Polymerase stuttering

Polymerase stuttering is the process by which a polymerase transcribes a nucleotide several times without progressing further on the mRNA chain. It is often used in addition of poly A tails or capping mRNA chains by less complex organisms such as viruses.

Process

A polymerase may undergo stuttering as a probability controlled event, hence it is not explicitly controlled by any mechanisms in the translation process. Generally, it is a result of many short repeated frameshifts on a slippery sequence of nucleotides on the mRNA strand [Anderson EC, Hunt SL, Jackson RJ. "Internal initiation of translation from the human rhinovirus-2 internal ribosome entry site requires the binding of Unr to two distinct sites on the 5' untranslated region." J Gen Virol. 2007 Nov;88(Pt 11):3043-52.] . However, the frameshift is restricted to one (in some cases two [Mauro VP, Chappell SA, Dresios J. "Analysis of polymerase shunting during translation initiation in eukaryotic mRNAs." Methods Enzymol. 2007;429:323-54.] ) nucleotides with a pseudoknot or choke points on both sides of the sequence.

An example of the process is denoted below, with P representing a polymerase:

"Step 1" --->P ATCGTAGCAAATCGTAA } Original strand ATCGT } Growing new strand

"Step 2" --------------->P ATCGTAGCAAATCGTAA } Original strand ATCGTAGCAAATCGTAA } Growing new strand

"Step 3" P<- } Polymerase slips back one ATCGTAGCAAATCGTAA } Original strand ATCGTAGCAAATCGTAA } Growing new strand

"Step 4" ->P } Transcribes another A ATCGTAGCAAATCGTAA } Original strand ATCGTAGCAAATCGTAAA } Growing new strand

Note: Step 3 & 4 is repeated and new nucleotides are added to the 3' end.

Examples

A polymerase that exhibits this behavior is RNA-dependent RNA polymerase, present in many RNA viruses. Reverse transcriptase has also been observed to undergo this polymerase stuttering [Kurzynska-Kokorniak A, Jamburuthugoda VK, Bibillo A, Eickbush TH. "DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon." J Mol Biol. 2007 Nov 23;374(2):322-33. Epub 2007 Sep 20.] .

Literature