More on phase variation

More information on what phase variation is and how it works

How does phase variation work in C. jejuni?

A striking feature of the C. jejuni genome is the presence of a number of short, homonucleotide sequences consisting of a multiple copies (8 to 12) of the same nucleotide in a row (known as a tandem array). In almost every case these sequences have guanine (G) in the protein coding direction. There are 29 such poly-G tracts in the genome of the NCTC11168 strain (which was the first strain to be sequenced) and although this number varies between strains, at least 12 are found in every completely sequenced strain.
These tracts are hypervariable because errors can occur during duplication (see figure below). In normal copying, each base pairs up with its usual partner (G to C, C to G, A to T and T to A) and so an exact complement is formed. However, in slipped-strand mispairing the replication process goes awry and the strands briefly separate and then, when they re-anneal a "kink" can form in either the template strand or the new copy. When the kink forms in the new strand, an extra base is added, whereas when the kink forms in the original strand, one less base is added to the new strand causing a deletion.
Strand slippage mispairing
(Note that direct evidence for this mechanism is not yet available but it is widely accepted as the likely mechanism for this change)
Because, in most cases, these poly-G tracts are located in the coding region of the gene, adding or removing a base can cause a frameshift mutation which typically causes the early truncation of the protein, e.g.
PV and Gene Expression
In this example (which is actually sequence from the cj0031/2 gene), deleting a base from the original 10G tract allows translation to continue and the full length, functional gene to be produced. This would be described as going from the OFF state to the ON state but the mutation can just as easily occur in the opposite direction by inserting an extra base into the 9G tract. If a base was deleted from the 9G tract that would also produce an OFF phenotype.
Although, in C. jejuni most phase variable genes work in this way it is also possible for hypervariable tracts to be located in regulator elements where changes in tract prevent binding of the relevant proteins.

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