Team:Kyoto/LearnMore

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(RPU (Relative Promoter Unit))
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{{:Team:Kyoto/Header}}
{{:Team:Kyoto/Header}}
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==Lysis Cassette==
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==LearnMore==
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==Sam7 Mutation==
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===Lysis Cassette===
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==RPU (Relative Promoter Unit)==
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===Sam7 Mutation===
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===Overview===
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===RPU (Relative Promoter Unit)===
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====Overview====
Though BioBrick parts are standardized in terms of how individual parts are physically assembled into multi-component systems, many of them are not standardized in the point of characterization.  
Though BioBrick parts are standardized in terms of how individual parts are physically assembled into multi-component systems, many of them are not standardized in the point of characterization.  
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Unfortunately, it is known that the absolute activity of BioBrick promoters varies across experimental conditions and measurement instruments [[#PMID: 10298678|[1]]]. However, Kelly et al. found that this variation could be reduced by measuring the activity of promoters relative to <partinfo>J23101</partinfo> which is a promoter as an in vivo reference standard for promoter activity by ~50%. They defined a Relative Promoter Units (RPU) in order to report promoter characterization data in compatible units. In order to measure RPUs of promoters, the synthesis rate of Green Fluorescent Protein (GFP) encoded by mRNA transcribed from each promoter is observed.
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Unfortunately, it is known that the absolute activity of BioBrick promoters varies across experimental conditions and measurement instruments <sup>[[#ref1|[1]]]</sup>. However, Kelly et al. found that this variation could be reduced by measuring the activity of promoters relative to <partinfo>J23101</partinfo> which is a promoter as an in vivo reference standard for promoter activity by ~50%. They defined a Relative Promoter Units (RPU) in order to report promoter characterization data in compatible units. In order to measure RPUs of promoters, the synthesis rate of Green Fluorescent Protein (GFP) encoded by mRNA transcribed from each promoter is observed.
RPU is defined by equation 1:
RPU is defined by equation 1:
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[[Image:KyotoPromoterActivity001.png|300px|center]]
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[[Image:KyotoPromoterActivity001.png|600px|center]]
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===Derivation===
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====Derivation====
PoPS (Polymerase Per Second) is the unit of absolute “promoter activity”. It is defined  as the number of RNA polymerase molecules that pass by the final base pair of the promoter and continue along DNA as an elongation complex. PoPS<sup>SS</sup> is PoPS at the steady state of following system (d[M]/dt=0, d[I]/dt=0, d[G]/dt=0:
PoPS (Polymerase Per Second) is the unit of absolute “promoter activity”. It is defined  as the number of RNA polymerase molecules that pass by the final base pair of the promoter and continue along DNA as an elongation complex. PoPS<sup>SS</sup> is PoPS at the steady state of following system (d[M]/dt=0, d[I]/dt=0, d[G]/dt=0:
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[[Image:KyotoPromoterActivity002.png|300px|center]]
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[[Image:KyotoPromoterActivity002.png|600px|center]]
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[[Image:KyotoPromoterActivity003.png|300px|center]]
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[[Image:KyotoPromoterActivity003.png|600px|center]]
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[[Image:KyotoPromoterActivity004.png|300px|center]]
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[[Image:KyotoPromoterActivity004.png|600px|center]]
Where:
Where:
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By combining equation 2, 3, 4 and 5 at the steady state, equation 6 and 7 are obtained:
By combining equation 2, 3, 4 and 5 at the steady state, equation 6 and 7 are obtained:
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[[Image:KyotoPromoterActivity005.png|300px|center]]
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[[Image:KyotoPromoterActivity005.png|600px|center]]
Here Scell is define as the per cell mature GFP synthesis term.
Here Scell is define as the per cell mature GFP synthesis term.
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[[Image:KyotoPromoterActivity006.png|300px|center]]
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[[Image:KyotoPromoterActivity006.png|600px|center]]
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[[Image:KyotoPromoterActivity007.png|300px|center]]
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[[Image:KyotoPromoterActivity007.png|600px|center]]
Here G<sub>cell</sub> is define as the per cell mature GFP synthesis term.
Here G<sub>cell</sub> is define as the per cell mature GFP synthesis term.
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From equation 1 and 6 RPU is described as equation8.
From equation 1 and 6 RPU is described as equation8.
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[[Image:KyotoPromoterActivity008.png|300px|center]]
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[[Image:KyotoPromoterActivity008.png|600px|center]]
If the test promoter φ and the reference standard promoter are measured under the same culture conditions and both promoters are carried on the same backbone plasmid, following equations are approved.
If the test promoter φ and the reference standard promoter are measured under the same culture conditions and both promoters are carried on the same backbone plasmid, following equations are approved.
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[[Image:KyotoPromoterActivity009.png|300px|center]]
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[[Image:KyotoPromoterActivity009.png|600px|center]]
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[[Image:KyotoPromoterActivity010.png|300px|center]]
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[[Image:KyotoPromoterActivity010.png|600px|center]]
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[[Image:KyotoPromoterActivity011.png|300px|center]]
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[[Image:KyotoPromoterActivity011.png|600px|center]]
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[[Image:KyotoPromoterActivity012.png|300px|center]]
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[[Image:KyotoPromoterActivity012.png|600px|center]]
From equation 8, 9, 10, 11, and 12, equation 13 is accomplished.
From equation 8, 9, 10, 11, and 12, equation 13 is accomplished.
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[[Image:KyotoPromoterActivity013.png|300px|center]]
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[[Image:KyotoPromoterActivity013.png|600px|center]]
In addition, immature GFP is stable so that protein degradation is negligible compared to dilution due to cell growth (&gamma;<sub>I</sub>, &phi;=&mu;<sub>&phi;</sub> and &gamma;<sub>I,,J23101</sub>=&mu;<sub>J23101</sub>, where μis the cellular growth rate). Therefore, equation 13 can be modified to equation 14:
In addition, immature GFP is stable so that protein degradation is negligible compared to dilution due to cell growth (&gamma;<sub>I</sub>, &phi;=&mu;<sub>&phi;</sub> and &gamma;<sub>I,,J23101</sub>=&mu;<sub>J23101</sub>, where μis the cellular growth rate). Therefore, equation 13 can be modified to equation 14:
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[[Image:KyotoPromoterActivity014.png|300px|center]]
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[[Image:KyotoPromoterActivity014.png|600px|center]]
And if the growth rates of both strains are almost same, equation 15 is approved.
And if the growth rates of both strains are almost same, equation 15 is approved.
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[[Image:KyotoPromoterActivity015.png|300px|center]]
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[[Image:KyotoPromoterActivity015.png|600px|center]]
Accordingly, we can make equation 16 from equation15.
Accordingly, we can make equation 16 from equation15.
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[[Image:KyotoPromoterActivity016.png|300px|center]]
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[[Image:KyotoPromoterActivity016.png|600px|center]]
S<sub>cell</sub><sup>SS</sup> can be described by equation17:
S<sub>cell</sub><sup>SS</sup> can be described by equation17:
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[[Image:KyotoPromoterActivity017.png|300px|center]]
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[[Image:KyotoPromoterActivity017.png|600px|center]]
Therefore, RPU is described by equation 18:
Therefore, RPU is described by equation 18:
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[[Image:KyotoPromoterActivity018.png|300px|center]]
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[[Image:KyotoPromoterActivity018.png|600px|center]]
We can also establish equation20 from equation1, 6, 9, 10, 11 and 12.
We can also establish equation20 from equation1, 6, 9, 10, 11 and 12.
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[[Image:KyotoPromoterActivity019.png|300px|center]]
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[[Image:KyotoPromoterActivity019.png|600px|center]]
RPU can be calculated from equation 18 or equation 19. Therefore, we have to observe GFP synthesis rate and ABS (OD600) of both strains or to measure GFP concentration per cell and growth rate of both strains to measure RPU.
RPU can be calculated from equation 18 or equation 19. Therefore, we have to observe GFP synthesis rate and ABS (OD600) of both strains or to measure GFP concentration per cell and growth rate of both strains to measure RPU.
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===Note===
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====Note====
To see how to measure RPU practically, go [[Team:Kyoto/Protocols#Measurement|Protocols]]
To see how to measure RPU practically, go [[Team:Kyoto/Protocols#Measurement|Protocols]]
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===Reference===
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====Reference====
<div class="reference">
<div class="reference">
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====PMID: 10298678====
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#<a name="ref1"></a> [http://www.ncbi.nlm.nih.gov/pubmed/19298678 PMID: 19298678] Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, Endy D., ''Measuring the activity of BioBrick promoters using an in vivo reference standard.'', J Biol Eng. 2009 Mar 20;3:4.
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1. [http://www.ncbi.nlm.nih.gov/pubmed/19298678 PMID: 19298678] Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, Endy D., ''Measuring the activity of BioBrick promoters using an in vivo reference standard.'', J Biol Eng. 2009 Mar 20;3:4.
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</div>
</div>
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Revision as of 17:38, 21 October 2010

Contents

LearnMore

Lysis Cassette

Sam7 Mutation

RPU (Relative Promoter Unit)

Overview

Though BioBrick parts are standardized in terms of how individual parts are physically assembled into multi-component systems, many of them are not standardized in the point of characterization.

Unfortunately, it is known that the absolute activity of BioBrick promoters varies across experimental conditions and measurement instruments [1]. However, Kelly et al. found that this variation could be reduced by measuring the activity of promoters relative to <partinfo>J23101</partinfo> which is a promoter as an in vivo reference standard for promoter activity by ~50%. They defined a Relative Promoter Units (RPU) in order to report promoter characterization data in compatible units. In order to measure RPUs of promoters, the synthesis rate of Green Fluorescent Protein (GFP) encoded by mRNA transcribed from each promoter is observed.

RPU is defined by equation 1:

KyotoPromoterActivity001.png

Derivation

PoPS (Polymerase Per Second) is the unit of absolute “promoter activity”. It is defined as the number of RNA polymerase molecules that pass by the final base pair of the promoter and continue along DNA as an elongation complex. PoPSSS is PoPS at the steady state of following system (d[M]/dt=0, d[I]/dt=0, d[G]/dt=0:

KyotoPromoterActivity002.png
KyotoPromoterActivity003.png
KyotoPromoterActivity004.png

Where:

  • [M] is the concentration of mRNA,
  • [I] is the concentration of immature GFP,
  • [G] is the concentration of mature GFP,
  • γM is the mRNA degradation rate,
  • a is the GFP maturation rate,
  • γI is the degradation rate of immature GFP
  • n is the copy number of the plasmid containing the promoter
  • ρ is the rate of synthesis of immature GFP in absolute units of protein per second per mRNA.

By combining equation 2, 3, 4 and 5 at the steady state, equation 6 and 7 are obtained:

KyotoPromoterActivity005.png

Here Scell is define as the per cell mature GFP synthesis term.

KyotoPromoterActivity006.png
KyotoPromoterActivity007.png

Here Gcell is define as the per cell mature GFP synthesis term.

From equation 1 and 6 RPU is described as equation8.

KyotoPromoterActivity008.png

If the test promoter φ and the reference standard promoter are measured under the same culture conditions and both promoters are carried on the same backbone plasmid, following equations are approved.

KyotoPromoterActivity009.png
KyotoPromoterActivity010.png
KyotoPromoterActivity011.png
KyotoPromoterActivity012.png

From equation 8, 9, 10, 11, and 12, equation 13 is accomplished.

KyotoPromoterActivity013.png

In addition, immature GFP is stable so that protein degradation is negligible compared to dilution due to cell growth (γI, φ=μφ and γI,,J23101J23101, where μis the cellular growth rate). Therefore, equation 13 can be modified to equation 14:

KyotoPromoterActivity014.png

And if the growth rates of both strains are almost same, equation 15 is approved.

KyotoPromoterActivity015.png

Accordingly, we can make equation 16 from equation15.

KyotoPromoterActivity016.png

ScellSS can be described by equation17:

KyotoPromoterActivity017.png

Therefore, RPU is described by equation 18:

KyotoPromoterActivity018.png

We can also establish equation20 from equation1, 6, 9, 10, 11 and 12.

KyotoPromoterActivity019.png

RPU can be calculated from equation 18 or equation 19. Therefore, we have to observe GFP synthesis rate and ABS (OD600) of both strains or to measure GFP concentration per cell and growth rate of both strains to measure RPU.

Note

To see how to measure RPU practically, go Protocols

Reference

  1. <a name="ref1"></a> [http://www.ncbi.nlm.nih.gov/pubmed/19298678 PMID: 19298678] Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, Endy D., Measuring the activity of BioBrick promoters using an in vivo reference standard., J Biol Eng. 2009 Mar 20;3:4.