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At least 937 records · Page 52Linked to original sources
PubMed1987

Characterization of the maintenance functions of IncFIV plasmid R124.

The genetic arrangement of the regions involved in R124 replication and incompatibility have been located and their homology to the IncFI basic replicons has been assessed. We show that R124 has homology with all three basic replicons, RepFIA, RepFIB, and RepFIC, and that these regions, FIVA, RepFIVB, and RepFIVC, are widely separated on the R124 genome. Cloning of autonomously replicating fragments has shown that RepFIVB and RepFIVC are functional in R124 and express incompatibility. The FIVA region was unable to form a functional replicon and when cloned into pUC8 lacked incompatibility activity. A fourth region of R124 was identified, which although not essential for replication stabilized mini-R124 plasmid replication and exhibited incompatibility with R124. This region, designated IncIV, showed no homology to RepFIA, RepFIB, or RepFIC. Incompatibility expression of IncIV required only the EcoRI fragment E13 but the strength of the reaction was modified in the presence of other fragments. The replication and incompatibility properties of an R124 deletion derivative indicated that R124 can switch its replication to either RepFIVB or RepFIVC when in the presence of an incompatible plasmid. The ambiguous incompatibility reactions reported for R124 is a result of the expression of the two functional replicons, RepFIVB and RepFIVC, and that expressed by IncIV.

Chromosome Mapping↗
PubMed2006

Hemin potentiates the anti-hepatitis C virus activity of the antimalarial drug artemisinin.

We report that the antimalarial drug artemisinin inhibits hepatitis C virus (HCV) replicon replication in a dose-dependent manner in two replicon constructs at concentrations that have no effect on the proliferation of the exponentially growing host cells. The 50% effective concentration (EC(50)) for inhibition of HCV subgenomic replicon replication in Huh 5-2 cells (luciferase assay) by artemisinin was 78+/-21 microM. Hemin, an iron donor, was recently reported to inhibit HCV replicon replication [mediated by inhibition of the viral polymerase (C. Fillebeen, A.M. Rivas-Estilla, M. Bisaillon, P. Ponka, M. Muckenthaler, M.W. Hentze, A.E. Koromilas, K. Pantopoulos, Iron inactivates the RNA polymerase NS5B and suppresses subgenomic replication of hepatitis C virus, J. Biol. Chem. 280 (2005) 9049-9057.)] at a concentration that had no adverse effect on the host cells. When combined, artemisinin and hemin resulted, over a broad concentration range, in a pronounced synergistic antiviral activity. Also at a concentration (2 microM) that alone had no effect on HCV replication, hemin still potentiated the anti-HCV activity of artemisinin.

Antimalarials↗
PubMed2005

Cloning and characterization of a region responsible for the maintenance of megaplasmid pTAV3 of Paracoccus versutus UW1.

Using cointegrate formation, we constructed a basic replicon of the megaplasmid/mini-chromosome pTAV3 of Paracoccus versutus UW1. It is composed of two adjacent modules, responsible for plasmid replication (rep) and partitioning (par). Functional analysis of the par region identified a determinant of incompatibility (inc2), whose presence is crucial for proper partitioning (the partitioning site). Database searches revealed that the only known replicon with significant homology to that of pTAV3 is encoded by the chromosome cII of Rhodobacter sphaeroides 2.4.1. Incompatibility studies showed that closely related basic replicons are also encoded by megaplasmids (above 400 kb) harbored by four strains of P. pantotrophus. Basic replicons of the pTAV3-type are able to maintain large bacterial genomes, therefore they appear to be good candidates for the construction of vectors specific for Alphaproteobacteria.

Base Sequence↗
PubMed2003

Analysis of pCU1 replication origins: dependence of oriS on the plasmid-encoded replication initiation protein RepA.

The broad-host-range replicon of the plasmid pCU1 has three origins of vegetative replication called oriB, oriS, and oriV. In the multi-origin replicon, individual origins can distinguish among replication factors provided by the host. It has been found that during replication in Escherichia coli polA(-) host, oriS was the only active origin of a mutant pCU1 derivative bearing a mutation in the gene encoding replication initiation protein RepA. To further investigate the capacity of oriS to function in an E. coli polA(-) host we constructed a number of clones of the basic replicon of pCU1 containing oriS as the only replication origin. An oriS construct created with pUC18 could transform the polA(-) strain when RepA was supplied in trans. When the oriS region (between nucleotides 290 and 832) was ligated to an antibiotic resistance Omega fragment, the construct could be recovered as a plasmid from polA(+) strain if functional RepA was provided in trans. Our results therefore indicate that the basic replicon of pCU1, containing oriS as the sole origin, does require RepA to initiate plasmid replication in E. coli

Bacterial Proteins↗
PubMed1997

Effects of bizelesin (U-77,779), a bifunctional alkylating minor groove binder, on replication of genomic and simian virus 40 DNA in BSC-1 cells.

Bizelesin, an AT-specific DNA-alkylating antitumor drug, is a potent inhibitor of genomic DNA replication in BSC-1 cells. Fifty percent inhibition of DNA synthesis was observed at 10 nM bizelesin compared to 160 nM needed for 50% inhibition of RNA synthesis while no inhibition of protein synthesis was observed up to 200 nM. Sedimentation analysis of nascent genomic DNA showed that bizelesin inhibited new replicon initiation and had significantly less effect on replicon maturation. Bizelesin also suppressed the intracellular synthesis of simian virus 40 (SV40) DNA in virus-infected BSC-1 cells. The analysis of nascent SV40 intermediates synthesized after bizelesin treatment confirmed an initiation-specific inhibition. The inhibitory effects on cellular DNA replication occurred at bizelesin levels resulting in infrequent adducts (one adduct per several replicons). Only one bizelesin adduct per several SV40 molecules was needed for a potent inhibition of intracellular SV40 replication. In contrast, only partial inhibition of SV40 replication in vitro was observed with bizelesin-treated naked SV40 DNA as a template. Overall, the results indicate that infrequent bizelesin lesions impede the cellular replication apparatus at the level of the initiation of new replicons.

Animals↗
PubMed2001

The shuffling function of resolvases.

Redistribution (shuffling) of genetic material between replicons requires consecutive recombination at four points, two of which (X, X') are involved in the replicon fusion and the other two (Y, Y'), in the cointegrate resolution. The fusion of replicons by bacterial resolvases makes the second recombination round at sites Y and Y' problematic because of the high probability of the reverse reaction. Structural differences of the res sites recognized by resolvase could delay the reverse reaction, thus enhancing the probability of recombination at sites Y, Y', but the direct reaction ensuring it (i.e. the fusion of replicons via different res sites) has not been described yet. Here, a genetic system to test intermolecular recombination at heterogeneous res sites has been developed. The system was based on the res site (RS2) of the novel resolution system, cinH-RS2, encoded by pKLH2, pKLH204 and pKLH205. As its partner, the res site of RP4 located in the par locus, the res site of transposon gammadelta or Tn1721, the incomplete site RS1 consisting only of the (crossover) subsite resI also found in pKLH2/204/205 and others were used. Except for the pairing of RS2 x gammadelta res, recombination was observed in each case even when the homology shared by partners did not exceed 35% (as in RS2 x par). In the latter case, the presence in cis of an additional, enhancer-like-acting element was required. Pairing of crossover subsites during site-specific recombination occurred in either orientation, depending on the structure of res partners and the kind of resolvase acting on the sites. With the complete res sites, the antiparallel alignment resulted in the production of an unusual res having the accessory subsites II and III at both sides of I, and a res lacking II and III. The wide range of frequencies was observed not only in the fusion formation but also in the dissociation of the resulting cointegrates. Hence, the resolvase-mediated interreplicon exchange of the DNA segments by fusion via an inefficient reaction (at sites X, X') and dissociation via an efficient one (at sites Y, Y') become possible.

Artificial Gene Fusion↗
PubMed1999

Alphavirus vectors for gene expression and vaccines.

Alphavirus expression vectors are finding novel uses in research. They are showing increasing promise as vaccines and are being developed for diagnostic assays of other viruses. Some highlights over the past couple of years include improvements in packaging of replicons, targeting of Sindbis virus replicons, stable cell lines that can be induced to produce replicons, and the isolation of noncytopathic variants of Sindbis virus replicons. Reports that alphavirus vectors can efficiently infect neurons in rat hippocampal slices should increase their use in neurobiological studies.

Alphavirus↗
PubMed2004

Induced oxidative stress and activated expression of manganese superoxide dismutase during hepatitis C virus replication: role of JNK, p38 MAPK and AP-1.

Activation of cellular kinases and transcription factors mediates the early phase of the cellular response to chemically or biologically induced stress. In the present study we investigated the oxidant/antioxidant balance in Huh-7 cells expressing the HCV (hepatitis C virus) subgenomic replicon, and observed a 5-fold increase in oxidative stress during HCV replication. We used MnSOD (manganese-superoxide dismutase) as an indicator of the cellular antioxidant response, and found that its activity, protein levels and promoter activity were significantly increased, whereas Cu/ZnSOD was not affected. The oxidative stress-induced protein kinases p38 MAPK (mitogen-activated protein kinase) and JNK (c-Jun N-terminal kinase) were activated in the HCV repliconcontaining cells and in Huh-7 cells transduced with Ad-NS5A [a recombinant adenovirus encoding NS5A (non-structural protein 5A)], coupled with a 4-5-fold increase in AP-1 (activator protein-1) DNA binding. Ava.1 cells, which encode a replication-defective HCV replicon, showed no significant changes in MnSOD, p38 MAPK or JNK activity. The AP-1 inhibitors dithiothreitol and N -acetylcysteine, as well as a dominant negative AP-1 mutant, significantly reduced AP-1 activation, demonstrating that this activation is oxidative stress-related. Exogenous NS5A had no effect on AP-1 activation in vitro, suggesting that NS5A acts at the upstream targets of AP-1 involving p38 MAPK and JNK signalling cascades. AP-1-dependent gene expression was increased in HCV subgenomic replicon-expressing Huh-7 cells. MnSOD activation was blocked by inhibitors of JNK (JNKI1) and p38 MAPK (SB203580), but not by an ERK (extracellular-signal-regulated kinase) inhibitor (U0126), in HCV-replicating and Ad-NS5A-transduced cells. Our results demonstrate that cellular responses to oxidative stress in HCV subgenomic replicon-expressing and Ad-NS5A-transduced cells are regulated by two distinct signalling pathways involving p38 MAPK and JNK via AP-1 that is linked to increased oxidative stress and therefore to an increased antioxidant MnSOD response.

Cell Line↗
PubMed1997

The poison-antidote stability system of the broad-host-range Thiobacillus ferrooxidans plasmid pTF-FC2.

In plasmid pTF-FC2, three small open reading frames (ORFs) are situated between the repB (primase) gene and the repA (helicase) gene of its IncQ-type replicon. Disruption of each of the three ORFs followed by tests for plasmid stability and host cell growth indicated that the ORFs encoded a poison-antidote plasmid stability system. The three genes were named pasA, pasB and pasC (plasmid addiction system), in which PasA is the antidote, PasB the toxin and PasC a protein that appears to enhance the ability of the antidote to neutralize the toxin. Disruption of the pasA gene resulted in two different spontaneous deletions, which inactivated the stability system but did not alter the host range or plasmid copy number. This indicated that the three small ORFs were not involved in plasmid replication. When placed behind a tac promoter, induction of pasB was found to be highly lethal to host cells, which suggests that the Pas system acts by killing plasmid-free host cells rather than by retarding the growth of plasmid-free segregants, as occurs in the ParD system of R1. In spite of this, the presence of the Pas poison-antidote system resulted in a relatively modest threefold stabilization of the pTF-FC2 host replicon and a similar increase in the stabilization of an unstable heterologous R1 plasmid replicon. The Pas system is a poison-antidote plasmid stability module, which appears to have become integrated within the pTF-FC2 replicon module.

Amino Acid Sequence↗
PubMed1984

Topological repression of gene activity by a transposable element.

The ebgA (evolved beta-galactosidase) gene of Escherichia coli was isolated as part of a 9.6-kilobase (kb) sequence cloned into plasmid pBR322. The position of the ebgA gene within that 9.6-kilobase sequence was identified by insertional inactivation by means of the transposon gamma-delta. In addition to the gamma-delta insertions that inactivate ebgA by disrupting the coding sequence, seven additional gamma-delta insertions reduce expression of the gene by a factor of greater than 200 by insertions elsewhere into the replicon. One of these insertions is into the pBR322 sequence itself. This action at a distance to reduce expression requires that gamma-delta is cis with respect to the ebgA gene. The effect is independent of the orientation or position of gamma-delta within the replicon, but it does depend both upon the orientation of the ebgA-bearing sequence within the replicon and upon the total size of the replicon. Transcription readthrough (promoter occlusion) does not explain this phenomenon, and we suggest that the presence of gamma-delta may alter the local supercoiling in the region of the ebgA promoter in such a way as to inhibit transcription. This repression by a transposable element appears to represent a novel mechanism for altering gene expression.

DNA Restriction Enzymes↗
PubMed1997

Recombinational construction in Escherichia coli of infectious adenoviral genomes.

A two-step gene replacement procedure was developed that generates infectious adenoviral genomes through homologous recombination in Escherichia coli. As a prerequisite, a human adenovirus serotype 5 (Ad5)-derived genome was first introduced as a PacI restriction fragment into an incP-derived replicon which, in contrast to ColE1-derivatives (e.g., pBR322 or pUC plasmids), is functional in a polA mutant of E. coli. Any modification can be introduced at will following two consecutive homologous recombinations between the incP/Ad5 replicon and the ColE1 plasmid. The overall procedure requires only the in vitro engineering of the ColE1-derivative by flanking the desired modification with small stretches of identical sequences. In the first step, a cointegrate between the tetracycline-resistant incP/Ad5 replicon and the kanamycin-resistant ColE1-derivative is selected by growing the polA host in the presence of both antibiotics. Resolution of this cointegrate is further selected in sucrose growth conditions due to the loss of a conditional suicide marker (the sacB gene of Bacillus subtilis) present in the ColE1 plasmid, leading to unmodified and modified incP/Ad5 replicons that can be differentiated upon restriction analysis. Consecutive rounds of this two-step cloning procedure allowed the introduction of multiple independent modifications within the virus genome, with no requirement for an intermediate virus. The potential of this procedure is demonstrated by the recovery of several E1E3E4-deleted adenoviruses following transfection of the corresponding E. coli-derived genomes in IGRP2 cells.

Adenovirus E1 Proteins↗
PubMed1998

Rapid, high level protein production using DNA-based Semliki Forest virus vectors.

Semliki Forest virus (SFV) vectors can be produced faster, and have a wider host range, than baculovirus vectors. However, the original SFV system requires in vitro manipulation of RNA. We have generated a system that is wholly DNA-based. Both the replicon vector, encoding SFV polymerase and the protein of interest, and the helper vector, encoding viral structural proteins, were modified so that expression was RNA polymerase II-dependent. Transfection of the modified replicon plasmid alone generated 20-30-fold more protein than obtained from a simple expression vector. Expression required the SFV replicase, which amplifies replicon RNA. The SFV-based vector generated 10-20-fold more protein than a plasmid based on Sindbis virus. Cotransfection of SFV replicon and helper vectors generated viral titers of around 10(6) infectious particles/ml. A single electroporation, plated on one 10-cm plate, generated enough virus (10(7) particles) to produce >500 microg of protein. Wild type, replication proficient virus was not detected in three tests utilizing almost 10(8) viral particles, a distinct advantage over a DNA Sindbis-based system in which over half the virus particles generated are fully infectious. The new SFV vectors significantly enhance the utility of this expression system.

Animals↗
PubMed2004

Synergistic inhibition of intracellular hepatitis C virus replication by combination of ribavirin and interferon- alpha.

Treatment of hepatitis C virus (HCV) infection with interferon (IFN)- alpha and ribavirin combination therapy results in superior clinical antiviral responses than does monotherapy with IFN. To explore the virological basis of the effects of combination therapy, we analyzed the effects of IFN- alpha and ribavirin, singly and in combination, on intracellular HCV replication by use of an HCV replicon system. A new replicon that expressed a selectable chimeric reporter protein comprising firefly luciferase and neomycin phosphotransferase was constructed. The replicon was highly sensitive to IFN-alpha (50% inhibitory concentration [IC(50)], 0.5 U/mL). Therapy with ribavirin showed weak suppression of HCV replication at a lower concentration (IC(50), 126 mu mol/L). The nucleotide sequence diversity of the replicon was increased significantly by therapy with ribavirin, suggesting that error-prone HCV replication was induced by the drug. Importantly, use of a clinically achievable concentration of ribavirin (approximately 10 mu mol/L) in combination with IFN showed strong synergistic inhibitory effects on HCV replication. Our results suggest that the direct effects of ribavirin on the genetic stability of the HCV subgenome and its synergistic action combined, with IFN-alpha, may explain the improved clinical responses to combination therapy.

Amino Acid Sequence↗
PubMed2006

In vitro antiviral activity of SCH446211 (SCH6), a novel inhibitor of the hepatitis C virus NS3 serine protease.

BACKGROUND: Current hepatitis C virus (HCV) therapies may cure approximately 60% of infections. They are often contraindicated or poorly tolerated, underscoring the need for safer and more effective drugs. A novel, alpha-ketoamide-derived, substrate-based inhibitor of the HCV serine protease (SCH446211) was developed. Compared with earlier reported inhibitors of similar chemical class, it has a P1'-P2' extension which provides extended interaction with the protease active site. The aim of this study was to evaluate the in vitro antiviral activity of SCH446211. METHODS: Binding constant of SCH446211 to HCV NS3 protease was measured with the chromogenic substrate in vitro cleavage assay. Cell-based activity of SCH446211 was evaluated in replicon cells, which are Huh-7 hepatoma cells stably transfected with a subgenomic HCV RNA as reported previously. After 72 h of incubation with SCH446211, viral transcription and protein expression were measured by real-time RT-PCR (TaqMan), quantitative in situ hybridization, immunoblot and indirect immunofluorescence. RESULTS: The binding constant of SCH446211 to HCV NS3 protease was 3.8 +/- 0.4 nM. HCV replication and protein expression were inhibited by SCH446211 in replicon cells as consistently shown by four techniques. In particular, based on quantitative real-time RT-PCR measurements, the IC50 and IC90 of SCH446211 were estimated to be 40 +/- 20 and 100 +/- 20 nM (n = 17), respectively. Long-term culture of replicon cells with SCH446211 reduced replicon RNA to <0.1 copy per cell. SCH446211 did not show cellular toxicity at concentrations up to 50 microM. CONCLUSIONS: SCH446211 is a potent inhibitor of HCV protease in vitro. Its extended interaction with the HCV NS3 protease active site is associated with potent in vitro antiviral activity. This observation is potentially a useful guide for development of future potent inhibitors against HCV NS3 protease.

Antiviral Agents↗
PubMed1999

Plant cell-directed control of virion sense gene expression in wheat dwarf virus.

We have used particle bombardment (biolistics) to deliver replication-competent wheat dwarf virus (WDV)-based constructs, carrying reporter gene sequences fused to the virion sense promoter (Pv) or the CaMV 35S promoter, to suspension culture cells and immature zygotic embryos of wheat. While the replication of WDV double-stranded DNA forms (replicons) was equivalent between wheat suspension culture cells and embryos, GUS reporter gene activity was 20-40 times higher in the embryo cultures. Maximum expression of WDV replicons occurred in the embryonic axis tissue of wheat embryos but their expression in suspension cells was compromised, compared with transiently maintained input plasmid DNA containing the same sequences. From these studies, we propose that WDV replicons are subject to a host cell-controlled competency for virion sense transcription. The term competency is used to distinguish between the phenomenon described here and control of gene expression by specific transcription factors. Control of competency is independent of Pv, the replacement 35S promoter and of the complementary sense control of virion sense expression involving specific sequences in Pv. We propose that factors controlling the competency for replicon expression may be present in cells which, as well as maintaining high rates of DNA synthesis, are totipotent. Cell type control of active chromatin, methylation of specific sequences in WDV minichromosomes and/or interaction of virus-encoded proteins with specific host factors are considered as possible mechanisms.

Caulimovirus↗
PubMed2002

Characterization of the replicator region of megaplasmid pTAV3 of Paracoccus versutus and search for plasmid-encoded traits.

The replicon of the pTAV3 megaplasmid (approx. 400 kb) of Paracoccus versutus has been localized to a 4center dot3 kb EcoRI restriction fragment and its entire nucleotide sequence determined. The G+C content of the entire sequence is 66 mol%, which is within the range (62-66 mol%) previously determined for P. versutus total DNA. ORF1 encodes a replication initiation protein Rep (47.2 kDa), which shares substantial similarity with putative proteins of the Coxiella burnetii plasmids QpH1 and QpDV, and the replication protein of Pseudomonas syringae plasmid pPS10. ORF2, located in the opposite transcriptional orientation to ORF1, encodes a putative protein that shares similarity to a subfamily of ATPases involved in plasmid partitioning. The highest similarity was observed with homologous proteins (RepA) encoded by the repABC family of replicons found in several plasmids of Agrobacterium, Rhizobium and Paracoccus spp. The predicted product of ORF3 was similar to AcoR, Nif and NtrC transcriptional activators. A strong incompatibility determinant (inc) was localized between ORF1 (rep) and ORF2 (parA). The origin of replication of pTAV400 contains a short A+T-rich region and several imperfect palindromic sequences. Curing experiments demonstrated that the megaplasmid bears genes required for growth in minimal media and can therefore be referred to as a mini-chromosome. Megaplasmids pTAV3 of P. versutus UW1 and pKLW2 of Paracoccus pantotrophus DSM 11073 were found to carry closely related, incompatible replicons. It has been shown that plasmid pORI6 (containing oriV of pTAV3 cloned into plasmid pABW1, which does not replicate in Paracoccus spp.) can be trans activated not only by pTAV3, but also by pKLW2. Using pORI6, it was demonstrated that replication systems related to pTAV3 are also present in the replicons of Paracoccus alcaliphilus JCM 7364, Paracoccus thiocyanatus IAM 12816 and Paracoccus methylutens DM 12.

Amino Acid Sequence↗
PubMed1993

Molecular analysis of the Lactococcus lactis subspecies lactis CNRZ270 bidirectional theta replicating lactose plasmid pUCL22.

pUCL22 is the lactose protease plasmid of Lactococcus lactis ssp. lactis CNRZ270. The nucleotide sequence of its replication region Rep22 contains a non-transcribed region, the replication origin, followed by a gene encoding a putative 388-amino-acid protein named Rep22A. The promoter regions of the rep22A and pC194 cat genes share strong similarities and the pUCL22 replicon exerted trans or cis negative control on the pC194 cat gene expression in L. lactis. We suggest that Rep22A binds to its own promoter as well as to the pC194 cat promoter and thus is autoregulated. We show that pUCL22 replicates mainly by a bidirectional theta mechanism in L. lactis, and is representative of a widely distributed replicon family, members of which could be co-resident. We propose that compatibility between these closely related replicons results from minor replication protein modifications coupled with base changes in their respective binding sites, supporting the co-existence of numerous related replicons in lactococcal strains.

Amino Acid Sequence↗
PubMed1995

A transcription terminator signal necessary for plasmid ColIb-P9 replication.

Replication of the IncI alpha plasmid ColIb-P9 requires the repZ gene, which encodes an essential, unstable initiator protein termed RepZ. Although many functional features of the ColIb-P9 replicon resemble those of structurally unrelated IncFII plasmids R1 and NR1, the role of transcription of repZ towards the replication origin is poorly understood. Using a series of deletion and substitution mutants of the ColIb-P9 replicon, we found that RepZ prefers to act in cis and that a spacer sequence between repZ and the origin is required for replication. This spacer element, referred to as CIS, retained strong transcription terminator activity. Efficient transcription terminators, whether Rho-dependent or -independent, were capable of replacing CIS function for in vivo replication; ColIb-P9 replicated better as transcription terminated more efficiently within CIS. When the CIS element was substituted for by a strong Rho-dependent terminator, such as lambda tR1 or E. coli trp t', in vivo replication of these recombinant replicons became dependent on the Rho factor, in contrast to the authentic ColIb-P9 replicon.

Bacterial Proteins↗