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

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<h1>COMPOSITE PART</h1>
 +
<h2>OVERVIEW</h2>
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<p>We built and submitted a series of useful composite parts this year. The following six composite parts are the most significant with great application and research value.
 +
</p>
 +
<p>These six parts belong to six plasmids respectively, which are all the components of a light control system with three light control circuits, including a ‘sensor array’, a ‘circuit’, a ‘resource allocator’ and ‘actuators’.
 +
</p>
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<p>The first one, BBa_K2598050, is our best composite part, which contains three RBSs, CGG（BBa_K2598011）, T3（BBa_K2598015） and phIF regulated by 3 promoters, PcpcG2-172, PphlF, PfixK2 respectively. The phIF is a repressor to switch off the blue-light output promoter when blue-light sensor is switched on. The CGG, in the blue-light circuit, and T3, in the green-light circuit, are both ‘sigma’ fragments that are a significant part in the resource allocator, which have the DNA-binding domain and can combine core fragment that is another necessary part produced by theresource-allocation system connecting the inputs with the outputs to form a full-functional RNA polymerase. And when σCGG combines the core fragment, they form a full-functional RNA polymerase to induce the expression of the blue-light output. Similarly, combination of σT3 and the core fragment can induce the green-light output. And these ‘sigma’ fragments are orthogonal and almost do not effect each other.
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</p>
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<p>The second part, BBa_K2598049, codes three light sensors, Cph8*, CcaSR and YF1 + fixJ, which is carried on one plasmid, pJFR1(KX011464), under the promoters of J23106, J23108 and laclq35（BBa_K2598007）to sense red, green and blue light 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.
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</p>
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<p>The third part, BBa_K2598051, contains CI, another repressor to switch off the red-light output promoter when red-light sensor is switched on, K1F（BBa_K2510004）, the third ‘sigma’ fragments that can combine with core fragment to induce the red-light output. And these three ‘sigma’ fragments are orthogonal and almost do not effect each other. This part is regulated by PompC1157 and Pλ promoters.
 +
</p>
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<p>The forth part, BBa_K2598053, is the output part encoding three fluorescent proteins outputs, RFP, GFP and BFP, on one plasmid. 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.
 +
Based on the forth part, the fifth part, BBa_K2598052，changes three fluorescent proteins outputs to three kinds of enzymes, including gusA（BBa_K330002）, lacZ（BBa_I732005） and bFMO（BBa_K2598027） that can combine with substrate in the medium to produce red, green and blue color.
 +
</p>
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<p>Similarly，based on the forth part, the sixth part, BBa_K2598061, constructed by our team this year changes three fluorescent proteins outputs to three chromoproteins, including eforRed, amilGFP and aeBlue.
 +
</p>
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<p>All composite parts are all listed in the table below.
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</p>
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<div id="cell-free-parts-table">
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<table class="table table-hover" style="margin-left:-40px;">
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    <thead>
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      <tr>
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        <th>Type</th>
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        <th>Parts Name</th>
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        <th>Number</th>
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        <th>Description</th>
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      </tr>
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Revision as of 04:38, 17 October 2018

BASIC PART

Type Parts Name Number Description
promoter laclq35 BBa_K2598007 a promoter promotes expression of YF1 and fixJ
promoter PCGG 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 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 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
insulator BydvJ BBa_K2598010 ribozyme-based insulator
insulator RiboJ BBa_K2598014 ribozyme-based insulator
coding T7 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
coding CcaSR 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
coding CGG 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)
coding T3 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)
coding bFMO BBa_K2598027 bFMO is a bacterial flavin-containing monooxygenase that can catalyse tryptophan and render it blue
coding rain BBa_K2598058 encoding GDS, a enzyme catalyzing the conversion of Farnesyl diphosphate to Geosmin that has rain smell
coding mint BBa_K2598059 encoding BSMT1, a enzyme catalyzing the conversion of benzoic acid to methyl benzoate that has flower smell
coding lemon BBa_K2598060 encoding Limonene synthase 1, an enzyme catalyzing the conversion of Farnesyl diphosphate to (+)-Limonene that has lemon smell
teminator ECK120033737 BBa_K2598002 a strong teminator
teminator L3S2P11 BBa_K2598004 a strong teminator
teminator L3S2P55 BBa_K2598008 a strong teminator
teminator DT25 BBa_K2598012 a strong teminator
teminator L3S1P22 BBa_K2598017 a strong teminator
teminator DT11 BBa_K2598020 a strong teminator
teminator T7 BBa_K2598024 a strong teminator
teminator DT5 BBa_K2598028 a strong teminator
teminator DT16 BBa_K2598031 a strong teminator
teminator L3S3P11 BBa_K2598054 a strong teminator

COMPOSITE PART

OVERVIEW

We built and submitted a series of useful composite parts this year. The following six composite parts are the most significant with great application and research value.

These six parts belong to six plasmids respectively, which are all the components of a light control system with three light control circuits, including a ‘sensor array’, a ‘circuit’, a ‘resource allocator’ and ‘actuators’.

The first one, BBa_K2598050, is our best composite part, which contains three RBSs, CGG（BBa_K2598011）, T3（BBa_K2598015） and phIF regulated by 3 promoters, PcpcG2-172, PphlF, PfixK2 respectively. The phIF is a repressor to switch off the blue-light output promoter when blue-light sensor is switched on. The CGG, in the blue-light circuit, and T3, in the green-light circuit, are both ‘sigma’ fragments that are a significant part in the resource allocator, which have the DNA-binding domain and can combine core fragment that is another necessary part produced by theresource-allocation system connecting the inputs with the outputs to form a full-functional RNA polymerase. And when σCGG combines the core fragment, they form a full-functional RNA polymerase to induce the expression of the blue-light output. Similarly, combination of σT3 and the core fragment can induce the green-light output. And these ‘sigma’ fragments are orthogonal and almost do not effect each other.

The second part, BBa_K2598049, codes three light sensors, Cph8*, CcaSR and YF1 + fixJ, which is carried on one plasmid, pJFR1(KX011464), under the promoters of J23106, J23108 and laclq35（BBa_K2598007）to sense red, green and blue light 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.

The third part, BBa_K2598051, contains CI, another repressor to switch off the red-light output promoter when red-light sensor is switched on, K1F（BBa_K2510004）, the third ‘sigma’ fragments that can combine with core fragment to induce the red-light output. And these three ‘sigma’ fragments are orthogonal and almost do not effect each other. This part is regulated by PompC1157 and Pλ promoters.

The forth part, BBa_K2598053, is the output part encoding three fluorescent proteins outputs, RFP, GFP and BFP, on one plasmid. 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. Based on the forth part, the fifth part, BBa_K2598052，changes three fluorescent proteins outputs to three kinds of enzymes, including gusA（BBa_K330002）, lacZ（BBa_I732005） and bFMO（BBa_K2598027） that can combine with substrate in the medium to produce red, green and blue color.

Similarly，based on the forth part, the sixth part, BBa_K2598061, constructed by our team this year changes three fluorescent proteins outputs to three chromoproteins, including eforRed, amilGFP and aeBlue.

All composite parts are all listed in the table below.

Type Parts Name Number Description