plasmid

Reference identity

Record the reference sequence, aliases and supported parent-derivative relationships.

1. Which accession, sequence version or repository record defines this plasmid? definition
2. Which isolation or engineering records establish its origin and changes from a parent plasmid? provenance

Verified correspondence

Capture sequence coverage, discrepancies and unresolved mixtures.

1. What evidence links this preparation to the claimed plasmid sequence, and which regions remain unchecked? measurement
2. Does the material contain one supported plasmid variant, multiple variants or an unresolved mixture? boundary

Feature map

Locate supported sequence features and identify mapping uncertainty.

1. What sequence length, coordinate convention and strand orientation define the plasmid map? definition
2. Which feature boundaries, repeats, junctions or terminal regions are experimentally resolved? measurement

Observed molecular form

Record the evidence for architecture and the forms present in the material.

1. Is the reference plasmid circular or naturally linear, and what supports that assignment? definition
2. Which molecular forms and proportions were observed in this preparation, using what assay? measurement
3. Does observed linear DNA represent native architecture, deliberate linearisation, breakage or an unresolved origin? boundary

Replication competence

Record origins, dependencies and observed replication separately from sequence predictions.

1. Which origin or replicon and host or helper factors are required for replication? definition
2. In which host strains or cell lines is replication demonstrated rather than inferred from DNA persistence? boundary
3. What copy number was measured, with what denominator and host conditions? measurement

Maintenance evidence

Relate maintenance features and compatibility assignments to observed outcomes.

1. What retention and sequence stability were observed over how many generations, with or without selection? measurement
2. Which partition, maintenance or incompatibility assignments have supporting evidence? provenance
3. Does evidence support maintaining this plasmid alongside the specified co-resident plasmids? action

Functional dependencies

Distinguish intended or annotated capabilities from demonstrated activity.

1. Which coding and regulatory features support each claimed capability? definition
2. Which host factors, regulatory conditions or companion components does each capability require? boundary

Phenotype attribution

Link expression, selection phenotypes and host burden to the tested plasmid-host combination.

1. Which expression, selection or growth effects were measured in the specified host and conditions? measurement
2. What comparison supports attributing those effects to this plasmid rather than the host background or another element? provenance

Mobility evidence

Record transfer classification, assistance requirements and the limits of observation.

1. What evidence supports self-transmissibility, assisted mobilization or an unresolved mobility classification? provenance
2. Which donor, recipient and helper contexts bound the observed transfer capability? boundary

Genomic location

Determine whether plasmid identity is supported across observed genomic states.

1. Is the sequence observed as a separate molecule, an integrated region, both or an unresolved assembly? measurement
2. What evidence distinguishes this entity from a chromosome, chromid, phage-plasmid or other mobile element? boundary
3. If an integrated copy is recorded, what evidence links it to the reference plasmid and any extrachromosomal form? provenance

Material fitness

Record the measurements needed to judge the particular preparation.

1. What concentration, available amount, integrity and relevant contaminant measurements describe this preparation? measurement
2. What preparation, storage and handling history could explain its present molecular condition? provenance

Supported next action

Qualify a proposed analysis, modification, propagation or transfer for this plasmid and context.

1. Which identity, host compatibility and preparation criteria must be satisfied for the proposed action? action
2. Which encoded functions, mobility properties and applicable use restrictions affect whether the action is permitted? action
3. What unresolved evidence prevents a decision, and what verification would resolve it? action

Kinds and varieties

Reported by the breadth pass; each item needs checking against its source before it becomes normative.

• conjugative (self-transmissible) plasmid
• mobilizable plasmid
• non-mobilizable / cryptic plasmid
• fertility (F) plasmid
• resistance (R) plasmid
• Col (bacteriocin) plasmid
• virulence plasmid
• cloning / expression vector (engineered plasmid)

1. Which of these kinds and varieties hold for the sense of plasmid this model covers, and on what evidence? provenance

Identifiers and schemes

Reported by the breadth pass; each item needs checking against its source before it becomes normative.

• Wikidata - Q172778 - Item for the class plasmid, not for an individual molecule.
• MeSH - D010957 - Descriptor Plasmids.
• Novick plasmid designation - p + laboratory initials + number (e.g. pBR322, pUC19, pET28a) - 1976 ASM proposal; lowercase p prefix is the usual lab and literature form.
• Incompatibility (Inc) group - Inc plus letter and optional subtype (e.g. IncF, IncP-1, IncA/C, IncX3) - Groups plasmids that cannot be stably co-maintained; historically separate catalogues for enterobacteria, Pseudomonas, and Staphylococcus.
• MOB / relaxase class - MOBF, MOBP, MOBQ, MOBH, MOBC, MOBV - Sequence-based typing of conjugative and mobilizable plasmids by the relaxase gene.
• INSDC / GenBank accession - nucleotide accession for a sequenced plasmid (e.g. AY350745.1) - The practical identifier for a particular plasmid sequence in public databases.

1. Which of these identifiers and schemes hold for the sense of plasmid this model covers, and on what evidence? provenance

Standards and regulation

Reported by the breadth pass; each item needs checking against its source before it becomes normative.

• NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules (National Institutes of Health, April 2024), including Institutional Biosafety Committee review of recombinant plasmid work at covered institutions.
• FDA and EMA GMP expectations for pharmaceutical plasmid DNA, as summarised in manufacturing reviews: typically more than 90% supercoiled (ccc) isoform, host genomic DNA below 1% of bulk, endotoxin not exceeding 40 EU/mg pDNA.
• Uniform Nomenclature for Bacterial Plasmids (Novick, Clowes, Cohen, Curtiss, Datta and Falkow, 1976; American Society for Microbiology) - the community standard for naming plasmids and Inc groups, not a statute.

1. Which of these standards and regulation hold for the sense of plasmid this model covers, and on what evidence? provenance

Real-world use

Reported by the breadth pass; each item needs checking against its source before it becomes normative.

• Hospital and livestock bacteria spread multi-drug resistance on conjugative and mobilizable R plasmids.
• Molecular-biology laboratories propagate cloned inserts on small high-copy vectors such as pUC19, pBR322 and pET derivatives in E. coli.
• Manufacturers produce kilogram-scale plasmid DNA as a drug substance (DNA vaccines, gene-therapy plasmids) or as the template for in-vitro transcription of mRNA.
• Agrobacterium Ti/Ri plasmids are the working vehicle for transferring T-DNA into plants.
• Degradative plasmids (for example TOL in Pseudomonas putida) allow catabolism of xenobiotics in environmental isolates.
• Pathogens carry virulence plasmids (for example Bacillus anthracis pXO1/pXO2, Shigella invasion plasmids, Agrobacterium Ti) that determine disease phenotypes used in diagnostics and surveillance.

1. Which of these real-world use hold for the sense of plasmid this model covers, and on what evidence? provenance

Typical measurements

Reported by the breadth pass; each item needs checking against its source before it becomes normative.

• length - about 1-400 for ordinary plasmids; megaplasmids several thousand; database extremes from ~0.2 to >10 000 - kbp
• copy number (PCN) - low-copy about 1-2 per chromosome equivalent; high-copy tens to hundreds; observed span ~1 to >1000 - copies per cell
• supercoiled (ccc) isoform fraction - GMP bulk often specified >90 - %
• host genomic DNA in purified pDNA - GMP specification typically <1 of bulk - %
• endotoxin in purified pDNA - GMP limit commonly 40 or lower - EU/mg
• GC content - most bacterial plasmids roughly 30-70; curated-database extremes about 12-87 - %

1. Which of these typical measurements hold for the sense of plasmid this model covers, and on what evidence? provenance

Failure modes and hazards

Reported by the breadth pass; each item needs checking against its source before it becomes normative.

• Segregational loss of the plasmid at cell division, especially low-copy replicons that lack partition or toxin-antitoxin systems.
• Incompatibility: a second plasmid of the same Inc group is displaced without continuous selection.
• Horizontal spread of antibiotic-resistance and virulence genes via conjugation, mobilisation, transduction or transformation.
• Metabolic burden and reduced host fitness from high copy number or large inserts.
• Relaxation of supercoiling to open-circular or linear DNA, which lowers transfection and biological activity of prepared pDNA.
• Residual plasmid DNA, endotoxin or host nucleic acid contaminating recombinant protein or mRNA products.
• Integration of an episomal plasmid (classic F) into the chromosome, producing Hfr-like donors and unexpected genome rearrangements.

1. Which of these failure modes and hazards hold for the sense of plasmid this model covers, and on what evidence? provenance

Regional variation

Reported by the breadth pass; each item needs checking against its source before it becomes normative.

• Inc-group catalogues were built separately for Enterobacteriaceae, Pseudomonas and Staphylococcus and are not a single interchangeable code.
• Clinical writing still uses "R factor"; molecular biology uses named plasmids and Inc/replicon types.
• Linear plasmids are treated as ordinary in Streptomyces, Borrelia and some yeasts, while introductory bacteriology still presents plasmids as circular.
• Contained-use rules for recombinant plasmid work follow the NIH Guidelines in the United States and national GMM/GMO contained-use law in the EU and elsewhere; the practical paperwork is not the same.

1. Which of these regional variation hold for the sense of plasmid this model covers, and on what evidence? provenance

Neighbouring kinds and how to tell them apart

Reported by the breadth pass; each item needs checking against its source before it becomes normative.

• bacterial chromosome (including chromids / secondary chromosomes) - A chromosome encodes essential housekeeping genes and is not dispensable; a plasmid is lost without a lethal housekeeping gap. Chromids additionally use chromosome-like replication control (often DnaA-dependent), which typical plasmids do not.
• episome - An episome (classic sense) can integrate into the chromosome as well as replicate autonomously; a plasmid in the strict later sense is scored by stable extrachromosomal maintenance. Integration is the operational test. Many specialists now retire "episome" as a separate class.
• transposon / insertion sequence - A transposon has no independent origin of replication and can persist only after insertion into a replicon; a plasmid has its own replicon and can be recovered as free DNA.
• bacteriophage (and prophage) - A phage encodes virion/packaging functions and has an extracellular particle; a plasmid does not. Phage-plasmids sit on the boundary because they carry both plasmid replicon genes and phage structural genes.
• integrative and conjugative element (ICE) - An ICE lives in the chromosome for most of the cycle and only excises to transfer; a conjugative plasmid is a stably extrachromosomal replicon that can transfer without a required chromosomal integrated state.
• cosmid / BAC / other artificial cloning replicons - These are engineered hybrids (phage packaging signals, F or BAC origins, eukaryotic ARS) built for cloning capacity; they are distinguished by construction and intended host, not by being a naturally circulating plasmid type.

1. Which of these neighbouring kinds and how to tell them apart hold for the sense of plasmid this model covers, and on what evidence? provenance