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I need a rough estimate on how to translate RPU or Polymerases Per Second (PoPS) to mRNA count (or even better protein count) in E. coli.

I understand that any number we come up with will be a very rough estimate of it, but for now, I need a placeholder value to do some modeling on genetic circuits in E. coli until a more verifiable number comes about.

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  • $\begingroup$ Can please you explain (or provide a link to) what you mean by these terms as they are not very common? In general, mRNA count is easier to estimate than calculating the speed of polymerase. So you are better off counting mRNAs directly instead of extrapolating from these parameters. Protein count is even more difficult to estimate using these parameters. You can't have a good estimate of protein counts unless you know about translation initiation and elongation rates and protein degradation rates. $\endgroup$
    – WYSIWYG
    Feb 11 '20 at 8:40
  • $\begingroup$ Yes, of course, I added the links just now. I know it would be much better to have mRNA numbers and then simply estimate protein numbers using an average ratio for E. coli. However, there is a study I am basing of my work and we only are going to have RPU or PoPS to base of, so was wondering if anyone had any references or rough estimates as to how to translate these into mRNA numbers for E. coli $\endgroup$ Feb 11 '20 at 13:06
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I could not find any paper that discusses these issues. So this answer is just based on my guess.

From the this page:

Transcription rate is generally a parameter associated with a particular transcript and has units of transcripts per unit time. In contrast, PoPS is essentially transcription rate at a particular location on the DNA. The value of PoPS just downstream of a coding region should be equal to the coding region's transcription rate. However, there are certain positions at which a transcription rate doesn't necessarily make sense yet PoPS does. For instance, as biological engineers, we care about the rate at which RNA polymerase moves through a terminator (or the PoPS downstream of a terminator) but yet most people don't talk about the transcription rate of a terminator.

What we want is the transcription rate for every gene. You can estimate it using PoPS corresponding to that terminator.

Now, at steady state the mRNA concentration would be the rate of formation divided by the rate of degradation (removal): rf / rd.

Since the study that you are referring to, calculates PoPs, I would guess that it is based on some standard BioBricks parts. You are likely to have have mRNA degradation rates associated with these transcripts (even protein formation and degradation rates, possibly). If you don't have the mRNA degradation rate then at least for long lived mRNAs, you can assume the rate of removal to be same as the dilution rate (loge2 / doubling time). Substitute this in the equation for steady state and you should get mRNA concentration.

Steady state protein counts would be: mRNA counts × protein formation rate / protein removal rate.

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