Plasmid

A plasmid is a small DNA molecule that replicates independently of a cell's chromosomes, most often a circular double-stranded molecule found in bacteria. Plasmids are also found in archaea and some eukaryotes, such as the "2-micron" plasmid of baker's yeast. The term was coined by Joshua Lederberg in 1952.

Plasmids sit at the center of two very different stories. In nature, they are the main vehicles that spread antibiotic resistance between bacteria. In the laboratory, they are the workhorses of genetic engineering, used to clone genes, produce medicines, and build synthetic organisms.

Plasmids range from about a thousand base pairs to more than a million (megaplasmids). Every plasmid needs an origin of replication, a sequence where its copying begins (see origins of replication). Plasmids use the host's enzymes, including DNA polymerase, and copy themselves by one of two main routes:

• Theta replication, in which both strands are copied from the origin, as in the chromosome.
• Rolling-circle replication, in which one strand is nicked and copied as it is peeled off the circle.

Each plasmid keeps a characteristic copy number, from one or two per cell for large plasmids to hundreds for some small ones. Copy number is held steady by built-in control systems such as antisense RNAs and repeated binding sites. Plasmids that use the same control systems cannot stably coexist in one cell, a property called incompatibility that is used to classify them.

Plasmids have evolved ways to avoid being lost when cells divide:

• Partitioning systems actively pull plasmid copies into each daughter cell, much as a mitotic spindle separates chromosomes.
• Toxin–antitoxin systems act as "addiction modules": the plasmid encodes a stable toxin and an unstable antitoxin. A daughter cell that loses the plasmid can no longer make the antitoxin, and the remaining toxin kills or halts it.

Many plasmids spread by horizontal gene transfer:

• Conjugative plasmids, such as the F (fertility) plasmid of E. coli, carry genes for a mating apparatus that builds a pilus and transfers a copy of the plasmid into a recipient cell.
• Mobilizable plasmids cannot build the apparatus themselves but can hitch a ride when a conjugative plasmid is present.

Transfer can cross species and even genus boundaries, so a gene that arises in one bacterium can spread rapidly through a whole microbial community.

Plasmids are not required for basic survival, but they often carry genes that help under particular conditions:

• Antibiotic resistance (R plasmids): Genes for enzymes that destroy antibiotics, such as extended-spectrum β-lactamases and carbapenemases (for example NDM-1 and KPC), spread largely on plasmids. The plasmid-borne colistin resistance gene mcr-1, reported in 2015, raised alarm because colistin is a last-resort drug.
• Virulence: The anthrax bacterium's toxin and capsule genes sit on two plasmids, pXO1 and pXO2.
• New metabolism: Some plasmids let bacteria break down pollutants such as toluene, which is useful in bioremediation.
• Interacting with plants: The Ti plasmid of Agrobacterium tumefaciens transfers a segment of DNA into plant cells, causing crown gall tumors.

In 1973, Stanley Cohen and Herbert Boyer used a plasmid to carry foreign DNA into E. coli, an early landmark of recombinant DNA technology (see introduction to recombinant DNA technology). Modern cloning vectors are engineered plasmids that combine:

• an origin of replication suited to the host;
• a selectable marker, usually an antibiotic resistance gene, so that only cells carrying the plasmid survive;
• a multiple cloning site with many unique restriction sites for inserting genes;
• often a reporter system, such as blue-white screening with the lacZα gene, to identify successful inserts.

Plasmids are used to manufacture insulin and other protein drugs. They also serve as templates for mRNA vaccines and DNA vaccines, and they deliver gene-editing tools such as CRISPR-Cas systems. The Ti plasmid, disarmed of its tumor genes, remains a standard way to make genetically modified plants. Together these uses make plasmids a foundation of biotechnology and synthetic biology.