Plasmids

1. vertical is parent to progeny transfer, and involves the entire genome
2. horizontal is from one strain or species to another, and rarely (if ever) involves the entire genome.  Rather, it deals with the transfer of one or a few genes.
   1. significance of horizontal transfer in infectious disease
   2. selfish DNA
   3. pathogenicity islands and the "gene theory of disease"
   4. Plasmids are a major player in horizontal transfer
3. Definition: plasmids are extrachromosomal DNA elements that replicate independently of the bacterial cell's chromosome. They are usually small, circular, double-stranded molecules, foundin all types of bacteria (perhaps all species, although not all strains, of bacteria). The number of copies varies from plasmid type to plasmid type, and a cell can have more than one type of plasmid. They contain genes that are non-essential, but often beneficial, to the bacterium.
4. Naming plasmids based on phenotypes is the historical approach, but has problems
   1. approach is natural because phenotypes are easiest to determine, and the first plasmids (F and R plasmids) were discovered on this basis.
   2. examples of plasmid types based on phenotypes
      1. F or conjugative plasmids
      2. R (resistance) plasmids
      3. Degradative plasmids (like Tol)
      4. Bacteriocin producing
      5. Virulence plasmids
      6. many others
5. However, these are extrinsic properties of the plasmids.  they are more like cassettes inserted into a cassette player. for now, we will cover intrinsic properties of plasmids, i.e., the nature of the replicon (the DNA that can self-replicate)
   1. ori (origin of replication) is analogous to oriC in E. coli. This is not a gene, its a sequence that is recognized by initiation proteins. Different plasmids have different types of origins. Host range is usually a function of the ori
   2. rep is a gene
      1. it encodes one or more Rep proteins that allow replication to initiate at the origin
      2. so ori and rep are the minimal unit of a replicon. Most plasmids have more to them, however, due to the problem of partitioning.
   3. cop/rop: when cells divide, the cytoplasm is squeezed in half.  Plasmids have means to ensure that they are in both halves of the cytoplasm (i.e., to ensure that they are partitioned correctly)
      1. copy number is one strategy, regulated by the cop or rop locus
      2. relaxed plasmids have high copy number, and the rop locus only kicks in when the number of plasmids is so high that the cell can't grow well. Stringent plasmids maintain a low copy number (e.g., F is found in only one copy per cell), so must have a more sophisticated partitioning function.
   4. par loci mediate partitioning though mechanism other than simply high copy number
      1. common theme is exemplified by hok/sok system.
      2. hok and sok are par genes on a particular E. coli plasmid. The product of the hok gene is a small protein (Hok), which kills the cell by itself. sok is transcribed to produce unstable antisense RNA, which serves as an inhibitor of Hok. If the plasmid is inherited correctly, sok RNA will inhibit Hok, and the cell will survive. If the plasmid is not partitioned, Hok will kill the plasmid-less cell.
6. The intrinsic properties of plasmids are reflected in "incompatibility groups"
   1. replicons of the same type will not coexist in a cell
   2. therefore, if two plasmids can exist in the same cell, they are said to be in different "incompatibility groups"  or Inc.
7. plasmids can be experimentally removed from a cell, by a process called curing
   1. plasmid curing can be achieved with high copy number (relaxed) plasmids by growing cells for many generations without a selective agent (e.g., antibiotic)
   2. curing can be accelerated with the addition of acridines like ethidium bromide or acridine orange