Difference between revisions of "Part:BBa K2505004"
 
(17 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
 
 
__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K2505004 short</partinfo>
 
<partinfo>BBa_K2505004 short</partinfo>
−
 
−
<span style="margin-left: 25px;">This gene codes complete iP synthesis enzymes. This gene was introduced to human cell, EA.hy926 cell and produces iP as a signaling molecule. atipt4 gene and log1 gene is derived from <i>A.thaliana</i>, optimized for <i>H.sapiens</i> codon in reference to the codon usage. AtIPT4 is an enzyme(adenylate dimethylallyltransferase [EC:2.5.1.112]: cytokinin synthase) that necessary for a synthesis of iP(isopentenyl adenine: kind of cytokinin). LOG1 is an enzyme(putative lysine decarboxylase family) that necessary for maturation of iP precursor.
 
−
 
−
===Characterization===
 
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here
−
===Usage and Biology===
+
 
  
 
<!-- -->
 
<!-- -->
Line 19: Line 14:
 
<partinfo>BBa_K2505004 parameters</partinfo>
 
<partinfo>BBa_K2505004 parameters</partinfo>
 
<!-- -->
 
<!-- -->
 +
 +
 +
These two genes(<i>atipt4</i> and <i>log1</i>) are derived from <i>Arabidopsis thaliana</i> and encode enzymes necessary for synthesizing iP (isopentenyladenine) in mammalian cells. iP is a kind of cytokinins that are signaling molecules (Phytohormones) in plants and play important roles in cell growth and differentiation. When these genes are introduced to human cells, EA.hy926, the cells produce iP heterologously. The DNA sequences of these genes are optimized for expressing in human cells considering the codon usage. AtIPT4 has the adenylate dimethylallyltransferase ('''[http://www.genome.jp/dbget-bin/www_bget?ec:2.5.1.112 [EC:2.5.1.112] ]''': cytokinin synthase) activity and catalyzes the transfer of an isopentenyl group from dimethylallyl diphosphate (DMAPP) to ATP and ADP, producing cytokinin nucleotides. Note that cytokinin nucleotides are the immature form. LOG1 has the phosphoribohydrolase activity and converts inactive cytokinin nucleotides to the biologically active free-base forms.
 +
 +
IVS (intervining sequence) is one kind of introns and is important for increasing the mRNA stability in eukaryotic cells. IRES (internal ribosome entry site) is an RNA element that allows translation initiation in a cap-independent mannerThe term “polyA” indicates the polyadenylation signal that  is important for the nuclear export, translation, and stability of mRNA.
 +
<p>The DNA sequences of these genes(<i>atipt4</i> and <i>log1</i>) are optimized for expressing in human cells considering the codon usage.</p>
 +
 +
 +
<html>
 +
</p>
 +
</html>
 +
__TOC__
 +
==Characterization==
 +
In this assay, we investigated whether human cells (the EA.hy926 cell line) receive AHL, a signaling molecule that is synthesized in and exported from E. coli and induce the transcription of <i>atIPT4</i> and <i>log1</i> genes to synthesize iP.
 +
 +
AHLs, which stand for [N-]acyl-homoserine lactones, are small signaling molecules and are employed in the bacterial “Quorum Sensing”. Among several kinds of AHLs, 3OC8HSL (C8) was chosen in the assay.
 +
 +
In order to achieve C8-dependent transcription in human cells, a chimeric transcription factor named RelA/NLS/<i>traR</i> was constructed. This protein is comprised of the transcription activating domain of RelA (a kind of human NF-kB family), nuclear localization signal (NLS), and full-length <i>traR</i>. This protein can bind to an appropriate enhancer sequence to activate transcription only in the presence of C8 (see below for details).
 +
 +
Isopentenyladenine (iP) is kind of a cytokinin, and we use it as a signal molecule from human to E. coli cells and for the inter-kingdom communication. Cytokinins are the signaling molecules (or Phytohormones) that plants produce and play important roles in cell growth and differentiation. In the case of <i>Arabidopsis thaliana</i>, extracellular iP is received by a transmembrane receptor, AHK4.
 +
 +
AHK4 has a histidine kinase activity, and binding of iP to AHK4 triggers auto-phosphorylation of AHK4 and the following histidine-to-aspartate phosphorelay. As a consequence, transcription from target genes is induced and/or repressed so that physiological states of plants are changed.
 +
Surprisingly, the histidine kinase activity of AHK4 has shown to be activated depending on iP even in E. coli cells (Suzuki et al. 2001, Lukáš Spíchal et al. 2004). This fact encouraged us to use iP as a signaling molecule in our project (See the AHK4 assay page).
 +
 +
==Result==
 +
The transformed cells were treated or not treated with different concentrations of C8. Then, the mRNA level of <i>atIPT4</i> and <i>log1</i> was analyzed using quantitative RT-PCR. As shown in Figure 1, the CMV minimal promoter was activated following the addition of C8.
 +
[[File:Tokyo_Tech_humancell result.png|thumb|left|600px| '''Figure 1:''' '''Result of the quantitative RT-PCR''' <br style="clear: both" />The term“Cont”means the control cells that are not electroporated, while “EP” means the electroporated cells. the concentrations of C8 used are indicated blow the bars. ]]<br>
 +
<br style="clear: both" />
 +
==Discussion==
 +
We confirmed that the transcription of <i>atIPT4</i> and <i>log1</i>) genes were induced by C8 addition and the degree of induction depends on C8 concentration.
 +
 +
==Material and Method==
 +
===Plasmids===
 +
* Sample
 +
<span style="margin-left: 20px;">pCAG-<i>relA</i>/NLS/<i>traR</i>-polyA (pMC1neo-polyA)
 +
 +
<span style="margin-left: 20px;">(trabox)7-CMVmin-<i>atIPT4</i>-IVS-IRES-<i>log1</i>-polyA(pIRESneo3)
 +
 +
===Construction===
 +
*Cell line
 +
<span style="margin-left: 20px;">All the plasmids were prepared in <i>Homo sapiens</i> EA.hy926 cell line.
 +
 +
===Medium===
 +
*DMEM 10% FBS
 +
*DMEM 10% FBS G418 (400 μg/mL)
 +
 +
===The primers for quantitative RT-PCR===
 +
*<i>atIPT4</i>
 +
Forward: 5’- gtgcaacgacaaaatggtgg-3’
 +
Reverse: 3’-cctgaagatcacgaccaatcg-5’
 +
 +
*<i>log1</i>
 +
Forward: 5’-ggactgatctctcaggctgtg-3’
 +
Reverse: 3’-cggtagcagatatgcatcagc-5’
 +
 +
 +
===Protocol===
 +
1. The EA.hy 926 cells were cultured to about 1.0 * 10<sup>7</sup> cells/dish (the dish size is 10 cm in diameter) and used for electroporation.
 +
 +
2. C8 was added to the dish at final concentration of 0, 20, or 40 μM and incubated further for 24 hours.
 +
 +
3. After harvesting the cells, total RNAs were purified according to the ordinary AGPC (Acid guanidinium thiocyanate-phenol-chloroform) method, and cDNAs were obtained by reverse transcription(Table. 1).
 +
 +
4. qPCR was performed using the above cDNA(Table. 2).
 +
 +
[[File:Tokyo_Tech_transcription.png|thumb|left|250px| '''Table 1''': '''Mixture components of Reverse transcription''' <br style="clear: both" />After mixing, samples were heated at 42° C. for 20 min, 99 ° C. for 5 min, 4 ° C. for 5 min, then stored at -20 ° C. ]]<br>
 +
[[File:Tokyo_Tech_qPCR.png|thumb|righit|250px| '''Table 2''': '''Mixture components of qPCR''' <br style="clear: both" />※SYBR：KAPA SYBR FAST qPCR kit ]]<br>
 +
<br style="clear: both" />
 +
 +
===AGPC methods===
 +
①Vortex the collected cells in the tube for 10 to 15 sec.
 +
 +
②Add 1/10 volume of Na acetate.
 +
 +
③Add 1.4-times volume of Phenol/Chloroform/Isoamyl alcohol.
 +
 +
④Vortex every 10 minutes.
 +
 +
⑤Centrifuge at 15000 rpm, 10 min, 4 ° C.
 +
 +
⑥Recover the aqueous layer and mix with 400 uL isopropanol.
 +
 +
⑦Leave at -20 ° C for 1 hour.
 +
 +
⑧Centrifuge at 15000 rpm, 10 min, 4 ° C and remove supernatant.
 +
 +
⑨Add 400 uL of 75% ethanol, centrifuge at 15000 rpm, 10 min, 4 ° C and remove supernatant.
 +
 +
⑩Dry the pellet and dissolve with 10 uL of pH = 7.4 TE buffer
 +
 +
 +
==Reference==
 +
Kakimoto, T. (2001) Identification of plant cytokinin biosynthetic enzymes as dimethylallyl diphosphate:ATP/ADP isopentenyltransferases. Plant Cell Physiol. 42:677-85.
 +
 +
Kakimoto, T. (2001) Identification of plant cytokinin biosynthetic enzymes as dimethylallyl diphosphate:ATP/ADP isopentenyltransferases. Plant Cell Physiol. 42:677-85.
 +
 +
Kurakawa, T., Ueda, N., Maekawa, M., Kobayashi, K., Kojima, M., Nagato, Y., ... Kyozuka, J. (2007). Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature, 445(7128), 652-655.
 +
 +
Suzuki, T., Miwa, K., Ishikawa, K., Yamada, H., Aiba, H. and Mizuno, T. (2001) The Arabidopsis Sensor His-kinase, AHK4, Can Respond to Cytokinins. Plant Cell Physiol. 42: 107-113.
 +
 +
Spíchal, L., Rakova, N.Y., Riefler, M., Mizuno, T., Romanov, G.A.,Strnad, M. and Schmülling, T. (2004) Two Cytokinin Receptors of Arabidopsis thaliana, CRE1/AHK4 and AHK3, Differ in their Ligand Specifity in a Bacterial Assay. Plant Cell Physiol. 45: 1299-1305.
 +
 +
Kurakawa, T., Ueda, N., Maekawa, M., Kobayashi, K., Kojima, M., Nagato, Y., ... Kyozuka, J. (2007). Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature, 445(7128), 652-655.
 +
 +
Suzuki, T., Miwa, K., Ishikawa, K., Yamada, H., Aiba, H. and Mizuno, T. (2001) The Arabidopsis Sensor His-kinase, AHK4, Can Respond to Cytokinins. Plant Cell Physiol. 42: 107-113.
 +
 +
Spíchal, L., Rakova, N.Y., Riefler, M., Mizuno, T., Romanov, G.A.,Strnad, M. and Schmülling, T. (2004) Two Cytokinin Receptors of Arabidopsis thaliana, CRE1/AHK4 and AHK3, Differ in their Ligand Specifity in a Bacterial Assay. Plant Cell Physiol. 45: 1299-1305.

Latest revision as of 18:24, 1 November 2017

atipt4-IVS-IRES-log1-polyA

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 1193
    Illegal XhoI site found at 2243
    Illegal XhoI site found at 2255
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 739
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 881



These two genes(atipt4 and log1) are derived from Arabidopsis thaliana and encode enzymes necessary for synthesizing iP (isopentenyladenine) in mammalian cells. iP is a kind of cytokinins that are signaling molecules (Phytohormones) in plants and play important roles in cell growth and differentiation. When these genes are introduced to human cells, EA.hy926, the cells produce iP heterologously. The DNA sequences of these genes are optimized for expressing in human cells considering the codon usage. AtIPT4 has the adenylate dimethylallyltransferase ([http://www.genome.jp/dbget-bin/www_bget?ec:2.5.1.112 [EC:2.5.1.112] ]: cytokinin synthase) activity and catalyzes the transfer of an isopentenyl group from dimethylallyl diphosphate (DMAPP) to ATP and ADP, producing cytokinin nucleotides. Note that cytokinin nucleotides are the immature form. LOG1 has the phosphoribohydrolase activity and converts inactive cytokinin nucleotides to the biologically active free-base forms.

IVS (intervining sequence) is one kind of introns and is important for increasing the mRNA stability in eukaryotic cells. IRES (internal ribosome entry site) is an RNA element that allows translation initiation in a cap-independent mannerThe term “polyA” indicates the polyadenylation signal that is important for the nuclear export, translation, and stability of mRNA.

The DNA sequences of these genes(atipt4 and log1) are optimized for expressing in human cells considering the codon usage.


Characterization

In this assay, we investigated whether human cells (the EA.hy926 cell line) receive AHL, a signaling molecule that is synthesized in and exported from E. coli and induce the transcription of atIPT4 and log1 genes to synthesize iP.

AHLs, which stand for [N-]acyl-homoserine lactones, are small signaling molecules and are employed in the bacterial “Quorum Sensing”. Among several kinds of AHLs, 3OC8HSL (C8) was chosen in the assay.

In order to achieve C8-dependent transcription in human cells, a chimeric transcription factor named RelA/NLS/traR was constructed. This protein is comprised of the transcription activating domain of RelA (a kind of human NF-kB family), nuclear localization signal (NLS), and full-length traR. This protein can bind to an appropriate enhancer sequence to activate transcription only in the presence of C8 (see below for details).

Isopentenyladenine (iP) is kind of a cytokinin, and we use it as a signal molecule from human to E. coli cells and for the inter-kingdom communication. Cytokinins are the signaling molecules (or Phytohormones) that plants produce and play important roles in cell growth and differentiation. In the case of Arabidopsis thaliana, extracellular iP is received by a transmembrane receptor, AHK4.

AHK4 has a histidine kinase activity, and binding of iP to AHK4 triggers auto-phosphorylation of AHK4 and the following histidine-to-aspartate phosphorelay. As a consequence, transcription from target genes is induced and/or repressed so that physiological states of plants are changed. Surprisingly, the histidine kinase activity of AHK4 has shown to be activated depending on iP even in E. coli cells (Suzuki et al. 2001, Lukáš Spíchal et al. 2004). This fact encouraged us to use iP as a signaling molecule in our project (See the AHK4 assay page).

Result

The transformed cells were treated or not treated with different concentrations of C8. Then, the mRNA level of atIPT4 and log1 was analyzed using quantitative RT-PCR. As shown in Figure 1, the CMV minimal promoter was activated following the addition of C8.

Figure 1: Result of the quantitative RT-PCR
The term“Cont”means the control cells that are not electroporated, while “EP” means the electroporated cells. the concentrations of C8 used are indicated blow the bars.


Discussion

We confirmed that the transcription of atIPT4 and log1) genes were induced by C8 addition and the degree of induction depends on C8 concentration.

Material and Method

Plasmids

  • Sample

pCAG-relA/NLS/traR-polyA (pMC1neo-polyA)

(trabox)7-CMVmin-atIPT4-IVS-IRES-log1-polyA(pIRESneo3)

Construction

  • Cell line

All the plasmids were prepared in Homo sapiens EA.hy926 cell line.

Medium

  • DMEM 10% FBS
  • DMEM 10% FBS G418 (400 μg/mL)

The primers for quantitative RT-PCR

  • atIPT4
Forward: 5’- gtgcaacgacaaaatggtgg-3’
Reverse: 3’-cctgaagatcacgaccaatcg-5’
  • log1
Forward: 5’-ggactgatctctcaggctgtg-3’
Reverse: 3’-cggtagcagatatgcatcagc-5’


Protocol

1. The EA.hy 926 cells were cultured to about 1.0 * 107 cells/dish (the dish size is 10 cm in diameter) and used for electroporation.

2. C8 was added to the dish at final concentration of 0, 20, or 40 μM and incubated further for 24 hours.

3. After harvesting the cells, total RNAs were purified according to the ordinary AGPC (Acid guanidinium thiocyanate-phenol-chloroform) method, and cDNAs were obtained by reverse transcription(Table. 1).

4. qPCR was performed using the above cDNA(Table. 2).

Table 1: Mixture components of Reverse transcription
After mixing, samples were heated at 42° C. for 20 min, 99 ° C. for 5 min, 4 ° C. for 5 min, then stored at -20 ° C.

Table 2: Mixture components of qPCR
※SYBR：KAPA SYBR FAST qPCR kit


AGPC methods

①Vortex the collected cells in the tube for 10 to 15 sec.

②Add 1/10 volume of Na acetate.

③Add 1.4-times volume of Phenol/Chloroform/Isoamyl alcohol.

④Vortex every 10 minutes.

⑤Centrifuge at 15000 rpm, 10 min, 4 ° C.

⑥Recover the aqueous layer and mix with 400 uL isopropanol.

⑦Leave at -20 ° C for 1 hour.

⑧Centrifuge at 15000 rpm, 10 min, 4 ° C and remove supernatant.

⑨Add 400 uL of 75% ethanol, centrifuge at 15000 rpm, 10 min, 4 ° C and remove supernatant.

⑩Dry the pellet and dissolve with 10 uL of pH = 7.4 TE buffer


Reference

Kakimoto, T. (2001) Identification of plant cytokinin biosynthetic enzymes as dimethylallyl diphosphate:ATP/ADP isopentenyltransferases. Plant Cell Physiol. 42:677-85.

Kakimoto, T. (2001) Identification of plant cytokinin biosynthetic enzymes as dimethylallyl diphosphate:ATP/ADP isopentenyltransferases. Plant Cell Physiol. 42:677-85.

Kurakawa, T., Ueda, N., Maekawa, M., Kobayashi, K., Kojima, M., Nagato, Y., ... Kyozuka, J. (2007). Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature, 445(7128), 652-655.

Suzuki, T., Miwa, K., Ishikawa, K., Yamada, H., Aiba, H. and Mizuno, T. (2001) The Arabidopsis Sensor His-kinase, AHK4, Can Respond to Cytokinins. Plant Cell Physiol. 42: 107-113.

Spíchal, L., Rakova, N.Y., Riefler, M., Mizuno, T., Romanov, G.A.,Strnad, M. and Schmülling, T. (2004) Two Cytokinin Receptors of Arabidopsis thaliana, CRE1/AHK4 and AHK3, Differ in their Ligand Specifity in a Bacterial Assay. Plant Cell Physiol. 45: 1299-1305.

Kurakawa, T., Ueda, N., Maekawa, M., Kobayashi, K., Kojima, M., Nagato, Y., ... Kyozuka, J. (2007). Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature, 445(7128), 652-655.

Suzuki, T., Miwa, K., Ishikawa, K., Yamada, H., Aiba, H. and Mizuno, T. (2001) The Arabidopsis Sensor His-kinase, AHK4, Can Respond to Cytokinins. Plant Cell Physiol. 42: 107-113.

Spíchal, L., Rakova, N.Y., Riefler, M., Mizuno, T., Romanov, G.A.,Strnad, M. and Schmülling, T. (2004) Two Cytokinin Receptors of Arabidopsis thaliana, CRE1/AHK4 and AHK3, Differ in their Ligand Specifity in a Bacterial Assay. Plant Cell Physiol. 45: 1299-1305.