PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Plasmid structure”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17Linked to original sources
PubMed1989

Comparative analysis of the HTLV-I Rex and HIV-1 Rev trans-regulatory proteins and their RNA response elements.

The Rex proteins of types I and II human T-cell leukemia viruses (HTLV-I, HTLV-II) are required for expression of the viral structural gene products, gag and env and, thus, are essential for the replication of these pathogenic retroviruses. The action of Rex is sequence specific, requiring the presence of a cis-acting Rex response element located in the 3' long terminal repeat. This element corresponds to a predicted RNA secondary structure and functions in an orientation-dependent but position-independent manner. Rex acts through this response element to stimulate the nuclear export of the unspliced or singly spliced viral mRNA species encoding the virion structural proteins that are normally excluded from the cytoplasm. Although the Rex proteins of HTLV-I and HTLV-II can also function via the related Rev response element present in the env gene of the type I human immunodeficiency virus (HIV-1), the analogous HIV-1 Rev protein is unable to act on the HTLV-I Rex response element. This nonreciprocal pattern of genetic complementation by Rex and Rev suggests that these viral trans-regulators may interact directly with their RNA response elements.

Base Sequence↗
PubMed1982

Cloning, partial sequencing, and expression of glyceraldehyde-3-phosphate dehydrogenase gene in chick embryonic heart muscle cells.

Two recombinant plasmids containing structural gene sequences of chick embryonic heart glyceraldehyde-3-phosphate dehydrogenase (GAP dehydrogenase) were constructed and characterized. The plasmids pGAP 30 and pGAP 36 have inserts of 1200 and 950 base pairs, respectively. The identity of the clones was established by hybrid-arrested and hybrid-selection translation assays, and by immunoprecipitation of hybrid-selected translation product with GaP dehydrogenase antiserum. Hybridization of labeled pGAP 30 DNA to size-fractionated chick heart poly(A) RNA occurred at the region on the gel corresponding to the mobility of GAP dehydrogenase mRNA. Base sequence analysis of plasmid pGAP 30 and the comparison of the amino acid sequence derived from it with that of pig muscle GAP dehydrogenase revealed that the amino acid sequence of GAP dehydrogenase is strictly conserved between the chick and pig muscle tissues. Expression of GAP dehydrogenase mRNA in developing chick heart cells in cultures was monitored by in situ hybridization. The GAP dehydrogenase mRNA was present in 5-h-old dividing myoblasts, in contrast to mRNAs specific for contractile proteins, which appear late in myoblast development paralleling morphogenetic differentiation of myoblasts into myocytes (Jakowlew, S. B., Khandekar, P., Datta, K., Narula, S. K., Arnold, H. H., and Siddiqui, M. A. Q. (1982) J. Mol. Biol. 156, 673-682).

Amino Acid Sequence↗
PubMed2002

Approaches to investigating the ecology of plasmids in marine bacterial communities.

To better understand prokaryotic gene flux in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of plasmid populations in marine bacterial communities, information on the distribution, diversity, and ecological traits of marine plasmids is necessary. This mini-review highlights recent insights gained into the molecular diversity and ecology of plasmids occurring in marine microbial communities.

DNA↗
PubMed1991

Structural similarity and distribution of small cryptic plasmids of Lactobacillus curvatus and L. sake.

Plasmid profiles of strains of Lactobacillus curvatus and L. sake isolated from meat or sauerkraut were analysed to investigate plasmid homology and distribution in relation to the ecology of these organisms in fermenting foods. A hybridisation probe was constructed by cloning of pLc2, a cryptic, 2.6-kbp plasmid from L. curvatus LTH683, into the Escherichia coli plasmid pRV50. In Southern hybridisations with the digoxygenine labeled pLc2 probe, pLc2-related small plasmids were frequently detected in meat-borne strains of L. casei subsp. pseudoplantarum, L. curvatus, L. sake, L. alimentarius, L. farciminis and L. halotolerans and in L. curvatus and L. sake isolated from sauerkraut. Among 27 Lactobacillus type strains originally isolated from habitats other than meat this type of homology was detected only with plasmids of L. buchneri and L. mali. Restriction-enzyme mapping of six small cryptic plasmids from L. curvatus and L. sake revealed strong structural homology but no similarity to previously characterized plasmids of lactobacilli. The presence of a variable region in addition to a conserved one and the occurrence of deletions during cloning of pLc2 suggest that vectors derived from these plasmids are likely to be structurally unstable.

Cloning, Molecular↗
PubMed2001

Non-oxidative mechanisms are responsible for the induction of mutagenesis by reduction of Cr(VI) with cysteine: role of ternary DNA adducts in Cr(III)-dependent mutagenesis.

Intracellular reduction of carcinogenic Cr(VI) generates Cr-DNA adducts formed through the coordination of Cr(III) to DNA phosphates (phosphotriester-type adduct). Here, we examined the role of Cr(III)-DNA adducts in mutagenesis induced by metabolism of Cr(VI) with cysteine. Reduction of Cr(VI) caused a strong oxidation of 2', 7'-dichlorofluoroscin (DCFH) and extensive Cr-DNA binding but no DNA breakage. Cr-DNA adducts induced unwinding of supercoiled plasmids and structural distortions in the DNA helix as detected by decreased ethidium bromide binding. Propagation of Cr-treated pSP189 plasmids in human fibroblasts led to a dose-dependent formation of the supF mutants and inhibition of replication. Blocking of Cr(III)-DNA binding by occupation of DNA phosphates with Mg(2+) or by sequestration of Cr(III) by inorganic phosphate or EDTA eliminated mutagenic responses and restored a normal yield of replicated plasmids. Dissociation of Cr(III) from DNA by a phosphate-based reversal procedure returned mutation frequency to background levels. The mutagenic responses at the different phases of the reduction reaction were unrelated to the amount of reduced Cr(VI) but reflected the number and the spectrum of Cr(III)-DNA adducts that were formed. Ternary cysteine-Cr(III)-DNA adducts were approximately 4-5 times more mutagenic than binary Cr(III)-DNA adducts. Although intermediate reaction products (CrV/IV, thiyl radicals) were capable of oxidizing DCFH, they were insufficiently reactive to damage DNA. Single-base substitutions at G/C pairs were the predominant type of Cr-induced mutations. The majority of mutations occurred at the sites where G had adjacent purine in the 3' or 5' position. Overall, our results present the first evidence that Cr(III)-DNA adducts play the dominant role in the mutagenicity caused by the metabolism of Cr(VI) by a biological reducing agent.

Base Sequence↗
PubMed1981

An Escherichia coli mutant thermosensitive in the B subunit of DNA gyrase: effect on the structure and replication of the colicin E1 plasmid in vitro.

An E. coli strain which carries a mutation conferring clorobiocin resistance and temperature sensitivity for growth has recently been described and evidence has been presented suggesting that the mutation is located in the gyrB gene (Orr et al. 1979). The replication of the ColE1 plasmid was analysed in cell-free extracts from this thermosensitive strain. These extracts were totally deficient in the replication of exogenous plasmid DNA and were unable to maintain the superhelical structure of the plasmid DNA. Both defects could be fully complemented by addition of purified gyrB protein.

Bacterial Proteins↗
PubMedDate not supplied

[A study of chloramphenicol resistance in "Salmonella" and identification of the relevant R plasmid (author's transl)].

Seventy nine strains of salmonella of human origin were tested for antibiotic-resistance. Eighteen strains (11 Salmonella typhi-murium, 4 S. saint-paul and 3 S. dublin) were multiresistant, particularly to chloramphenicol. All the strains were able to transfer their resistance by conjugation. Thirteen conjugation R plasmids were classified into five incompatibility groups: I1, N, H1, M and B. Molecular studies showed that the DNA structures of the four IncI1R plasmids differed from one another and also partly from the plasmid DNA structures of other IncI1R plasmid DNA isolated from salmonellae. In conclusion, chloramphenicol resistance was conferred by various R factors, and the R factors of the I1 incompatibility group appeared to have different plasmid structures.

Chloramphenicol↗
PubMed1986

Nucleotide sequence of the structural genes for an anion pump. The plasmid-encoded arsenical resistance operon.

The structural genes for the arsenical pump of the conjugative R-factor R773 contained on a HindIII fragment of 4.3 kilobase pairs were cloned into bacteriophage M13. A series of ordered deletions was created using Bal31 digestion, and the nucleotide sequence of the operon determined. Three open reading frames for genes arsA, arsB, and arsC were found. The arsA gene encodes a hydrophilic protein of 63,169 Da with two potential adenylate-binding sites. The arsB gene encodes a potentially membrane protein of 45,577 Da. The arsC gene encodes a 15,811-Da hydrophilic protein. The arsA and arsC gene products correspond to cytosolic proteins previously identified from minicell experiments. Isolated ArsA protein was shown to bind to dye-agarose columns which act as affinity resins for nucleotide-binding proteins. A model is proposed in which these gene products form an anion translocating ATPase for extrusion of arsenite and arsenate from resistant cells.

Adenosine Triphosphatases↗
PubMed1984

[Conjugative R-plasmid resistance of Salmonella].

A total of 4801 Salmonella strains of 67 serovars isolated from various sources in 1968-1982 were studied for their sensitivity to 12 drugs. The Salmonella strains of groups A, B, C, D and E amounted to 0.8, 84.6, 6.4, 5.8 and 2.0 per cent, respectively. The Salmonella strains of the other groups amounted to 0.4 per cent. During the 5-year periods, the number of the antibiotic resistant Salmonella strains increased from 57.7 to 93.4 per cent. The conjugative drug resistance was detected in 16 out of the 67 serovars. The Salmonella strains usually resistant to 4-10 drugs were the donors of this conjugative drug resistance. The strains of S. typhimurium responsible for the hospital infections were characterized by the highest levels of the antibiotic polyresistance and the greatest variety of the conjugative R plasmids. The structure of the multiple and conjugative drug resistance of the organisms causing salmonellosis was more frequently defined by the conjugative plasmids of the antibiotic resistance of the S. typhimurium serovar. The Salmonella R plasmids determined various levels of the antibiotic resistance. The highest resistance levels were observed to benzylpenicillin, chloramphenicol and erythromycin and the lowest resistance levels to tetracycline.

Animals↗
PubMedDate not supplied

[Characteristic features of the structure of co-integrating plasmids and simple insertions formed during transposition of the IS1 element in transposon Tn9'].

Earlier we have studied unstable dissociating IS1/Tn9'-mediated cointegrates between the plasmids pDK57 (pBR322::Tn9') and pRP3.1, a deletion derivative of RP1, and two types of such cointegrates containing three and four copies of IS1 were revealed. In the present paper we studied the structure of stable IS1/Tn9'-mediates cointegrates and simple insertions formed by interaction between the plasmids pDK57 and pRP3.1 in the E. coli recA- cells. It was shown, that the stable cointegrates were formed by insertion of pDK57 in different loci of pRP3.1 and these cointegrates contain three copies of IS1, i.e. one copy of IS1 and a copy of Tn9' at the junction of the two replicons. The cointegrates are formed predominantly due to the activity of the left copy of Tn9', which occupies a proximal position in regard to the promoter of the cat gene. It was found that the integration of pDK57 into the kan gene region of pRP3.1 leading to the formation of the KmS cointegrates occurs only in one of the two possible orientations. Meanwhile the insertions of the transposon Tn9' into the kan region of pRP3.1 leading to simple insertions occurs in the orientation opposite to the orientation of the transposon in the KmS cointegrates. It is proposed that simple insertions are not the products of direct transposition of Tn9', but they are formed from unstable cointegrates under the action of IS1-specific resolvase.

Conjugation, Genetic↗
PubMed1990

Flanking AT-rich tracts cause a structural distortion in Z-DNA in plasmids.

The effect of neighboring AT-rich sequences on the right-handed B to left-handed Z transition was investigated in plasmids. The supercoil stabilized Z-DNA structure in (CG) tracts 36 and 40 base pairs (bp) in length revealed an unexpected conformational aberration at defined C residues proximal to one end (colL) when the inserts were bilaterally flanked by an 80% AT-rich segment (90 bp on one side and 331 bp on the other). The presence of the perturbed Z-conformation required (CG) stretches longer than 32 bp and bilateral flanking by the AT-rich tracts, since plasmids with the (CG) tracts unilaterally flanked had an orthodox Z-structure. The thermodynamics of the negative super-coil-induced transitions were influenced only slightly by the neighboring AT-rich regions. Hence, the nature of Z-conformations in plasmids is markedly influenced by intrinsic structural features of the (Pur-Pyr) tract and by seemingly modest changes in the properties of neighboring sequences over a distance of several helical turns.

Adenine↗
PubMed1981

Plasmid DNA in Treponema pallidum (Nichols): potential for antibiotic resistance by syphilis bacteria.

A plasmid DNA structure (approximate molecular weight = 7.5 X 10(6)) was identified in the human pathogen Treponema pallidum (Nichols). The inability to isolate this plasmid from rabbit host tissue and the total lack of DNA homology of the plasmid with rabbit DNA has confirmed its Treponema pallidum origin. The observation documents a newly recognized and potentially significant genetic capability for Treponema pallidum.

Animals↗
PubMed2003

Structural changes in RepA, a plasmid replication initiator, upon binding to origin DNA.

RepA protein is the DNA replication initiator of the Pseudomonas plasmid pPS10. RepA dimers bind to an inversely repeated operator sequence in repA promoter, thus repressing its own synthesis, whereas monomers bind to four directly repeated sequences (iterons) to initiate DNA replication. We had proposed previously that RepA is composed of two winged-helix (WH) domains, a structural unit also present in eukaryotic and archaeal initiators. To bind to the whole iteron sequence through both domains, RepA should couple monomerization to a conformational change in the N-terminal WH, which includes a leucine zipper-like sequence motif. We show for the first time that, by itself, binding to iteron DNA in vitro dissociates RepA dimers into monomers and alters RepA conformation, suggesting an allosteric effect. Furthermore, we also show that similar changes in RepA are promoted by mutations that substitute two Leu residues of the putative leucine zipper by Ala, destabilizing the hydrophobic core of the first WH. We propose that this mutant (RepA-2L2A) resembles a transient folding intermediate in the pathway leading to active monomers. These findings, together with the known activation of other Rep-type proteins by chaperones, are relevant to understand the molecular basis of plasmid DNA replication initiation.

Amino Acid Motifs↗
PubMed1987

Chromosome- and plasmid-mediated gentamicin resistance in Staphylococcus aureus encoded by Tn4001.

DNA sequences corresponding to the 4.7-kb gentamicin, tobramycin and kanamycin resistance (GmrTmrKmr) transposon Tn4001 have been detected on a series of nine structurally-related plasmids that mediate this phenotype in Australian isolates of Staphylococcus aureus. Tn4001 sequences have also been demonstrated on the chromosomes of GmrTmrKmr isolates that do not possess these plasmids, and the exhibited diversity of chromosomal sites occupied by this element implies that Tn4001 has transposed to the chromosome on numerous occasions in vivo. These results suggest that the rapid emergence of nosocomial GmrTmrKmr S. aureus in the early 1980s may have been the result of the transposition of Tn4001 from a chromosomal site to a readily disseminated plasmid.

Chromosomes, Bacterial↗
PubMed2005

Plasmid delivery in vivo from porous tissue-engineering scaffolds: transgene expression and cellular transfection.

Tissue engineering scaffolds capable of sustained plasmid release can promote gene transfer locally and stimulate new tissue formation. We have investigated the scaffold design parameters that influence the extent and duration of transgene expression and have characterized the distribution of transfected cells. Porous scaffolds with encapsulated plasmid were fabricated from poly(lactide-co-glycolide) with a gas foaming procedure, with wet granulation employed to mix the components homogeneously prior to foaming. Wet granulation enhanced plasmid incorporation relative to standard procedures and also enhanced in vivo transgene expression, possibly through the increased loading and maintenance of the scaffold pore structure. The plasmid loading regulated the quantity and duration of transgene expression, with expression for 105 days achieved at the highest dosage. Expression was localized to the implantation site, though the distribution of transfected cells varied with time. Transfected cells were initially observed at the scaffold periphery (day 3), then within the pores and adjacent to the polymer (day 17), and finally throughout the scaffold interior (day 126). Delivery of a plasmid encoding VEGF increased the blood vessel density relative to control. Correlating scaffold design with gene transfer efficiency and tissue formation will facilitate application of plasmid-releasing scaffolds to multiple tissues.

Animals↗
PubMedDate not supplied

[Incompatibility group P-7 plasmids responsible for biodegradation of naphthalene and salicylate in fluorescent pseudomonads].

Analysis of seven plasmids (77 to 135 kbp in size) of the P-7 incompatibility group that are responsible for the biodegradation of naphthalene and salicylate has shown that the main natural host of IncP-7 plasmids is the species Pseudomonas fluorescens. The IncP-7 plasmids are structurally diverse and do not form groups, as is evident from their cluster analysis. The naphthalene catabolism genes of six of the IncP-7 plasmids are conservative and homologous to the catabolic genes of NAH7 and pDTG1 plasmids. The pAK5 plasmid contains the classical nahA gene, which codes for naphthalene dioxygenase, and the salicylate 5-hydroxylase gene (nagG) sequence, which makes the conversion of salicylate to gentisate possible.

Biodegradation, Environmental↗