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Microbiology Spectrum Feb 2015Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid... (Review)
Review
Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid carriage, only a fraction of a local population carries plasmids or is permissive to plasmid uptake. Plasmids provide various accessory traits which might be beneficial under particular conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness toward environmental changes. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens. Here we summarize the state-of-the-art methods to study the occurrence, abundance, and diversity of plasmids in environmental bacteria. Increasingly, cultivation-independent total-community DNA-based methods are being used to characterize and quantify the diversity and abundance of plasmids in relation to various biotic and abiotic factors. An improved understanding of the ecology of plasmids and their hosts is crucial in the development of intervention strategies for antibiotic-resistance-gene spread. We discuss the potentials and limitations of methods used to determine the host range of plasmids, as the ecology of plasmids is tightly linked to their hosts. The recent advances in sequencing technologies provide an enormous potential for plasmid classification, diversity, and evolution studies, but numerous challenges still exist.
Topics: Adaptation, Biological; Bacteria; Ecology; Environmental Microbiology; Gene Transfer, Horizontal; Genetic Variation; Host Specificity; Plasmids
PubMed: 26104560
DOI: 10.1128/microbiolspec.PLAS-0038-2014 -
Advances in Biochemical... 2004Many expression systems in research and industry use plasmids as vectors for the production of recombinant proteins or non-proteinous recombinant substances. Plasmids... (Review)
Review
Many expression systems in research and industry use plasmids as vectors for the production of recombinant proteins or non-proteinous recombinant substances. Plasmids have an essential impact on productivity. Related factors are plasmid copy number, structural plasmid stability and segregational plasmid stability. Plasmid copy number determines the gene dosage accessible for expression and many plasmids lead generally to a high productivity. To analyze an expression system the quantification of plasmid copy number is very helpful. Therefore, different methods for the determination of plasmid copy number are described. Structural plasmid stability exists, when all generated plasmids have the correct base sequence. The analysis of structural instabilities is not trivial and some methods are reported. When all daughter cells get at least one plasmid during cell division, the culture is segregational stable. The development of plasmid free cells can lead to a significant loss in productivity. Different methods for lab scale and industrial scale help to avoid segregational instability. Since plasmids are used as pharmaceuticals, additional aspects of stability have to be taken into account. These include stability during downstream processing, stability after application and stability during storage and shipping.
Topics: Animals; Drug Stability; Gene Dosage; Gene Expression Profiling; Gene Expression Regulation; Gene Transfer Techniques; Genetic Engineering; Genetic Therapy; Humans; Plasmids
PubMed: 15088763
DOI: 10.1007/b12440 -
Microbiology Spectrum Sep 2017Plasmids mediate the horizontal transmission of genetic information between bacteria, facilitating their adaptation to multiple environmental conditions. An especially... (Review)
Review
Plasmids mediate the horizontal transmission of genetic information between bacteria, facilitating their adaptation to multiple environmental conditions. An especially important example of the ability of plasmids to catalyze bacterial adaptation and evolution is their instrumental role in the global spread of antibiotic resistance, which constitutes a major threat to public health. Plasmids provide bacteria with new adaptive tools, but they also entail a metabolic burden that, in the absence of selection for plasmid-encoded traits, reduces the competitiveness of the plasmid-carrying clone. Although this fitness reduction can be alleviated over time through compensatory evolution, the initial cost associated with plasmid carriage is the main constraint on the vertical and horizontal replication of these genetic elements. The fitness effects of plasmids therefore have a crucial influence on their ability to associate with new bacterial hosts and consequently on the evolution of plasmid-mediated antibiotic resistance. However, the molecular mechanisms underlying plasmid fitness cost remain poorly understood. Here, we analyze the literature in the field and examine the potential fitness effects produced by plasmids throughout their life cycle in the host bacterium. We also explore the various mechanisms evolved by plasmids and bacteria to minimize the cost entailed by these mobile genetic elements. Finally, we discuss potential future research directions in the field.
Topics: Adaptation, Physiological; Bacteria; Bacterial Physiological Phenomena; Biological Evolution; Gene Transfer, Horizontal; Plasmids
PubMed: 28944751
DOI: 10.1128/microbiolspec.MTBP-0016-2017 -
Methods in Enzymology 2013The purpose of this protocol is the isolation of plasmid DNA from bacteria. The boiling method for isolating plasmids by Holmes and Quigley (1981) is presented here....
The purpose of this protocol is the isolation of plasmid DNA from bacteria. The boiling method for isolating plasmids by Holmes and Quigley (1981) is presented here. This method is rapid and simple and it allows for a large number of samples to be processed simultaneously (up to 40 samples). Thus, it is appropriate for the preparation of bacterial plasmids in order to screen a large number of colonies or small cultures for the presence of recombinant DNA inserts. The protocol can be effectively scaled up for the preparation of plasmids from liter cultures.
Topics: DNA, Bacterial; Escherichia coli; Plasmids
PubMed: 24011041
DOI: 10.1016/B978-0-12-418687-3.00010-0 -
Microbiology Spectrum Dec 2014The stable maintenance of low-copy-number plasmids in bacteria is actively driven by partition mechanisms that are responsible for the positioning of plasmids inside the... (Review)
Review
The stable maintenance of low-copy-number plasmids in bacteria is actively driven by partition mechanisms that are responsible for the positioning of plasmids inside the cell. Partition systems are ubiquitous in the microbial world and are encoded by many bacterial chromosomes as well as plasmids. These systems, although different in sequence and mechanism, typically consist of two proteins and a DNA partition site, or prokaryotic centromere, on the plasmid or chromosome. One protein binds site-specifically to the centromere to form a partition complex, and the other protein uses the energy of nucleotide binding and hydrolysis to transport the plasmid, via interactions with this partition complex inside the cell. For plasmids, this minimal cassette is sufficient to direct proper segregation in bacterial cells. There has been significant progress in the last several years in our understanding of partition mechanisms. Two general areas that have developed are (i) the structural biology of partition proteins and their interactions with DNA and (ii) the action and dynamics of the partition ATPases that drive the process. In addition, systems that use tubulin-like GTPases to partition plasmids have recently been identified. In this chapter, we concentrate on these recent developments and the molecular details of plasmid partition mechanisms.
Topics: Biological Transport; Cell Division; Plasmids
PubMed: 26104442
DOI: 10.1128/microbiolspec.PLAS-0023-2014 -
Nature Ecology & Evolution Dec 2021
Topics: Plasmids
PubMed: 34857893
DOI: 10.1038/s41559-021-01613-x -
Nature Reviews. Microbiology Sep 2023
Topics: Sugars; Plasmids
PubMed: 37433958
DOI: 10.1038/s41579-023-00952-9 -
PloS One 2020There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to...
There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. A challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly. This work describes an approach to plasmid design where a plasmid is specified as simply a DNA sequence or list of features. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson assembly®. It finds existing DNA sequences in both user-specified and public DNA databases: iGEM, Addgene, and DNASU. Such a software application is introduced and characterized against all post-2005 iGEM composite parts and all Addgene vectors submitted in 2018 and found to reduce costs by 34% versus a purely synthetic plasmid design approach. The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs.
Topics: DNA; Databases, Genetic; Genetic Vectors; Plasmids; Software
PubMed: 31917791
DOI: 10.1371/journal.pone.0223935 -
Plasmid Mar 2005Plasmid partition systems are essential for the stability and thus the survival of low-copy-number plasmids in growing bacterial populations. The partition reaction is... (Review)
Review
Plasmid partition systems are essential for the stability and thus the survival of low-copy-number plasmids in growing bacterial populations. The partition reaction is responsible for proper intracellular distribution of plasmids in the bacterial cell cycle. One common step in most partition models is the pairing of plasmids to each other by partition components. Here, evidence that supports the pairing of plasmids via their partition complexes is reviewed, and discussed in light of recent observations that many plasmids, including those without active partition systems are clustered in limited groups inside bacterial cells.
Topics: Bacterial Proteins; DNA Replication; Plasmids
PubMed: 15737399
DOI: 10.1016/j.plasmid.2004.12.009 -
Canadian Journal of Microbiology May 2018Plasmids are extrachromosomal DNA elements that can be found throughout bacteria, as well as in other domains of life. Nonetheless, the evolutionary processes underlying... (Review)
Review
Plasmids are extrachromosomal DNA elements that can be found throughout bacteria, as well as in other domains of life. Nonetheless, the evolutionary processes underlying the persistence of plasmids are incompletely understood. Bacterial plasmids may encode genes for traits that are sometimes beneficial to their hosts, such as antimicrobial resistance, virulence, heavy metal tolerance, and the catabolism of unique nutrient sources. In the absence of selection for these traits, however, plasmids generally impose a fitness cost on their hosts. As such, plasmid persistence presents a conundrum: models predict that costly plasmids will be lost over time or that beneficial plasmid genes will be integrated into the host genome. However, laboratory and comparative studies have shown that plasmids can persist for long periods, even in the absence of positive selection. Several hypotheses have been proposed to explain plasmid persistence, including host-plasmid co-adaptation, plasmid hitchhiking, cross-ecotype transfer, and high plasmid transfer rates, but there is no clear evidence that any one model adequately resolves the plasmid paradox.
Topics: Adaptation, Physiological; Bacteria; Evolution, Molecular; Models, Genetic; Plasmids
PubMed: 29562144
DOI: 10.1139/cjm-2017-0609