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I was looking at the iGEM Bioregistry of Terminator parts which offer varying degrees of termination efficiency. I am wondering why studies into combinatorial synthesis of genetic circuits for metabolic engineering include terminators as a variable component within their designs, such as this paper by Woodruff et al., 2017? This must come at great complexity cost to overall library size, where I would of assumed one would take the most efficient terminator and fix it within the design. How could terminator strength or sequence effect optimisation of a metabolic pathway in an impactful manner such that this extra complexity becomes worthwhile?

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    $\begingroup$ My guess is that they used different terminators to ensure sequence variability. Cloning several copies of an identical sequence into a plasmid can lead to spontaneous loop-outs, causing the additional copies to get lost over time. And for why less efficient terminators are kept in Parts Registry: why would you remove well-characterized parts and thereby lose potentially valuable data? You can only appreciate the efficiency of one part by comparing it to another. $\endgroup$
    – gaspanic
    Apr 10, 2021 at 11:20
  • $\begingroup$ @gaspanic Interesting, thank you for your thoughts! $\endgroup$
    – JEJS
    Apr 11, 2021 at 14:15

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To add to gaspanic's answer, not all terminators work equally well under all conditions. So if terminators weren't characterized in the organism or tissue you are working in the efficiency might be different. Additionally, though rarely people might be looking to design with a leaky terminator mimicking bacterial use of leaky terminators to use one DNA sequence to create two mRNAs of different length.

[Edit] Sources for further reading

Example of terminator efficacy differences between different species

Example of terminator differences between tissues

Terminator Attenuation - stopping of termination only sometimes

Leaky stop codons as a molecular tool

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    $\begingroup$ Your answer may or may not be correct, but we have no way of knowing because it is just an assertion, with no supporting evidence. Please read the Help on Answering Questions. $\endgroup$
    – David
    Apr 12, 2021 at 22:35
  • $\begingroup$ Sorry, I thought this was widely accepted enough that it didn't need specific references for the assertions. $\endgroup$ Apr 13, 2021 at 0:04
  • $\begingroup$ @PlantPromoter This is very true that part behaviour can vary not only strain to strain but system to system (metabolically engineered system). I guess if you have the ability to implement such complexity nothing is to be lost. I don't think in this case of Woodruff et al., that readthrough would create any benefit to their system because all transcriptional units have their own promoters. $\endgroup$
    – JEJS
    Apr 13, 2021 at 8:55

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