ColE1 RNA II is the primer-precursor transcript used to initiate DNA replication of the Colicin E1 plasmid. Part of the nascent RNA forms a persistent hybrid with the template DNA near the replication start. Ribonuclease H processes the hybridized transcript to generate an RNA primer, from which DNA synthesis can proceed. Thus a transcript can help start replication without encoding a protein.[ref]
Control of ColE1 plasmid replication: the process of binding of RNA I to the primer transcript by J. Tomizawa. Abstract: primer-promoter transcript, persistent RNA–DNA hybrid and RNAase H processing.
The regulatory transcript ColE1 RNA I binds ColE1 RNA II and can prevent the hybrid needed for primer formation. The important distinction is between making an RNA molecule and making a usable primer: a transcript can be present but take a pairing or folding pathway that blocks productive initiation.[ref]
Control of ColE1 plasmid replication: the process of binding of RNA I to the primer transcript by J. Tomizawa. RNA I binding inhibits RNA II hybridization; identification of the RNA-binding product.
An idealized bookkeeping example separates the steps. If 100 precursor transcripts are made but only 30 reach the primer-producing state, the number of transcripts is 100 while the number of productive primer events is 30. This is not a measured efficiency or a complete kinetic model; it illustrates why total transcript abundance does not directly count successful DNA replication initiations. Changes in RNA production, RNA pairing or processing can have different mechanisms even if they all reduce final plasmid yield.
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