-
Methods in Molecular Biology (Clifton,... 2020Plasmids identification and classification is an essential parameter in current bacterial typing. The most widely used PCR-based methods are the PCR-based replicon...
Plasmids identification and classification is an essential parameter in current bacterial typing. The most widely used PCR-based methods are the PCR-based replicon typing (PBRT) and the degenerate primer MOB typing (DPMT). PBRT targets the replicons on the plasmids and DPMT targets the relaxase genes. A finer resolution of phylogenetic relatedness can be obtained by plasmid multiLocus sequence typing available for the major plasmid types occurring in Enterobacteriaceae.
Topics: Alleles; Bacterial Typing Techniques; Humans; Molecular Typing; Multilocus Sequence Typing; Phylogeny; Plasmids; Polymerase Chain Reaction
PubMed: 31584172
DOI: 10.1007/978-1-4939-9877-7_22 -
Molecular Microbiology Sep 2007The mitotic apparatus that a plasmid uses to ensure its stable inheritance responds to the appearance of an additional copy of the plasmid's centromere by segregating it... (Review)
Review
The mitotic apparatus that a plasmid uses to ensure its stable inheritance responds to the appearance of an additional copy of the plasmid's centromere by segregating it from the pre-existing copies: if the new copy arises by replication of the plasmid the result is partition, if it arrives on a different plasmid the result is incompatibility. Incompatibility thus serves as a probe of the partition mechanism. Coupling of distinct plasmids via their shared centromeres to form mixed pairs has been the favoured explanation for centromere-based incompatibility, because it supports a long-standing assumption that pairing of plasmid replicas is a prerequisite for their partition into daughter cells. Recent results from molecular genetic and fluorescence microscopy studies challenge this mixed pairing model. Partition incompatibility is seen to result from various processes, including titration, randomized positioning and a form of mixed pairing that is based on co-activation of the same partition event rather than direct contact between partition complexes. The perspectives thus opened onto the partition mechanism confirm the continuing utility of incompatibility as an approach to understanding bacterial mitosis. The results considered are compatible with the view that direct pairing of plasmids is not essential to plasmid partition.
Topics: Models, Genetic; Plasmids; Species Specificity; Transcription, Genetic
PubMed: 17714446
DOI: 10.1111/j.1365-2958.2007.05882.x -
Critical Reviews in Biotechnology 2000The idea that plasmids replicate within hosts at the expense of cell metabolic energy and preformed cellular blocks depicts plasmids as a kind of molecular parasites... (Review)
Review
The idea that plasmids replicate within hosts at the expense of cell metabolic energy and preformed cellular blocks depicts plasmids as a kind of molecular parasites that, even when they may eventually provide plasmid-carrying strains with growth advantages over plasmid-free strains, doom hosts to bear an unavoidable metabolic burden. Due to the consistency with experimental data, this idea was rapidly adopted and used as a basis of different hypotheses to explain plasmid-host interactions. In this article we critically discuss current ideas about plasmid effects on host metabolism, and present evidence suggesting that the complex interaction between plasmids and hosts is related to the alteration of the cellular regulatory status.
Topics: Escherichia coli; Plasmids
PubMed: 10890453
DOI: 10.1080/07388550008984167 -
Developments in Biologicals 2000With the advent and progress of recombinant DNA technology into a variety of fields such as medical therapy, preventive or curative vaccination or the induction of... (Review)
Review
With the advent and progress of recombinant DNA technology into a variety of fields such as medical therapy, preventive or curative vaccination or the induction of regeneration, the demand for large quantities of highly purified DNA is increasing. Traditional methods of purifying plasmids usually require sophisticated methodology if the DNA is to be separated from RNA and other contaminating organic components. In particular, methods for obtaining supercoiled covalently closed circular (CCC) plasmid DNA in pure form, cope with the requirement that other plasmid topologies also produced have to be separated from the final product. The innovative technology of capillary gel electrophoresis (CGE) contributes a sensitive tool to the short list of applicable quality control assays for clinical grade plasmid DNA.
Topics: Biotechnology; Electrophoresis, Capillary; Genetic Therapy; Humans; Pilot Projects; Plasmids; Quality Control; Vaccines, DNA
PubMed: 11713820
DOI: No ID Found -
Plasmid Mar 2011The lambdoid phage N15 of Escherichia coli is very unusual among temperate phages in that its prophage is not integrated into chromosome but is a linear plasmid molecule... (Review)
Review
The lambdoid phage N15 of Escherichia coli is very unusual among temperate phages in that its prophage is not integrated into chromosome but is a linear plasmid molecule with covalently closed ends. Upon infection the phage DNA circularises via cohesive ends, then phage-encoded enzyme, protelomerase, cuts at an inverted repeat site and forms hairpin ends (telomeres) of the linear plasmid prophage. Replication of the N15 prophage is initiated at an internally located ori site and proceeds bidirectionally resulting in formation of duplicated telomeres. Then the N15 protelomerase cuts duplicated telomeres generating two linear plasmid molecules with hairpin telomeres. Stable inheritance of the plasmid prophage is ensured by partitioning operon similar to the F factor sop operon. Unlike F sop, the N15 centromere consists of four inverted repeats dispersed in the genome. The multiplicity and dispersion of centromeres are required for efficient partitioning of a linear plasmid. The centromeres are located in N15 genome regions involved in phage replication and control of lysogeny, and binding of partition proteins at these sites regulates these processes. Two N15-related lambdoid Siphoviridae phages, φKO2 in Klebsiella oxytoca and pY54 in Yersinia enterocolitica, also lysogenize their hosts as linear plasmids, as well as Myoviridae marine phages VP882 and VP58.5 in Vibrio parahaemolyticus and ΦHAP-1 in Halomonas aquamarina. The genomes of all these phages contain similar protelomerase genes, lysogeny modules and replication genes, as well as plasmid-partitioning genes, suggesting that these phages may belong to a group diverged from a common ancestor.
Topics: Bacteriophages; Escherichia coli; Genome, Viral; Lysogeny; Plasmids; Prophages; Telomere; Virus Replication
PubMed: 21185326
DOI: 10.1016/j.plasmid.2010.12.004 -
Current Issues in Molecular Biology Oct 2003The selective pressure imposed by the use of antimicrobials in both human and veterinary medicine promotes the spread of multiple antimicrobial resistance. The... (Review)
Review
The selective pressure imposed by the use of antimicrobials in both human and veterinary medicine promotes the spread of multiple antimicrobial resistance. The dissemination of antimicrobial resistance in Salmonella enterica strains, causing severe enteritis in human, has been reported worldwide and is largely attributed to conjugative DNA exchange. In the present review, the relevance of plasmids to the dissemination of antimicrobial resistance in S. enterica is discussed. Recent examples of plasmid-mediated resistance to expanded-spectrum cephalosporins are reported to illustrate the severity of current situation in enteric pathogens. The exchanges between plasmid(s) and the bacterial chromosome and the integration of resistance genes into specialised genetic elements, called integrons, play a major role in acquisition and dissemination of resistance genes. The evolution of a plasmid through the acquisition of integrons is reported, describing novel mechanisms for short-term accumulation of resistance determinants in plasmids circulating in Salmonella.
Topics: Animals; Anti-Bacterial Agents; DNA Transposable Elements; Drug Resistance, Bacterial; Drug Resistance, Multiple, Bacterial; Evolution, Molecular; Humans; Integrons; Microbial Sensitivity Tests; Plasmids; Salmonella enterica
PubMed: 12921226
DOI: No ID Found -
Microbiology Spectrum Apr 2015The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and... (Review)
Review
The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and recombined and as sister chromosomes are moved into new daughter cell compartments during cell division. This article links the original discoveries of superhelical structure and molecular topology to non-B form DNA structure and contemporary biochemical and biophysical techniques. The emphasis is on the power of plasmids for studying DNA structure and function. The conditions that trigger the formation of alternative DNA structures such as left-handed Z-DNA, inter- and intra-molecular triplexes, triple-stranded DNA, and linked catenanes and hemicatenanes are explained. The DNA dynamics and topological issues are detailed for stalled replication forks and for torsional and structural changes on DNA in front of and behind a transcription complex and a replisome. The complex and interconnected roles of topoisomerases and abundant small nucleoid association proteins are explained. And methods are described for comparing in vivo and in vitro reactions to probe and understand the temporal pathways of DNA and chromosome chemistry that occur inside living cells.
Topics: Biochemical Phenomena; Biophysical Phenomena; DNA; Nucleic Acid Conformation; Plasmids
PubMed: 26104708
DOI: 10.1128/microbiolspec.PLAS-0036-2014 -
The Journal of Antimicrobial... May 2018Bacterial antimicrobial resistance (AMR) is constantly evolving and horizontal gene transfer through plasmids plays a major role. The identification of plasmid... (Review)
Review
Bacterial antimicrobial resistance (AMR) is constantly evolving and horizontal gene transfer through plasmids plays a major role. The identification of plasmid characteristics and their association with different bacterial hosts provides crucial knowledge that is essential to understand the contribution of plasmids to the transmission of AMR determinants. Molecular identification of plasmid and strain genotypes elicits a distinction between spread of AMR genes by plasmids and dissemination of these genes by spread of bacterial clones. For this reason several methods are used to type the plasmids, e.g. PCR-based replicon typing (PBRT) or relaxase typing. Currently, there are 28 known plasmid types in Enterobacteriaceae distinguished by PBRT. Frequently reported plasmids [IncF, IncI, IncA/C, IncL (previously designated IncL/M), IncN and IncH] are the ones that bear the greatest variety of resistance genes. The purpose of this review is to provide an overview of all known AMR-related plasmid families in Enterobacteriaceae, the resistance genes they carry and their geographical distribution.
Topics: Drug Resistance, Bacterial; Enterobacteriaceae; Gene Transfer, Horizontal; Genes, Bacterial; Genotype; Humans; Plasmids
PubMed: 29370371
DOI: 10.1093/jac/dkx488 -
Methods in Molecular Biology (Clifton,... 2022Gene editing is increasing its popularity day by day especially as an essential tool for the research. It is based on two recombination mechanisms in mammalian cells:...
Gene editing is increasing its popularity day by day especially as an essential tool for the research. It is based on two recombination mechanisms in mammalian cells: nonhomologous end-joining (NHEJ) and homology-directed repair (HDR). The first one can be used to silence a specific gene or a portion of it and the second one to insert new DNA, in presence of a donor template, in a targeted position in the genome. In order to exploit one of these two mechanisms, three major targeted nucleases have been developed: zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN), and CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein). The last one seems to be the most promising tool among the others for gene editing. By using the properties and versatility of the Cell Penetrating Peptide (CPP) PepFect14, we developed a protocol to deliver a plasmid encoding for CRISPR-Cas9 and Green Fluorescent Protein (GFP) in BHM cell line expressing luciferase (Bomirsky Hamster Melanoma pLuc). Aiming to knocking down the luciferase gene in the cell line and to expressing GFP. Having two fast and easy read-outs of the plasmid's activity at the same time. Furthermore, by labeling the CRISPR plasmid with Cy5 it is possible to have a visual confirmation of the cellular uptake of the pDNA/CPP complex, via fluorescent microscopy, as described.
Topics: Animals; CRISPR-Cas Systems; Cell-Penetrating Peptides; Gene Editing; Plasmids; Transcription Activator-Like Effector Nucleases
PubMed: 34766316
DOI: 10.1007/978-1-0716-1752-6_38 -
Plasmid 1998The term "plasmid" was introduced 45 years ago (J. Lederberg, 1952, Physiol. Rev. 32, 403-430) as a generic term for any extrachromosomal genetic particle. It was...
The term "plasmid" was introduced 45 years ago (J. Lederberg, 1952, Physiol. Rev. 32, 403-430) as a generic term for any extrachromosomal genetic particle. It was intended to clarify the classification of agents that had been thought of disjunctively as parasites, symbionts, organelles, or genes. For a decade or more it was confused with "episome," although that was carefully crafted (F. Jacob and E. L. Wollman, 1958, C. R. Acad. Sci. 247, 154-156) to mean agents with traffic in and out of chromosomes. Starting about 1970, plasmids became important reagents in molecular genetic research and biotechnology. They also play a cardinal role in the evolution of microbial resistance and of pathogenicity. The usage of the term has then escalated to its current peak of about 3000 published articles per year. The bedrock of genetic mechanism is no longer mitosis and meiosis of chromosomes; it is template-directed DNA assembly. This is often more readily studied and managed with the use of plasmids, which replicate autonomously outside the chromosomes. Some plasmids are also episomes, namely, they interact with the chromosomal genome, and other mobile elements may be transposed from one chromosomal locus to another without replicating autonomously.
Topics: Animals; History, 20th Century; Organelles; Plasmids; Symbiosis; Terminology as Topic
PubMed: 9473441
DOI: 10.1006/plas.1997.1320