Difference between revisions of "Part:BBa K1639002"
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GadE have three main activation mechanisms. The first of these is performed by evgA and ydeO. About GadE activation phase: | GadE have three main activation mechanisms. The first of these is performed by evgA and ydeO. About GadE activation phase: | ||
| − | '''1.'''EvgS (sensor kinase) activate EvgA (response regulator) | + | <br>'''1.'''EvgS (sensor kinase) activate EvgA (response regulator) |
| − | '''2.'''YdeO and evgA are independently from each other and GadE takes an active role in transcription activation. | + | <br>'''2.'''YdeO and evgA are independently from each other and GadE takes an active role in transcription activation. |
The second GadE activation circuit includes CRP,RpoS and two AraC-like regulators, GadXand GadW. | The second GadE activation circuit includes CRP,RpoS and two AraC-like regulators, GadXand GadW. | ||
These steps are as follows: | These steps are as follows: | ||
| − | '''1.'''GadX and GadW, are located downstream of gadA also GadX and GadW directly activate transcription of gadE | + | <br>'''1.'''GadX and GadW, are located downstream of gadA also GadX and GadW directly activate transcription of gadE |
| − | '''2.'''GadX and GadW also bind to the gadA and gadBC gad box sequences and seem to repress the gadA and gadBC promoters. (4) GadW inhibits this GadX’s repression Also GadX and GadW regulate indirectly GadA/BC transcriptional functions. | + | <br>'''2.'''GadX and GadW also bind to the gadA and gadBC gad box sequences and seem to repress the gadA and gadBC promoters. (4) GadW inhibits this GadX’s repression Also GadX and GadW regulate indirectly GadA/BC transcriptional functions. |
| − | '''3.'''The balance of power in this circuit is influenced by cAMP and CRP,which together inhibit the synthesis of RpoS. Growth under acidic conditions reduces the concentration of cAMP in the cell. RpoS increases GadX’s transcriptional function The increase in GadX then stimulates transcription of GadE and also down regulates GadW. | + | <br>'''3.'''The balance of power in this circuit is influenced by cAMP and CRP,which together inhibit the synthesis of RpoS. Growth under acidic conditions reduces the concentration of cAMP in the cell. RpoS increases GadX’s transcriptional function The increase in GadX then stimulates transcription of GadE and also down regulates GadW. |
The third activation of GadE contains TrmE and glucose. These steps are as follows: | The third activation of GadE contains TrmE and glucose. These steps are as follows: | ||
| − | '''1.'''The function of TrmE in the cell is not fully defined but it does have a clear effect on tRNA modification | + | <br>'''1.'''The function of TrmE in the cell is not fully defined but it does have a clear effect on tRNA modification |
| − | '''2.'''TrmE and glucose increase independently GadE’s transcriptional function | + | <br>'''2.'''TrmE and glucose increase independently GadE’s transcriptional function |
We discourse GadE’s regulation and then now we will discourse GadE’s effect mechanisms. GadA/BC’s effect mechanisms to acid resistance are as follows: | We discourse GadE’s regulation and then now we will discourse GadE’s effect mechanisms. GadA/BC’s effect mechanisms to acid resistance are as follows: | ||
'''1.'''The external pH is normally neutral but if external pH turns to acidic pH, internal pH begins to become acidic pH with HCl diffusion. | '''1.'''The external pH is normally neutral but if external pH turns to acidic pH, internal pH begins to become acidic pH with HCl diffusion. | ||
| − | '''2.'''If the external pH=2,5 and internal pH begins pH=4.2 ± 0.1. GDAR system will activate for acid resistance. | + | <br>'''2.'''If the external pH=2,5 and internal pH begins pH=4.2 ± 0.1. GDAR system will activate for acid resistance. |
| − | '''3.'''GadC is a transmembrane protein. The external pH begins to change from neutral pH to acidic pH, C-plug (is GadC’s subunit) will open. Then glutamate will take inside. | + | <br>'''3.'''GadC is a transmembrane protein. The external pH begins to change from neutral pH to acidic pH, C-plug (is GadC’s subunit) will open. Then glutamate will take inside. |
| − | [[File:ATOMS-Turkiye_ulcer_GadE_1.3.png|400px|thumb|left|]]'''4.'''Glutamate in cells convert to GABA by GadB/C that’s glutamate decarboxylase isozymes These steps are as follows: | + | [[File:ATOMS-Turkiye_ulcer_GadE_1.3.png|400px|thumb|left|]] |
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| + | '''4.'''Glutamate in cells convert to GABA by GadB/C that’s glutamate decarboxylase isozymes These steps are as follows: | ||
*This step contains pyridoxal phosphate-containing enzymes that replace the α-carboxyl groups of their amino acid substrates with a proton that is recruited from the cytoplasm. | *This step contains pyridoxal phosphate-containing enzymes that replace the α-carboxyl groups of their amino acid substrates with a proton that is recruited from the cytoplasm. | ||
*HCl that diffusion from outside dissociates H+ and Cl-. This H+ is used and CO² is released by the agency of GadA/B isozymes than this is the last stage of glutamate changes to GABA. Besides this is the most important and the last step for acid resistance. | *HCl that diffusion from outside dissociates H+ and Cl-. This H+ is used and CO² is released by the agency of GadA/B isozymes than this is the last stage of glutamate changes to GABA. Besides this is the most important and the last step for acid resistance. | ||
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[[File:ATOMS-Turkiye_ulcer_GadE_1.4.png|400px|thumb|right|]] | [[File:ATOMS-Turkiye_ulcer_GadE_1.4.png|400px|thumb|right|]] | ||
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| + | '''5.'''If H+ leaves HCl it is staying back Cl and it will be export from the transport of chlorine channel. | ||
| + | <br>'''6.'''The emitted CO² is taken out by diffusion. | ||
| + | <br>'''7.'''Finally, the uncovered GABA is thrown out from the transmembrane protein GadC.<br clear=all> | ||
<span class='h3bb'>Sequence and Features</span> | <span class='h3bb'>Sequence and Features</span> | ||
Revision as of 22:26, 20 September 2015
GadE
This part is activator of proteins responsible for acid resistance in E.coli. GadE is transcription factor of Gad operon and Gad operon express Glutamate Dependent Acid Resistance genes gadA, gadB, gadC.
Usage and Biology
Escherchia coli Natural Acid Resistance System E. coli possesses four phenotypically distinct systems of acid resistance. These systems: 1. Glutamate dependent acid resistance system (GDAR) 2. Arginine dependent acid resistance system (ADAR) 3. Lysine dependent acid resistance system (LDAR) 4. Ornithine dependent acid resistance system (ODAR)
The most effective one of these systems is the glutamate dependent system so we decided to focus on glutamate dependent system (GDAR).
The GDAR system has in the acid resistance complex pathways. We decided to do the certain pathways that how to do acid resistance with our results of research.
EvgA is the most effective positive regulator of GDAR. (Efficiency: evgA>ydeO>gadE) But evgA takes part in countless number different genes regulation and cellular processes (2,6,7) and also most of this cellular processes are unclear. We cannot predict the results of the overexpression of evgA so we chose gadE and using by overexpression of gadE we can induce glutamate depended acid resistance system.
Briefly talk about the impact of the GadE on the mechanism.
The central activator is the LuxR-family member GadE (formerly known as YhiE). GadE binds to a 20-bp sequence called the gad box, which is located 63-bp upstream of the transcriptional start sites of gadA and gadBC. (4)GadE and GadBox are an important point for GadA and GadBC. This means that GadE and GadBox are an important for acid resistance. The basis section of acid resistance is GadE’s regulation. At least 10 different regulatory take part in this regulation.
GadE have three main activation mechanisms. The first of these is performed by evgA and ydeO. About GadE activation phase:
1.EvgS (sensor kinase) activate EvgA (response regulator)
2.YdeO and evgA are independently from each other and GadE takes an active role in transcription activation.
The second GadE activation circuit includes CRP,RpoS and two AraC-like regulators, GadXand GadW.
These steps are as follows:
1.GadX and GadW, are located downstream of gadA also GadX and GadW directly activate transcription of gadE
2.GadX and GadW also bind to the gadA and gadBC gad box sequences and seem to repress the gadA and gadBC promoters. (4) GadW inhibits this GadX’s repression Also GadX and GadW regulate indirectly GadA/BC transcriptional functions.
3.The balance of power in this circuit is influenced by cAMP and CRP,which together inhibit the synthesis of RpoS. Growth under acidic conditions reduces the concentration of cAMP in the cell. RpoS increases GadX’s transcriptional function The increase in GadX then stimulates transcription of GadE and also down regulates GadW.
The third activation of GadE contains TrmE and glucose. These steps are as follows:
1.The function of TrmE in the cell is not fully defined but it does have a clear effect on tRNA modification
2.TrmE and glucose increase independently GadE’s transcriptional function
We discourse GadE’s regulation and then now we will discourse GadE’s effect mechanisms. GadA/BC’s effect mechanisms to acid resistance are as follows:
1.The external pH is normally neutral but if external pH turns to acidic pH, internal pH begins to become acidic pH with HCl diffusion.
2.If the external pH=2,5 and internal pH begins pH=4.2 ± 0.1. GDAR system will activate for acid resistance.
3.GadC is a transmembrane protein. The external pH begins to change from neutral pH to acidic pH, C-plug (is GadC’s subunit) will open. Then glutamate will take inside.
4.Glutamate in cells convert to GABA by GadB/C that’s glutamate decarboxylase isozymes These steps are as follows:
- This step contains pyridoxal phosphate-containing enzymes that replace the α-carboxyl groups of their amino acid substrates with a proton that is recruited from the cytoplasm.
- HCl that diffusion from outside dissociates H+ and Cl-. This H+ is used and CO² is released by the agency of GadA/B isozymes than this is the last stage of glutamate changes to GABA. Besides this is the most important and the last step for acid resistance.
5.If H+ leaves HCl it is staying back Cl and it will be export from the transport of chlorine channel.
6.The emitted CO² is taken out by diffusion.
7.Finally, the uncovered GABA is thrown out from the transmembrane protein GadC.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BamHI site found at 2
Illegal XhoI site found at 540 - 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]