Drew Reams studies unselected duplication formation, and recently found an eel in the DNA!
Recall that duplication formation is a fundamental small-effect driver of evolutionary adaptation, and TIDs may be the primum mobile of most or all duplications. Drew’s “recalcitrant” duplication strains — those with joints not easily determined by multiplex PCR — are a class which should include TIDs. To analyze them, he sequences their genomes by Illumina technology.
We think TID formation often begins with a snap-back of a 3′ end at a short inverted repeat, forming a stem-loop structure which then initiates DNA synthesis using self as template.
A subsequent template switch restores the fork and finishes the TID. See the excellent article in our Encyclopedia.
The extensive secondary structures at such symmetric TID joints are toxic and rarely observed. Instead, remodelling asymmetric deletions are selected spontaneously, yielding “SJ” (“short junction”) joints. David Leach has shown that sbcCD backgrounds tolerate such structures by not cutting them with the endonuclease product.
Drew wondered what would happen to duplication frequencies in such backgrounds, which may allow the cell to survive the two initial steps of TID formation and increase the yield of duplications. To enhance stem-loop persistance, he also made the cells recQ to prevent stem melting.
He observed a 2-fold increase in duplications in both the chromosome and wild type F’128. The latter contains two IS3 elements and nearly all spontaneous duplications happen by recombination between them. If at least one were removed, the duplication frequency increased by an order of magnitude compared to sbcCD+ recQ+ cells. Something definitely happens in the absence of sbcCD and recQ when IS recombination is blocked
One sequenced duplication was in F’128 of strain DR397. It had a lacZ read depth 3-fold greater than the chromosome with remaining plasmid DNA about 9-fold greater. In addition, there was a large deletion extending from traI up to lacZ accounting for ~20% of the plasmid.
When we inspected the anomalous read-pair data, we discovered two symmetrical TID joins. We were able to confirm these by showing that reads right at the edge of the deletion window fully contained these joints.
Drew’s suspicions were vindicated. Removing activities which cut stem loop structures or prevent them from folding encourages secondary structure formation and reduces counterselection of the long symmetrical products of snap back and strand switching.
But, what’s the meaning of the enormous deletion? There are a couple of models which come to mind.
Model 1: A snapback at traI followed by another at lac, 5′ resection and ligation of ends will produce a product that matches our observations. It would look something like the following:
Model 2: A snapback at traI and strand switch at lac will restore the replication fork and lead to a TID. Eventual remodelling by recombination of the flanking repeats will yield our observed product:
Other related models are possible, with the order of the snapbacks and strand switches reversed, with double strand switches instead of snapbacks, etc. Nevertheless, we favor the second model above, as it only involves two steps to get the essential intermediate, while many generations can pass before selection of the final product.
An interesting aspect of the TID model is the inevitability of the remodeling event. When the origin is itself in the TID, counterselection on a large number of unnecessary genes leads easily to their deletion by recombination. The resulting fitness increase will lead to expansion in the population of the symmetric inversion and eventual extinction of the TID.-- Eric Kofoid