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Results for “extrachromosomal element”

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PubMed1985

Two mammalian cell systems for propagation of the hepatitis B virus genome in extrachromosomal and chromosomally integrated states: production of the surface and e antigens.

A recombinant plasmid consisting of (i) the entire genome of hepatitis B virus (HBV) DNA, (ii) the replication origin of SV40 virus, and (iii) a deletion derivative of pBR322 was introduced either into COS cells of monkey origin which constitutively express SV40 large T antigen, or into thymidine kinase(TK)-deficient mouse L cells together with the TK DNA of Herpes simplex virus. In the COS cell system, the transfecting recombinant DNA replicates via SV40 origin and is maintained in an autonomously replicating state. The cells carrying these extrachromosomal elements express the hepatitis B surface antigen gene at moderate rate, and release the products into the culture medium. However, neither core antigen nor e antigen expression was detected in this system. In the L cell system, the transformed L cells carry the recombinant DNA in a chromosomally integrated state. Such cells express the surface antigen gene at high rate, and release the products into the culture medium. This system also excretes the e antigen into the culture medium. The core antigen was not detected.

Animals↗

PubMed1998

Genomic organization analysis of acidophilic chemolithotrophic bacteria using pulsed field gel electrophoretic techniques.

The genomic organization of acidophilic chemolithotrophic bacteria belonging to the genus Thiobacillus, Thiomonas and Leptospirillum was studied using pulsed field gel electrophoresis techniques (PFGE). The electrophoretic analysis of intact DNA prepared from different strains showed that all have a circular chromosome, with sizes ranging from 1.9 Mb for Leptospirillum ferrooxidans ATCC 49879, the smallest genome for an acidophilic strict chemolithoautotrophic microorganism, to 3.8 Mb for Thiomonas cuprina DSM 5495, the largest in this study. The number of extrachromosomal elements present varied from none, as observed in several isolates of Leptospirillum ferrooxidan, to five in Thiobacillus thiooxidans ATCC 8085. The mixotroph Thiomonas cuprina DSM 5495 was found to have a linear 50 kb megaplasmid which was inducible when the bacteria was grown in chemolithotrophic conditions. Low-frequency restriction fragment analysis (LFRFA) of different acidophilic chemolithotrophs and related species was carried out by PFGE to determine macrorestriction patterns for rare cutters (SpeI, XbaI, SwaI, PmeI), which were then used for taxonomic identification (karyotyping), genome size determination, and generation of physical and genetic maps.

Chromosome Mapping↗

PubMed1978

[Genetic structure of Staphylococcus epidermidis strain No. 17 possessing penicillinase and bacteriocinogenic activity].

The studies on the genetic structure of Staphylococcus epidermidis, strain 17 showed that this strain possessed a factor of bactericinogenicity of the one type, which was an extrachromosomal element not bound with penicillinase activity. The loss of the bacteriocinogenicity factor spontaneously or under the effect of acridine orange at a temperature of 37 degrees C was not observed. Passages of the strain at a temperature of 44 degrees C for 5 days and acridine orange proved to be the most effective eliminating factors. The loss of the bacteriocinogenicity plasmid did not result in changing any biochemical properties of the strain but was accompanied by a loss of the immunity to bacteriocin of the initial strain. The study of the growth regularities of the initial strain and its variant deprived of the bacteriocinogenicity plasmid showed that multiplication of the cells in the presence of the plasmid practically started without the latent period.

Acridine Orange↗

PubMed1994

Molecular characterization of Theileria parasites: application to the epidemiology of theileriosis in Zimbabwe.

Forty Theileria schizont-infected lymphocyte culture isolates from Zimbabwe were characterized using a panel of antischizont monoclonal antibodies (MAbs) and 4 Theileria parva DNA probes containing cloned extrachromosomal element, Tpr repetitive, ribosomal and telomeric sequences. The Theileria isolates were assigned as T. parva or T. taurotragi on the basis of reactivities with MAbs and restriction fragment length polymorphisms (RFLPs) detected using the extra-chromosomal element probe. Cattle-derived T. parva isolates were relatively homogeneous on the basis of reactivities with MAbs and RFLPs detected using Tpr repetitive and ribosomal DNA probes. In contrast to previous results from Kenya, most of the cattle-derived isolates from Zimbabwe exhibited very similar Tpr restriction fragment patterns, although the Tpr genotypes of buffalo-derived isolates were heterogeneous. This suggests that selection for a particular Tpr genotype may be occurring in cattle. Many isolates with similar Tpr genotypes were differentiated by RFLPs detected using the telomeric DNA probe. The T. parva Boleni immunizing stock was distinguished from all other isolates by telomeric RFLPs. The T. parva Boleni Tpr repetitive DNA probe cross-hybridized with T. taurotragi DNA and detected RFLPs between different T. taurotragi isolates.

Animals↗

PubMed1974

Multienzyme systems of DNA replication.

Replication is accomplished by multienzyme systems whose operations are usefully considered in respect to three stages of the process: initiation, elongation, anid termination. 1) Initiation entails synthesis of a short RNA fragment that serves as primer for the elongation step of DNA synthesis. This stage, probed by SS phage DNA templates, reveals three distinctive and highly specific systems in E. coli. The Ml3 DNA utilizes RNA polymerase in a manner that may reflect how plasmid elements are replicated in the cell. The ØX174 DNA does not rely on RNA-polymerase, but requires instead five distinctive proteins which may belong to an apparatus for initiating a host chromosome replication cycle at the origin. The G4 DNA, also independent of RNA polymerase, needs simply the dnaG protein for its distinctive initiation and may thus resemble the system that initiates the replication fragments at the nascent growing fork. In each case it is essential that in vitro the DNA-unwinding protein coat the viral DNA and influence its structure. 2) Elongation is achieved in every case by the multisubunit, holoenzyme form of DNA polymerase III. Copolymerase III, which is an enzyme subunit, and adenosine triphosphate are required to form a proper complex with the primer template but appear dispensable for the ensuing chain growth by DNA polymerase (33). 3) Termination requires excision of the RNA priming fragment, filling of gaps and sealing of interruptions to produce a covalently intact phosphodiester backbone. DNA polymerase I has the capacity for excision and gapfilling and DNA ligase is required for sealing. What once appeared to be a simple DNA polymerase-mediated conversion of a single-strand to a duplex circle (34) is now seen as a complex series of events in which diverse multienzyme systems function. Annoyance with the difficulties in resolving and reconstituting these systems is tempered by the conviction that these are the very systems used ,by the cell in replicating its chromosome and extrachromosomal elements. Thus, understanding of the regulation of replication events in the cell, their localization at membrane surfaces and integration with cell division, and their coordination with phage DNA maturation and particle assembly will all be advanced by knowledge of the components of the replicative machinery.

Cell-Free System↗

PubMed1993

CpG island mapping of a mouse double-minute chromosome.

The development of double-minute chromosomes (DMs) and subsequent gene amplification are important genomic alterations resulting in increased oncogene expression in a variety of tumors. The molecular mechanisms mediating the development of these acentric extrachromosomal elements have not been completely defined. To elucidate the mechanisms involved in DM formation, we have developed strategies to map amplified circular DM DNA. In this study, we present a long-range restriction map of a 980-kb DM. A cell line cloned from mouse EMT-6 cells was developed by stepwise selection for resistance to methotrexate. This cloned cell line contains multiple copies of the 980-kb DM carrying the dihydrofolate reductase (DHFR) gene. A long-range restriction map was developed in which a hypomethylated CpG-rich region near the DHFR gene served as a landmark. This strategy was combined with plasmid-like analysis of ethidium bromide-stained pulsed-field gels and indicated that a single copy of the DHFR gene was located near a hypomethylated region containing SsII and NotI sites. At least 490 kb of this DM appears to be composed of unrearranged chromosomal DNA.

Animals↗

PubMed1976

Spontaneous chromosome mutation and screening of mutator factors in Drosophila melanogaster.

(1) The marked inversion technique was used, and 38 major autosome sets of Drosophila melanogaster were extracted from populations of Jugoslavia, Taiwan and Japan. Spontaneous mutations were allowed to accumulate on the major chromosomes for 25 generations. Then the second chromosomes were tested to determine whether or not they were associated with such known mutator factors as the male crossing-over factor, SD, and the extrachromosomal element delta. Chromosome mutations were examined by salivary gland chromosome analysis, and viability mutations were done by the marked autosomal translocation method. (2) In 8 out of 38 major autosome lines, 5 inversions occurred in the second chromosomes, 4 inversions in the third chromosomes, and 1 reciprocal translocation between the second and the third chromosomes. Chromosome mutation rates were, therefore, 0.0063 per second chromosome per generation and 0.0053 per third chromosome per generation. Since there was no signficant difference in the rates, chromosome mutations seem to be occurring approximately equally in both major autosomes. (3) Lethal mutation rates were estimated to be 0.0097 per major autosome per generation. (4) Twenty-four second chromosome lines out of 37 demonstrated male crossing-over among the cinnabar and brown interval; the average frequencies were 0.0031 for all lines and 0.0034 when non-recombination lines were excluded. (5) One second chromosome exhibited delta retaining ability (ID), but no second chromosome carried SD.

Animals↗

PubMed1983

[Multiplication of a DNA fragment in Streptomyces antibioticus--producer of oleandomycin].

Two strains of Str. antibioticus producing oleandomycin were studied. Strain 326 was obtained from the initial laboratory strain and strain 1607 from strain 326 as a result of multistage selection aimed at increasing the antibiotic production capacity. Extrachromosomal ring DNA could be identified in strain 1607. The identified DNA was designated as eSA1 or extrachromosomal element of Streptomyces antibioticus 1. The molecular weight of this DNA is 21.3 Md. It is represented by 1 copy per chromosome. No eSA1 was isolated from strain 326 at CsCl-EtBr gradient. Hybridization studies according to Southern with the use as a probe of 32-eSA1 DNA showed that strain 326 contained 1 copy of eSA1 per chromosome in the integrated state. The hybridization studies, electron microscopy and analysis of the total DNA in CsC1-EtBr gradient showed that eSA1 in strain 1607 was tandemly multireplicated in the chromosome content. In the autonomous state its number was approximately equal to 1 copy per chromosome. The presence of eSA1 in strain 1607 in the autonomous state probably results from its segregation during homologous recombination due to tandem multireplication. The data are indicative of multiplication in strain 1607 of the chromosome fragment 23.3 Md in size. It is suggested that an increase in the oleandomycin production capacity of strain 1607 is associated with multiplication of the DNA fragment (eSA1) containing the genes determining production of the antibiotic.

Chromosomes, Bacterial↗

PubMed1993

Molecular dissection of an extrachromosomal amplicon reveals a circular structure consisting of an imperfect inverted duplication.

A mouse fibroblast line, B-1/50, with a 4300-fold amplification of the adenosine deaminase gene locus (Yeung et al., 1983, J. Biol. Chem. 258: 8338-8345), was shown by in situ hybridization to harbor the amplified sequences on variously sized extrachromosomal elements. We show here that the smallest circle is approximately 500 kb. We describe a facile screening technique for identifying cosmid and yeast artificial chromosome (YAC) clones derived from the amplicon. A closed molecular map was generated by arranging the cosmids and YACs into a contig spanning over 250 kb of the adenosine deaminase gene locus. YACs from the two ends of this contig were shown to delimit a 250-kb inverted duplication. Long-range mapping of a SalI partial digest of B-1/50 DNA is also consistent with the interpretation that the 500-kb adenosine deaminase amplicon in B-1/50 cells is an inverted duplication. The finding that this amplicon is the only or predominant structure containing amplified sequences in the B-1/50 cell line suggests that such structures are not inherently prone to high frequency rearrangement, even when present at such high copy number. This study provides the first molecular description of the structure of an episome involved in mammalian gene amplification. The implications of this finding for models of gene amplification and episome formation are discussed.

Adenosine Deaminase↗

PubMed1983

A preliminary model of double-minute-mediated gene amplification.

A mathematical model of double minute (dm) population dynamics has been developed based upon current concepts of the saltatory replication, random partitioning, nuclear exclusion and loss, and cellular growth inhibition of these extrachromosomal elements. A highly accurate approximate analytical solution has been obtained for the dm frequency distribution at steady state and preliminary analysis of transient states has been performed. The steady state solution has been fit to experimental frequency data of the SW527N carcinoma line, the excellent goodness of fit (X2 = 2.6, d.f. = 29) providing preliminary evidence for the consistency of this set of mechanisms. Two special cases are examined in which extrareplicative dms are produced on both the chromosome and existing dms at equal rates or on the chromosome alone. The model predicts that the population--average rate of extrareplicative dm production is 0.039 +/- S.E. 0.009 dms/hr/cell in the first case and is tenfold higher than when such replication occurs on the chromosome alone (0.0043 +/- S.E. 0.0004 dms/hr/cell). Allowable ranges of the extent of dm-related growth inhibition and dm loss are determined for the SW527N cell line. It is found that dm-related growth inhibition can be nearly as high as that observed for the S180 sarcoma lines (on the order of 0.5% per dm lengthening of the doubling time) or as low as zero.

Animals↗

PubMed1973

Molecular nature of R-factor deoxyribonucleic acid isolated from Salmonella typhimurium minicells.

In earlier reports it was shown that a variety of extrachromosomal elements harbored in the Escherichia coli minicell producer segregate into the minicells. We show in this report that the fi(+) R factor R-100-1 (derepressed derivative of R-100) similarly segregates into minicells produced by a Salmonella typhimurium strain. Four distinct classes of covalently closed circular deoxyribonucleic acid molecules are found in minicells derived from the R(+)Salmonella minicell producer. The sum of the average molecular weights or contour lengths of the circular molecules in two of the classes is equal to the average molecular weight or contour length of those in a third class. The data suggest that R-100-1 dissociates into resistance determinants (i.e., genes that specify the molecules that confer resistance) and the resistance transfer factor (i.e., genes responsible for the transferability of the R factor to a recipient). In contrast, only one molecular species is found in minicells derived from the R(+) (R-100-1) Escherichia coli minicell producer. The fourth size class consists of small covalently closed circles (minicircles), which were originally found in the R(-)Salmonella minicell producer and are shown in this report to be enhanced in number in R(+)Salmonella minicells.

Bromides↗

PubMed1994

The dominant PNM2- mutation which eliminates the psi factor of Saccharomyces cerevisiae is the result of a missense mutation in the SUP35 gene.

The PNM2- mutation of Saccharomyces cerevisiae eliminates the extrachromosomal element psi. PNM2 is closely linked to the omnipotent suppressor gene SUP35 (also previously identified as SUP2, SUF12, SAL3 and GST1). We cloned PNM2- and showed that PNM2 and SUP35 are the same gene. We sequenced the PNM2- mutant allele and found a single G-->A transition within the N-terminal domain of the protein. We tested the effects of various constructs of SUP35 and PNM2- on psi inheritance and on allosuppressor and antisuppressor functions of the gene. We found that the C-terminal domain of SUP35 protein (SUP35p) could be independently expressed; expression produced dominant antisuppression. Disruption of the N-terminal domain of PNM2- destroyed the ability to eliminate psi. These results imply that the domains of SUP35p act in an antagonistic manner: the N-terminal domain decreases chain-termination fidelity, while the C-terminal domain imposes fidelity. Two transcripts were observed for SUP35, a major band at 2.4 kb and a minor band at 1.3 kb; the minor band corresponds to 3' sequences only. We propose a model for the function of SUP35, in which comparative levels of N- and C-terminal domains of SUP35p at the ribosome modulate translation fidelity.

Amino Acid Sequence↗

PubMed1984

Evolutionary relationships among genes for antibiotic resistance.

The genes that determine resistance to antibiotics are commonly found encoded by extrachromosomal elements in bacteria. These were described first in Enterobacteriaceae and subsequently in a variety of other genera; their spread is associated with the increased use of antibiotics in human and animal medicine. Antibiotic-resistance genes that determine the production of enzymes which modify (detoxify) the antibiotics have been detected in antibiotic-producing organisms. It has been suggested that the producing strains provided the source of antibiotic-resistance genes that were then 'picked-up' by recombination. Recent studies of the nucleotide sequence of certain antibiotic-resistance genes indicate regions of strong homology in the encoded proteins. The implications of these similarities are discussed.

Amino Acid Sequence↗

PubMed1992

Fasciation induction by the phytopathogen Rhodococcus fascians depends upon a linear plasmid encoding a cytokinin synthase gene.

Rhodococcus fascians is a nocardiform bacteria that induces leafy galls (fasciation) on dicotyledonous and several monocotyledonous plants. The wild-type strain D188 contained a conjugative, 200 kb linear extrachromosomal element, pFiD188. Linear plasmid-cured strains were avirulent and reintroduction of this linear element restored virulence. Pulsed field electrophoresis indicated that the chromosome might also be a linear molecule of 4 megabases. Three loci involved in phytopathogenicity have been identified by insertion mutagenesis of this Fi plasmid. Inactivation of the fas locus resulted in avirulent strains, whereas insertions in the two other loci affected the degree of virulence, yielding attenuated (att) and hypervirulent (hyp) bacteria. One of the genes within the fas locus encoded an isopentenyltranferase (IPT) with low homology to analogous proteins from Gram-negative phytopathogenic bacteria. IPT activity was detected after expression of this protein in Escherichia coli cells. In R.fascians, ipt expression could only be detected in bacteria induced with extracts from fasciated tissue. R.fascians strains without the linear plasmid but containing this fas locus alone could not provoke any phenotype on plants, indicating additional genes from the linear plasmid were also essential for virulence. These studies, the first genetic analysis of the interaction of a Gram-positive bacterium with plants, suggest that a novel mechanism for plant tumour induction has evolved in R.fascians independently from the other branches of the eubacteria.

Alkyl and Aryl Transferases↗

PubMed1993

Three cases of human herpesvirus-6 latent infection: integration of viral genome in peripheral blood mononuclear cell DNA.

Saliva and peripheral blood mononuclear cells from three patients, two with lymphoproliferative disorders and one suffering from multiple sclerosis, were examined for the presence of human herpesvirus-6 (HHV-6) genome by using the polymerase chain reaction and Southern blot analysis. The search for anti-HHV-6 antibodies, carried out in the sera of the same cases by an immunofluorescence assay, was negative in two cases at the lowest dilution used (1:40). These three patients had a high number of HHV-6 specific sequences in uncultured peripheral blood mononuclear cells, which are thought to be a normal site of viral latency although, in healthy individuals, the infected cells are extremely rare. In order to gain some insight into the state of the viral genome in this latent HHV-6 infection, we used pulsed field gel electrophoresis to separate HHV-6 DNA directly from HHV-6 (strain GS) infected HSB-2 cells and from the peripheral blood mononuclear cells of these three patients. Our study showed the presence of intact viral genome, of the expected length of 170 kb, persisting as free extrachromosomal element in the HSB-2 cells but not in patients' peripheral blood mononuclear cells. On the other hand, in strong contrast with the results obtained in infected HSB-2 DNA, the restriction analysis of the three patients' peripheral blood mononuclear cell DNA showed fragments of molecular weight constantly higher than the 170 kb segment, indicating that the viral sequences are linked to high molecular weight cellular DNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed1996

Integration of foreign DNA in an intergenic region of the archaeon Methanosarcina mazei without effect on transcription of adjacent genes.

Transformation systems for methanogenic archaea are scarce, none has been reported for the genus Methanosarcina, and plasmids useful as vectors for cloning foreign DNA into methanogens that stably replicate as extrachromosomal elements are not available. We developed an integration vector for transformation of a member of the genus Methanosarcina, i.e. Methanosarcina mazei, using a segment (Int alpha; 1015 bp) which encompasses the intergenic region (431 bp) between the stress (heat-shock) genes grpE and dnaK. This segment also includes the 3' end (270 bp) of the grpE protein-coding region and the 5' end (314 bp) of the dnaK protein-coding region. Int alpha has an EcoRI site, useful for cloning, situated in the 3' direction beyond the grpE transcription termination region, and far upstream from the dnaK promoter. This location of the site, and the monocistronic mode of transcription of grpE and dnaK in M. mazei, suggested to us that a foreign insert in the site would not affect transcription of either flanking gene. A puromycin-resistance cassette (pac cassette) was inserted in the EcoRI site of Int alpha already inserted in pUC18, to obtain a vector which integrated the pac cassette in the chromosome between grpE and dnaK. The pac gene was transcribed and the transformants acquired puromycin resistance. Constitutive and heat-shock-induced transcription of grpE and dnaK in the transformants was the same as in wild-type cells. The two vectors found with transforming ability differed in the orientation of the pac cassette but both had M. mazei's DNA on each flank of the cassette, with the same orientation as that of the homologous segments in the chromosome.

Bacterial Proteins↗

PubMed1998

Identification of PhoP-PhoQ activated genes within a duplicated region of the Salmonella typhimurium chromosome.

Salmonellae virulence requires the PhoP-PhoQ two-component regulatory system. PhoP-PhoQ activate the transcription of genes following phagocytosis by macrophages which are necessary for survival within the phagosome environment. Thirteen previously undefined PhoP-activated gene fusions generated by MudJ and TnphoA (pag A, and E-P, respectively) were cloned and sequenced. Most pag products show no similarity to proteins in the database, while others are predicted to encode: a UDP-glucose dehydrogenase (pagA); a protein with similarity to the product of an E. coli aluminium-induced gene (pagH); a protein encoded within a Salmonella-unique region adjacent to the sinR gene (pagN); a protein similar to a product of the Yersinia virulence plasmid (pagO); and a protein with similarity to CrcA which is necessary for resistance of E. coli to camphor (pagP). Of the pag characterized, only pagK, M and O were closely linked. pagJ and pagK were shown to be unlinked but nearly identical in DNA sequence, as each was located within a 1.6 kb DNA duplication. The translations of sequences surrounding pagJ and pagK show similarity to proteins from extrachromosomal elements as well as those involved in DNA transposition and rearrangement, suggesting that this region may have been or is a mobile element. The transcriptional start sites of pagK, M, and J were determined; however, comparison to other known pag gene promoters failed to reveal a consensus sequence for PhoP-regulated activation. DNA sequences hybridizing to a Salmonella typhimurium pagK specific probe were found in S. enteritidis but absent in other Salmonella serotypes and Enterobacteriaceae tested, suggesting that these genes are specific for broad host range Salmonellae that cause diarrhoea in humans. Cumulatively, these data further demonstrate: (1) that PhoP-PhoQ is a global regulator of the production of diverse envelope or secreted proteins; (2) that PhoP-PhoQ regulate the production of proteins of redundant function; and (3) that pag are often located in regions of horizontally acquired DNA that are absent in other Enterobacteriaceae.

Artificial Gene Fusion↗

PubMed1994

Escherichia coli F plasmid transfers to and replicates within Legionella pneumophila: an alternative to using an RP4-based system for gene delivery.

Derivatives of the self-transmissible F plasmid of Escherichia coli can be introduced into Legionella pneumophila by conjugation and maintained within only upon selection. In L. pneumophila. F-based replicons seem to exist as extrachromosomal elements since they were readily lost when F-containing L. pneumophila was grown on nonselective medium. The F-based plasmids were not self-transmissible in L. pneumophila. The mating defect may be due to an inability to form the F pilus since F-containing strains of L. pneumophila could neither be infected with the pilus-specific phage M13 nor transduced with f1-packaged ColE1 replicons. Currently, the most commonly used transfer system for introducing genetic information into L. pneumophila employs E. coli donors with a chromosomally integrated copy of RP4::Mu to mobilize plasmids bearing the RK2 origin of transfer (oriT). Use of this system to deliver TnphoA for mutagenesis of the L. pneumophila chromosome led to transconjugants that all contained cryptic DNA alterations that involved the plasmid RP4 and phage Mu. No TnphoA transposition was observed in L. pneumophila. The fact that F-mediated conjugation can be used to efficiently transfer plasmids containing the oriT of F to L. pneumophila provides an important alternative to the RP4-based plasmid transfer system and may avoid DNA anomalies in transconjugants that impede genetic analysis. Furthermore, our results demonstrate the promiscuous nature of the F conjugal transfer and replication systems.

Bacteriophage mu↗