum L.

We have examined by fibre autoradiography the spacing of replicons in pea root meristems during synchronized entry into S phase from arrest at the G1/S boundary. Pretreatment with the DNA cross-linking agent, psoralen, produces a marked shortening of replicon spacing, suggesting that premature arrest of the replication fork results in the recruitment of additional initiation points within a given replicon family. This is discussed in relation to models for the control of DNA replication.

Autoradiography↗

PubMed1989

Replicon size and rate of DNA replication fork movement are correlated in grasses.

In eukaryotes, most nuclear DNA replication proceeds bidirectionally from multiple origins of replication. A unit of DNA, replicated by two replication forks from a single origin, is termed a replicon. Using results from DNA fiber autoradiography we show a novel positive correlation between replicon size and the rate of replication fork movement in root meristem nuclei of 13 grass species. Although there is interspecific variation in replicon size, it is balanced by similar variation in the rate of replication fork progression.

Poaceae↗

PubMed1993

Staurosporine suppresses replicon initiation in mammalian cells.

Replication in cellular replicons of mouse Ehrlich ascites, human CCRF-CEM and hamster BHK-21 cells was analyzed, after exposition of the cells to staurosporine, by measuring the overall DNA synthesis rate, by alkaline sedimentation analysis of length distributions of growing daughter strand DNA and by DNA fibre autoradiography. The results consistently indicated that micromolar concentrations of staurosporine caused, in all three cell lines, a fast suppression of replicon initiation which was reversible if the drug treatment did not exceed about 2 h. The inhibition of initiation was accompanied by a slight reduction of rates of propagation of replication forks. The data are interpreted in terms of the existence of a so far unknown factor which seems to be involved relatively directly in the initiation process of cellular replicons and has to be activated, like the large T antigen of SV 40 for the replication initiation in the viral genome, by a specific phosphorylation event. Unlike several other protein phosphorylations of cellular regulation, the kinase concerned here seems to be inhibited only by relatively high staurosporine concentrations.

Alkaloids↗

PubMed1981

A novel role for site-specific recombination in maintenance of bacterial replicons.

If daughter copies of unit-copy replicons recombine with each other, a replicon dimer results that cannot be partitioned equally to daughter cells at cell division. We present evidence that dimer formation interferes with plasmid equipartition in the case of a miniplasmid derived from the unit-copy plasmid prophage of bacteriophage P1. Asymmetric partition occurs, leading to a relatively high rate of loss of the plasmid from the growing population. In contrast, the wild-type P1 plasmid is maintained very efficiently in host cells. We show that this efficient maintenance is due to the presence of the loxP-cre site-specific recombination system present on the intact P1 plasmid. This system promotes rapid recombination between two loxP sites on dimer molecules, resolving them into monomeric substrates for proper partition. We suggest that bacterial replicons that are maintained with great accuracy in recombination-proficient cells might also encode high-efficiency recombination systems.

Base Sequence↗

PubMed1985

Location of rep and inc sequences in the F secondary replicon.

Miniplasmids derived by deletion of DNA from the F plasmid secondary replicon have been tested for the ability to replicate and to express incompatibility with the IncFI plasmid, ColV3-K30. The results demonstrate that the minimal rep region of the secondary replicon lies within a 1.9-kb sequence (33.7F-35.6F kb), and that an inc region, presumably involved in replication control, is present in a 0.45-kb portion of the rep region (33.7F-34.15F kb). In addition, the secondary replicon was found not to require DNA polymerase I activity.

Chromosome Mapping↗