Polymerase stuttering

From Wikipedia, the free encyclopedia

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.

[edit] 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[1]. However, the frameshift is restricted to one (in some cases two[2]) 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.

[edit] 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[3].

[edit] Literature

  1. ^ 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.
  2. ^ Mauro VP, Chappell SA, Dresios J. "Analysis of polymerase shunting during translation initiation in eukaryotic mRNAs." Methods Enzymol. 2007;429:323-54.
  3. ^ 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.