Plasmid copy number

Plasmids must regulate their copy number (average number of plasmid copies per cell) to ensure that they do not excessively burden the host or become lost during cell division. Plasmids may be either high copy number plasmids or low copy number plasmids; the regulation mechanisms between these two types are often significantly different. Biotechnology applications may involve engineering plasmids to allow a very high copy number. For example, pBR322 is a low copy number plasmid (~20 copies/cell) from which several very high copy number cloning vectors (~1000 copies/cell) have been derived.[1]


High copy number plasmids, also called relaxed plasmids, require a system to ensure that replication is inhibited once the number of plasmids in the cell reaches a certain threshold. Relaxed plasmids are generally regulated through one of two mechanisms: antisense RNA or iteron binding groups. Low copy number plasmids, also called stringent plasmids, require tighter control of replication.

ColE1 derived plasmids: Antisense RNAEdit

In ColE1 derived plasmids, replication is primarily regulated through a small plasmid-encoded RNA called RNA I. A single promoter initiates replication in ColE1: the RNA II promoter. The RNA II transcript forms a stable RNA-DNA hybrid with the DNA template strand near the origin of replication, where it is then processed by RNaseH to produce the 3' OH primer that DNA polymerase I uses to initiate leading strand DNA synthesis. RNA I serves as a major plasmid-encoded inhibitor of this process whose concentration is proportional to plasmid copy number. RNA I is exactly complementary to the 5' end of the RNA II (because it is transcribed from the opposite strand of the same region of DNA as RNA II). RNA I and RNA II first form a weak interaction called a kissing complex. The kissing complex is stabilized by a protein called Rop (repressor of primer) and a double-stranded RNA-I/RNA-II RNA duplex is formed. This altered shape prevents RNA II from hybridizing to the DNA and being processed from RNaseH to produce the primer necessary for initiation of plasmid replication. More RNA I is produced when the concentration of the plasmid is high, and high concentration of RNA I inhibits replication, resulting in regulation of copy number.[2][3]

R1 and ColIb-p9 Plasmids: Antisense RNAEdit

Most plasmids require a plasmid-encoded protein, usually called Rep, to separate the strands of DNA at the origin of replication (oriV) to initiate DNA replication. Rep binds to specific DNA sequences in oriV which are unique to a plasmid type. The synthesis of Rep protein is controlled in order to limit plasmid replication and therefore regulate copy number. In R1 plasmids RepA can be transcribed from two different promoters. It is made from the first promoter until the plasmid reaches its copy number, upon which the protein CopB represses this primary promoter.[3] RepA expression is also regulated post-transcriptionally from the secondary promoter by an antisense RNA called CopA. CopA interacts with its RNA target in the RepA mRNA and forms a kissing complex and then a RNA-RNA duplex. The resultant double stranded RNA is cleaved by RNase III, preventing synthesis of RepA. The higher the concentration of the plasmid, the more CopA RNA is produced and the less RepA protein can be synthesized, increasing inhibition of plasmid replication.[4]

Col1b-P9: Antisense RNAEdit

Replication of the low-copy-number ColIb-P9 depends upon Rep, which is produced by expression of the repZ gene. repZ expression requires formation of a pseudoknot in the mRNA. repZ is repressed by a small antisense Inc RNA, which binds to repZ mRNA, forms an Inc RNA-mRNA duplex, and prevents formation of the pseudoknot to inhibit repZ translation into Rep. In this event, replication can no longer occur.[5]

pSC101: Iteron plasmidEdit

Iteron plasmids, including F and RK2-related plasmids, have oriV regions containing multiple (~3-7) repeats of 17-22 bp iteron sequences.[3]pSC101 represents a simple model of an iteron plasmid. Iteron plasmids control copy number through two combined methods, suitable for low copy number stringent plasmids. One method is control of RepA synthesis. RepA is the only plasmid-encoded protein required for replication in pSC101. RepA protein represses its own synthesis by binding to its own promoter region and blocking transcription of itself (transcriptional autoregulation). Thus, the more RepA is made, the more its synthesis is repressed, and subsequently limiting plasmid replication.[3] The coupling hypothesis proposes that the second method is coupling of plasmids through the Rep protein and iteron sequences. When the plasmid concentration is high, RepA plasmids bound to iterons form dimers in between two plasmids, "handcuffing" them at the origin of replication and inhibiting replication.[6]


Plasmids can be incompatible if they share the same replication control mechanism. Under these circumstances, both plasmids contribute to the total copy number and are regulated together. They are not recognized as distinct plasmids. As such, it becomes much more likely that one of the plasmids may be out-copied by the other and lost during cell division (the cell is "cured" of the plasmid).[3] This is particularly likely with low copy number plasmids. Plasmids can also be incompatible due to shared partitioning systems.


  1. ^ Boros, I; Pósfai, G; Venetianer, P (October 1984). "High-copy-number derivatives of the plasmid cloning vector pBR322". Gene. 30 (1–3): 257–60. doi:10.1016/0378-1119(84)90130-6. PMID 6096220.
  2. ^ Cesareni, G; Helmer-Citterich, M; Castagnoli, L (1991). "Control of ColE1 plasmid replication by antisense RNA". Trends in Genetics. 7 (7): 230–235. doi:10.1016/0168-9525(91)90370-6. PMID 1887504.
  3. ^ a b c d e Snyder, Larry; Peters, Joseph E.; Henkin, Tina M.; Champness, Wendy (2013). Molecular Genetics of Bacteria (4th ed.). ASM Press. ISBN 978-1555816278.
  4. ^ Blomberg, P; Nordström, K; Wagner, E. G. (1992). "Replication control of plasmid R1: RepA synthesis is regulated by CopA RNA through inhibition of leader peptide translation". The EMBO Journal. 11 (7): 2675–2683. PMC 556743. PMID 1378398.
  5. ^ Asano, K; Mizobuchi, K (1998). "Copy number control of IncIalpha plasmid ColIb-P9 by competition between pseudoknot formation and antisense RNA binding at a specific RNA site". The EMBO Journal. 17 (17): 5201–5213. doi:10.1093/emboj/17.17.5201. PMC 1170848. PMID 9724656.
  6. ^ Kunnimalaiyaan, S; Inman, R. B.; Rakowski, S. A.; Filutowicz, M (2005). "Role of π Dimers in Coupling ("Handcuffing") of Plasmid R6K's γ ori Iterons". Journal of Bacteriology. 187 (11): 3779–3785. doi:10.1128/JB.187.11.3779-3785.2005. PMC 1112066. PMID 15901701.