Difference between revisions of "Team:UCAS-China/Part Collection"

 
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        <th>fluorescent protein+promoter </th>
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        <th>sfGFP+PCGG</th>
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        <th>composite</th>
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        <th><a href="http://parts.igem.org/Part:BBa_K2598063">BBa_K2598063</a></th>
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        <th> sfGFP+PCGG +terminator</th>   
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        <th>fluorescent protein+promoter </th>
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        <th>tag-BFP+PT3</th>
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        <th>composite</th>
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        <th><a href="http://parts.igem.org/Part:BBa_K2598064">BBa_K2598064</a></th>
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        <th> tag-BFP+PT3 +terminator</th>   
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        <th>fluorescent protein+promoter </th>
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        <th>mRFP+PK1F</th>
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        <th>composite</th>
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        <th><a href="http://parts.igem.org/Part:BBa_K2598065">BBa_K2598065</a></th>
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        <th> mRFP+PK1F +terminator</th>   
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        <th>sensor+fluorescent protein </th>
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        <th>CcaSR+GFP</th>
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        <th>composite</th>
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        <th><a href="http://parts.igem.org/Part:BBa_K2598035">BBa_K2598035</a></th>
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        <th>green light sensor CcaSR+GFP</th>   
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        <th>fluorescent protein </th>
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        <th>pJFR4 (KX011467)</th>
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        <th>composite</th>
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        <th><a href="http://parts.igem.org/Part:BBa_K2598053">BBa_K2598053</a></th>
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        <th> This plasmid encodes three fluorescent proteins outputs, mRFP, GFP and BFP. It uses DT16（BBa_K2598031）, T7（BBa_K2598024） and DT5（BBa_K2598028） as terminators and PK1F（BBa_K2598030）, PCGG（BBa_K2598023） and PT3（BBa_K2598026） as promotors corresponding to red, green and blue light circuits respectively.</th>   
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         <th>enzyme</th>
 
         <th>enzyme</th>

Latest revision as of 03:53, 18 October 2018

PART COLLECTION

OVERVIEW

Our project is based on an excellent light control system that can convert light and sound signals into chemical signals, and finally produce scents and colors. The system consists of 4 modules, “sensor array”, circuit, “resource allocator” and actuators.

Firstly, the “sensor array” module combines 3 light sensors, Cph8* (asterisk), YF1 and CcaSR, which could be activated predominantly by red, blue and green light. These optogenetic tools enables our E. coli to response to light of different wavelengths respectively. Cph8 is a chimeric histidine kinase that is switched on by infrared (705 nm) light and off by red (650 nm) light. So it can be used as a red light sensor. CcaSR is a green-light sensor based on the membrane-associated histidine kinase CcaS and its response regulator CcaR, which can be switched on by green (535 nm) light, inducing the promoter PcpcG2-172 (BBa_K592003) and off by far-red (672 nm) light. YF1 is a fusion protein of YtvA (B subtilis) and FixL (B japonicum) that can sense blue light. The fixJ is the wild-type response regulator to YF1. They can form a blue light sensor and transfer the signal to next module.

Secondly, the circuit module has two NOT gates to invert signals from red and blue light sensor, in which two repressors CI and PhIF can be expressed respectively activated by red and blue input to switch off corresponding red and blue output promoters.

Next, the “resource allocator” module, connects the input with the output. The resource-allocation system is a split-phage RNA polymerase system, enabling signals easily connected to the circuit outputs. The resource-allocation system also allocate the resource and stabilize the transcription level in the cell. In the system, three well orthogonal sigma fragments which has specific DNA binding domain are expressed under the control of 3 sensors. And a core fragment is expressed by a constitutive promoter. Only when a core fragment conjugate with specific sigma fragment to form a full-functional RNA polymerase, then the transcription of corresponding output gene is initiated. In this way, we not only keep the proportion of the response product precisely through the compete among 3 sigma fragments but reduce the metabolic burden of E. coli and make the whole system work more orderly. Here we sincerely appreciate Dr. Christopher Voigt’s laboratory that created this system, and sent us plasmids to support our work this year.

Last, the “actuator” module implement the biological functions that are the outputs of the RGB sysytem. There are three output genes responding to three light sensors activated by different wavelength of light. In order to implement customized outcome, theoretically, you can change them into any genes you want.

To make it work more well, ribozyme-based insulators and 18 strong synthetic terminators are also added to the whole system. We collected all these parts together.

PARTS OF SENSOR

Type Parts Name Basic/Composite Number Description
CDS Cph8* basic BBa_K2598006 Cph8 is a chimeric histidine kinase that is switched on by infrared (705 nm) light and off by red (650 nm) light. So it can be used as a red light sensor. Here is promoter+Cph8+terminator
CDS CcaSR basic BBa_K2598005 This part is a green-light sensor based on the membrane-associated histidine kinase CcaS and its response regulator CcaR, which can be switched on by green (535 nm) light, inducing the promoter PcpcG2-172 (BBa_K592003) and off by far-red (672 nm) light. So it can be used as a green light sensor
CDS CcaSR composite BBa_K2598003 promoter+CcaSR+terminator
CDS YF1+fixJ composite BBa_K2598009 YF1 is a fusion protein of YtvA (B subtilis) and FixL (B japonicum) that can sense blue light. fixJ is the wild-type response regulator to YF1. They can form a blue light sensor and transfer the signal to next module
CDS ho1+pcyA composite BBa_K2598018 ho1 oxidizes the heme group using a ferredoxin cofactor, generating biliverdin Ixalpha and pcyA converts biliverdin IXalpha (BV) to phycocyanobilin (PCB), the immediate precursor of cyanobacterial phytochromes, which achieve phycocyanobilin biosynthetic process. Here is promoter+ho1+pcyA+terminator
insulator BydvJ basic BBa_K2598014 ribozyme-based insulator
insulator RiboJ basic BBa_K2598010 ribozyme-based insulator
promoter laclq35 basic BBa_K2598007 a promoter promotes expression of YF1 and fixJ
whole plasmid pJFR1 (KX011464) composite BBa_K2598049 This plasmid codes three light sensors, Cph8*, CcaSR and YF1, under the promoters of J23106, J23108 and laclq35 to sense red, green and blue light respectively

PARTS OF CIRCUIT

Type Parts Name Basic/Composite Number Description
repressor PhIF composite BBa_K2598016 PhIF is a repressor that can repress promoter, PPhIF(BBa_K1725000), of blue light output under promoter PfixK2 which can be activated by fixJ when blue light sensor is activated. Here is promoter+PhIF+terminator
repressor CI composite BBa_K2598021 CI is a repressor that can repress promoter, Pλ(BBa_K1145005), of red light output under promoter Pomp which can be activated by activated red light sensor. Here is promoter+CI+terminator
sensor+repressor YF1+fixJ+PhlF composite BBa_K2598039 blue light sensor YF1+fixJ(regulator to YF1)+repressor PhIF
sensor+repressor Cph8*+CI composite BBa_K2598038 red light sensor composite Cph8*+repressor CI

PARTS OF RNAP

Type Parts Name Basic/Composite Number Description
sigma fragment CGG basic BBa_K2598011 a T7 RNAP sigma fragment with DNA-binding domain that can be expressed when green light sensors are activated and be able to combine to non-active T7 RNAP core fragment (BBa_K2598001) to form a full-functional RNA polymerase and direct it to specific promoter PCGG(BBa_K2598023)
sigma fragment CGG composite BBa_K2598013 promoter+CGG+terminator
sigma fragment T3 basic BBa_K2598015 a T7 RNAP sigma fragment with DNA-binding domain that can be expressed when blue light sensors are activated and be able to combine to non-active T7 RNAP core fragment (BBa_K2598001) to form a full-functional RNA polymerase and direct it to specific promoter PT3(BBa_K2598026)
sigma fragment T3 composite BBa_K2598033 promoter+T3+terminator
sigma fragment K1F composite BBa_K2598022 K1F is a T7 RNAP sigma fragment with DNA-binding domain that can be expressed when red light sensors are activated and be able to combine to non-active T7 RNAP core fragment (BBa_K2598001) to form a full-functional RNA polymerase and direct it to specific promoter PK1F(BBa_K2598030). Here is promoter+K1F+terminator
sigma fragment+output T3+BFP composite BBa_K2598040 sigma fragment T3+a blue fluorescent protein BFP
sigma fragment+output CGG+GFP composite BBa_K2598041 sigma fragmentCGG+a green fluorescent protein GFP
sigma fragment+output K1F+mRFP composite BBa_K2598042 sigma fragment K1F+a red fluorescent protein mRFP
sensor+sigma fragment CcaSR+CGG composite BBa_K2598034 green light sensor CcaSR+sigma fragment CGG
core fragment T7 basic BBa_K2598000 Non-active T7 RNAP core fragment being able to combine to being able to combine to sigma fragment to form a full-functional RNA polymerase
core fragment T7 composite BBa_K2598001 promoter+T7+terminator
promoter PCGG basic BBa_K2598023 a promoter that can be regulated by the full-functional RNA polymerase consisting of T7 RNAP sigma fragment T3 and T7 RNAP core fragment and promotes blue light output
promoter PT3 basic BBa_K2598026  a promoter that can be regulated by the full-functional RNA polymerase consisting of T7 RNAP sigma fragment CGG and T7 RNAP core fragment and promotes green light output
promoter PK1F basic BBa_K2598030  a promoter that can be regulated by the full-functional RNA polymerase consisting of T7 RNAP sigma fragment K1F and T7 RNAP core fragment and promotes red light output
fluorescent protein+promoter sfGFP+PCGG composite BBa_K2598063 sfGFP+PCGG +terminator
fluorescent protein+promoter tag-BFP+PT3 composite BBa_K2598064 tag-BFP+PT3 +terminator
fluorescent protein+promoter mRFP+PK1F composite BBa_K2598065 mRFP+PK1F +terminator
teminator ECK120033737 basic BBa_K2598002 a strong teminator
teminator L3S2P11 basic BBa_K2598004 a strong teminator
teminator L3S2P55 basic BBa_K2598008 a strong teminator
teminator DT25 basic BBa_K2598012 a strong teminator
teminator L3S1P22 basic BBa_K2598017 a strong teminator
teminator DT11 basic BBa_K2598020 a strong teminator
teminator T7 basic BBa_K2598024 a strong teminator
teminator DT5 basic BBa_K2598028 a strong teminator
teminator DT16 basic BBa_K2598031 a strong teminator
teminator L3S3P11 basic BBa_K2598054 a strong teminator
whole plasmid pJFR2 (KX011465) composite BBa_K2598050 a strong teminator
whole plasmid pJFR3 (KX011466) composite BBa_K2598051 a strong teminator

PARTS OF ACTUATOR

Type Parts Name Basic/Composite Number Description
sensor+fluorescent protein CcaSR+GFP composite BBa_K2598035 green light sensor CcaSR+GFP
fluorescent protein pJFR4 (KX011467) composite BBa_K2598053 This plasmid encodes three fluorescent proteins outputs, mRFP, GFP and BFP. It uses DT16（BBa_K2598031）, T7（BBa_K2598024） and DT5（BBa_K2598028） as terminators and PK1F（BBa_K2598030）, PCGG（BBa_K2598023） and PT3（BBa_K2598026） as promotors corresponding to red, green and blue light circuits respectively.
enzyme lacZ composite BBa_K2598025 LacZ encodes beta-galactosidase, an intracellular enzyme that can cleaves X-gal into colorful products. It is often used for blue/white screeningof bacterial colonies, dilute X-Gal appear green at low concentrations. Here is PCGG+lacZ+terminator
enzyme bFMO basic BBa_K2598027 bFMO is a bacterial flavin-containing monooxygenase that can catalyse tryptophan and render it blue
enzyme bFMO composite BBa_K2598029 promoter+bFMO+terminator
enzyme gusA composite BBa_K2598032 gusA encodes beta-glucuronidase (GUS), an enzyme originated from Escherichia coli which can catalyze Rose-gluc into red substance. Here is PK1F+gusA+terminator
enzyme pJFR5 (KX011468) composite BBa_K2598052 This plasmid encodes three kinds of enzymes, including gusA, lacZ and bFMO
chromoprotein amilGFP composite BBa_K2598055 amilGFP is a yellow chromoprotein improved from green fluorescent protein. Here is promoter+amilGFP+terminator
chromoprotein eforRed composite BBa_K2598056 eforRed is a red chromoprotein. Here is promoter+eforRed+terminator
chromoprotein amilCP composite BBa_K2598057 amilCP is a blue chromoprotein . Here is promoter+amilCP+terminator
chromoprotein amilCP+amilGFP composite BBa_K2598043 promoter+amilCP+amilGFP+terminator. We use this part to mix color.
chromoprotein amilCP+eforRed composite BBa_K2598044 promoter+amilCP+eforRed+terminator. We use this part to mix color.
chromoprotein amilCP+fwyellow composite BBa_K2598045 fwYellow is a yellow chromoprotein. Here is promoter+amilCP+fwYellow+terminator. We use this part to mix color.
chromoprotein amilGFP+eforRed composite BBa_K2598046 promoter+amilGFP+eforRed+terminator. We use this part to mix color.
chromoprotein amilGFP+fwyellow composite BBa_K2598047 promoter+amilGFP+fwYellow+terminator. We use this part to mix color.
chromoprotein eforRed+fwyellow composite BBa_K2598048 promoter+eforRed+fwYellow+terminator. We use this part to mix color.
chromoprotein amilCP+amilGFP+eforRed composite BBa_K2598061 promoter+amilCP+amilGFP+eforRed+terminator. We use this part to mix color.
smell rain basic BBa_K2598058 encoding GDS, a enzyme catalyzing the conversion of Farnesyl diphosphate to Geosmin that has rain smell
smell mint basic BBa_K2598059 encoding BSMT1, a enzyme catalyzing the conversion of benzoic acid to methyl benzoate that has flower smell
smell lemon basic BBa_K2598060 encoding Limonene synthase 1, an enzyme catalyzing the conversion of Farnesyl diphosphate to (+)-Limonene that has lemon smell
smell rain+mint+lemon composite BBa_K2598062 PCGG+rain+terminator+PK1F+lemon+terminator+PT3+mint+terminator