Difference between revisions of "Part:BBa K1416004"

 
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A plasmid standard used in the 2014 UT Austin iGEM team's Expanded Genetic Code Measurement Kit. The plasmid contains an RFP domain fused to a GFP domain by a linker sequence that contains a UAG amber stop codon in the middle for non-canonical amino acid incorporation measurement.
 
A plasmid standard used in the 2014 UT Austin iGEM team's Expanded Genetic Code Measurement Kit. The plasmid contains an RFP domain fused to a GFP domain by a linker sequence that contains a UAG amber stop codon in the middle for non-canonical amino acid incorporation measurement.
  
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<!-- Add more about the biology of this part here
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===Usage and Biology===
 
===Usage and Biology===
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===How the reporter plasmid works===
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[[File:T--Aachen--pFRY.jpg|200px|thumb|left|<i>Fig 1</i>:Reporter Plasmid]]
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This reporter plasmid is one of a two plasmids containing screening system for determining efficiancy and fidelty of non-canonical amino acids (ncAA) incorporation via amber termination supression. One plasmid contains tRNA and corresponding aminoacylation-synthetase. The other one is this plasmid presented herein. It consists of am mRFP1 domain which is connected through a linker sequence containing a recoded amber stop codon with a sfGFP domain. The expression of the plasmid gives either a red fluorescence, or - if the ncAA will be incorporated at the recoded amber stop codon within the linker site - both a red and a green fluorescence.
 +
 +
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<b>Synthetase and tRNA</b> are constitutivly expressed in a plasmid with low copy replicon p15A, taking into account that expression results in metabolic stress, but are not under IPTG control for he purpose of avoiding abrupt and unpredictable effects considering extra time and energy needed for their assembly. Whereas the <b>reporter plasmid</b> containig two fluorescence proteins, is kept under operon control for IPTG induction likewise on a low copy plasmid with ColE1.
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[picture reporter plasmid]
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====Example of cultivation conditions with High Throughput measurement====
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 +
Exmample taken from [[http://2016.igem.org/Team:Aachen|Team Aachen 2016 - Evolving a new synthetase for DMNBS incorporation in E.coli]]
 +
 +
In order to evolve a new aminoacylation synthetase for DMNBS in E.coli, transforming a mutation library into competent cells, the following order works to get a maximum output and equal optical densities:
 +
 +
*<b>Transform</b> into competent cells containing already pFRY on M9 solid, growth: 2 days, 37°C
 +
*<b>Pick</b> into M9 liquid: <b>Masterplate</b>, growth: 2 days at 30°C, 900rpm,  shaking diameter: 50 mm
 +
*<b>Replicate</b> into M9 liquid, growth 2 days at 30°C, 900 rpm, shaking diameter: 50 mm
 +
*<b>Replicate</b> into M9 liquid <b>Screening plate</b>, growth 2 days at 30°C, 900 rpm, shaking diameter:50 mm
 +
**For positive screening, supplementation at the beginning:
 +
***Induction with 100 µM IPTG
 +
***2mM DMNBS as final concentration
 +
**For negative screening, supplementation at the beginning:
 +
***Induction with 100 µM IPTG
 +
 +
It was shown previously, that highest GFP formation is achieved with supplementation of IPTG and the ncAA at the beginning of incubation, but does results in decelerated growth (1). In fact, cultivation of BL21 DE3 gold containing two different plasmids show lower growth rates, when adding 100µM IPTG and 2mM DMNBS to M9 minimal medium, resulting overall in a growth phase of 42-48h at 30°C to reach maximum cell density.
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====Measurement: Wavelength====
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[[File:T--Aachen--mRFP1 scan.png|200px|thumb|left|<i>Fig 2</i>: normalized fluorescence spectrum of mRFP1]]
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[[File:T--Aachen--sfGFP scan.png|200px|thumb|left|<i>Fig 3</i>: normalized fluorescence spectrum of sfGFP]]
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Excitation and emission wavelegthes of mRFP1 and sfGFP were obtained from a conducted measurement with a Biolector set up (<i>Fig 2</i>, <i>Fig 3</i>).
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For screening with Tecan Plate Reader the following settings can be used:
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*OD: 600 nm
 +
*sfGFP 480/508 nm
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*mRFP1 584/605 nm
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*Slid: 8 nm
 +
 +
====Measurement: Evaluation====
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 +
 +
====With the reporter plasmid evaluated synthtases====
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*[[Part:BBa_K2020050|Y-RS, canonical amino acid]]
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*[[Part:BBa_K1416000|oNBY-RS]]
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*[[Part:BBa_K2020043|AzF-synthetase]]
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*[[Part:BBa_K2020046|CN-F synthetase]]
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*[[Part:BBa_K1416001|Iodo-Y synthetase]]
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*5HT-P synthetase
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*[[Part:BBa_K2020045|Nitro-Y synthetase]]
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*Amino-Y synthetase
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*DMNBS-RS clones:
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**[[Part:BBa_K2020052|DMNBS-RS Clone 1]]
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**[[Part:BBa_K2020053|DMNBS-RS Clone 2]]
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**[[Part:BBa_K2020054|DMNBS-RS Clone 3]]
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**[[Part:BBa_K2020055|DMNBS-RS Clone 4]]
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**[[Part:BBa_K2020056|DMNBS-RS Clone 5]]
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**[[Part:BBa_K2020057|DMNBS-RS Clone 6]]
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**[[Part:BBa_K2020058|DMNBS-RS Clone 7]]
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**[[Part:BBa_K2020059|DMNBS-RS Clone 8]]
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**[[Part:BBa_K2020060|DMNBS-RS Clone 9]]
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**[[Part:BBa_K2020061|DMNBS-RS Clone 10]]
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*OMe-Y-RS
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===Links===
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*[[Part:BBa_K2020040|Part K2020040 - Flourescent reporter for measurement of incorporation of ncAA]] : Whereas you find herunder the whole plasmid as a biobrick, we provide the two flourescent proteins connected through the linker sequence as a biobrick for self-assembly in a low copy plasmid.
 +
*[http://2014.igem.org/Team:Austin_Texas/kit Team Austin, Texas 2014 built this measurement kit and probed various synthetases]
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*[http://2016.igem.org/Team:Aachen Team Aachen 2016 evolved a new synthetase for incorporation of DMNBS in E.coli]
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 +
  
 
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Revision as of 10:17, 17 October 2016


pFRY: a Reporter Plasmid for Measuring ncAA Incorporation

A plasmid standard used in the 2014 UT Austin iGEM team's Expanded Genetic Code Measurement Kit. The plasmid contains an RFP domain fused to a GFP domain by a linker sequence that contains a UAG amber stop codon in the middle for non-canonical amino acid incorporation measurement.


Usage and Biology

How the reporter plasmid works

Fig 1:Reporter Plasmid

This reporter plasmid is one of a two plasmids containing screening system for determining efficiancy and fidelty of non-canonical amino acids (ncAA) incorporation via amber termination supression. One plasmid contains tRNA and corresponding aminoacylation-synthetase. The other one is this plasmid presented herein. It consists of am mRFP1 domain which is connected through a linker sequence containing a recoded amber stop codon with a sfGFP domain. The expression of the plasmid gives either a red fluorescence, or - if the ncAA will be incorporated at the recoded amber stop codon within the linker site - both a red and a green fluorescence.


Synthetase and tRNA are constitutivly expressed in a plasmid with low copy replicon p15A, taking into account that expression results in metabolic stress, but are not under IPTG control for he purpose of avoiding abrupt and unpredictable effects considering extra time and energy needed for their assembly. Whereas the reporter plasmid containig two fluorescence proteins, is kept under operon control for IPTG induction likewise on a low copy plasmid with ColE1. [picture reporter plasmid]


Example of cultivation conditions with High Throughput measurement

Exmample taken from Team Aachen 2016 - Evolving a new synthetase for DMNBS incorporation in E.coli

In order to evolve a new aminoacylation synthetase for DMNBS in E.coli, transforming a mutation library into competent cells, the following order works to get a maximum output and equal optical densities:

  • Transform into competent cells containing already pFRY on M9 solid, growth: 2 days, 37°C
  • Pick into M9 liquid: Masterplate, growth: 2 days at 30°C, 900rpm, shaking diameter: 50 mm
  • Replicate into M9 liquid, growth 2 days at 30°C, 900 rpm, shaking diameter: 50 mm
  • Replicate into M9 liquid Screening plate, growth 2 days at 30°C, 900 rpm, shaking diameter:50 mm
    • For positive screening, supplementation at the beginning:
      • Induction with 100 µM IPTG
      • 2mM DMNBS as final concentration
    • For negative screening, supplementation at the beginning:
      • Induction with 100 µM IPTG

It was shown previously, that highest GFP formation is achieved with supplementation of IPTG and the ncAA at the beginning of incubation, but does results in decelerated growth (1). In fact, cultivation of BL21 DE3 gold containing two different plasmids show lower growth rates, when adding 100µM IPTG and 2mM DMNBS to M9 minimal medium, resulting overall in a growth phase of 42-48h at 30°C to reach maximum cell density.


Measurement: Wavelength

Fig 2: normalized fluorescence spectrum of mRFP1
Fig 3: normalized fluorescence spectrum of sfGFP

Excitation and emission wavelegthes of mRFP1 and sfGFP were obtained from a conducted measurement with a Biolector set up (Fig 2, Fig 3).

For screening with Tecan Plate Reader the following settings can be used:

  • OD: 600 nm
  • sfGFP 480/508 nm
  • mRFP1 584/605 nm
  • Slid: 8 nm

Measurement: Evaluation

With the reporter plasmid evaluated synthtases

Links

  • Part K2020040 - Flourescent reporter for measurement of incorporation of ncAA : Whereas you find herunder the whole plasmid as a biobrick, we provide the two flourescent proteins connected through the linker sequence as a biobrick for self-assembly in a low copy plasmid.
  • [http://2014.igem.org/Team:Austin_Texas/kit Team Austin, Texas 2014 built this measurement kit and probed various synthetases]
  • [http://2016.igem.org/Team:Aachen Team Aachen 2016 evolved a new synthetase for incorporation of DMNBS in E.coli]


Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 5940
    Illegal XbaI site found at 2474
    Illegal XbaI site found at 3764
    Illegal PstI site found at 1388
    Illegal PstI site found at 1490
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 5940
    Illegal NheI site found at 1618
    Illegal PstI site found at 1388
    Illegal PstI site found at 1490
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 5940
    Illegal BamHI site found at 679
    Illegal BamHI site found at 1456
    Illegal XhoI site found at 1429
    Illegal XhoI site found at 5853
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 5940
    Illegal XbaI site found at 2474
    Illegal XbaI site found at 3764
    Illegal PstI site found at 1388
    Illegal PstI site found at 1490
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 5940
    Illegal XbaI site found at 2474
    Illegal XbaI site found at 3764
    Illegal PstI site found at 1388
    Illegal PstI site found at 1490
    Illegal AgeI site found at 555
    Illegal AgeI site found at 667
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI site found at 4054