Difference between revisions of "Team:UCAS-China/Composite Part"
m |
m |
||
| Line 222: | Line 222: | ||
<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>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> | </p> | ||
| − | < | + | <strong>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. |
| − | </ | + | </strong> |
<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. | <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. | ||
</p> | </p> | ||
Revision as of 12:19, 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.
| Parts Name | Number | Description |
|---|---|---|
| T7 | BBa_K2598001 | promoter+T7+terminator |
| CcaSR | BBa_K2598003 | promoter+CcaSR+terminator |
| Cph8* | 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 |
| YF1+fixJ | 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 |
| CGG | BBa_K2598013 | promoter+CGG+terminator |
| PhIF | 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 |
| ho1+pcyA | 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 |
| CI | 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 |
| K1F | 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 |
| lacZ | 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 |
| bFMO | BBa_K2598029 | promoter+bFMO+terminator |
| gusA | 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 |
| T3 | BBa_K2598033 | promoter+T3+terminator |
| CcaSR+CGG | BBa_K2598034 | green light sensor CcaSR+sigma fragment CGG |
| CcaSR+GFP | BBa_K2598035 | green light sensor CcaSR+GFP |
| Cph8*+CI | BBa_K2598038 | red light sensor composite Cph8*+repressor CI |
| YF1+fixJ+PhlF | BBa_K2598039 | blue light sensor YF1+fixJ(regulator to YF1)+repressor PhIF |
| T3+BFP | BBa_K2598040 | sigma fragment T3+a blue fluorescent protein BFP |
| CGG+GFP | BBa_K2598041 | sigma fragmentCGG+a green fluorescent protein GFP |
| K1F+mRFP | BBa_K2598042 | sigma fragment K1F+a red fluorescent protein mRFP |
| amilCP+amilGFP | BBa_K2598043 | promoter+amilCP+amilGFP+terminator. We use this part to mix color |
| amilCP+eforRed | BBa_K2598044 | promoter+amilCP+eforRed+terminator. We use this part to mix color |
| amilCP+fwyellow | BBa_K2598045 | fwYellow is a yellow chromoprotein. Here is promoter+amilCP+fwYellow+terminator. We use this part to mix color |
| amilGFP+eforRed | BBa_K2598046 | promoter+amilGFP+eforRed+terminator. We use this part to mix color. |
| amilGFP+fwyellow | BBa_K2598047 | promoter+amilGFP+fwYellow+terminator. We use this part to mix color |
| eforRed+fwyellow | BBa_K2598048 | promoter+eforRed+fwYellow+terminator. We use this part to mix color |
| pJFR1 (KX011464) | 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 |
| pJFR2 (KX011465) | BBa_K2598050 | This plasmid contains three RBSs, sigma fragment CGG, sigma fragment T3 and repressor PhIF regulated by 3 promoters, PcpcG2-172, PPhlF, PfixK2 respectively |
| pJFR3 (KX011466) | BBa_K2598051 | This part contains repressor CI and sigma fragment K1F regulated by PompC1157 and Pλ promoters |
| pJFR5 (KX011468) | BBa_K2598052 | This plasmid encodes three kinds of enzymes, including gusA, lacZ and bFMO |
| pJFR4 (KX011467) | 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. |
| amilGFP | BBa_K2598055 | amilGFP is a yellow chromoprotein improved from green fluorescent protein. Here is promoter+amilGFP+terminator |
| eforRed | BBa_K2598056 | eforRed is a red chromoprotein. Here is promoter+eforRed+terminator |
| amilCP | BBa_K2598057 | amilCP is a blue chromoprotein . Here is promoter+amilCP+terminator |
| amilCP+amilGFP+eforRed | BBa_K2598061 | promoter+amilCP+amilGFP+eforRed+terminator. We use this part to mix color |
| rain+mint+lemon | BBa_K2598062 | PCGG+rain+terminator+PK1F+lemon+terminator+PT3+mint+terminator |
