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| | In <i>td</i> gene of T4 phage, there is the group 1 intron. A part of the RNA transcribed from the group 1 intron is a ribozyme which catalyzes a splicing reaction, and this RNA splices itself. | | In <i>td</i> gene of T4 phage, there is the group 1 intron. A part of the RNA transcribed from the group 1 intron is a ribozyme which catalyzes a splicing reaction, and this RNA splices itself. |
| | The circular mRNA can be expressed in <i>E. coli</i> by cloning a domain which functions as ribozyme for splicing of the <i>td</i> gene, and putting it in the plasmid. This method is called “PIE method.” | | The circular mRNA can be expressed in <i>E. coli</i> by cloning a domain which functions as ribozyme for splicing of the <i>td</i> gene, and putting it in the plasmid. This method is called “PIE method.” |
| − | The circular mRNA without the termination codon sequence can be used to synthesize protein semi-permanently.</p><br>
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| − | <p> We succeeded in expression of the circular mRNA, and synthesizing long chain protein last year. But the long chain protein synthesized in last year was not functional because its holding had lost shape. So, this year, we design a linker sequence and synthesize a functional long chain protein. On the other hand, the probability was just a few percent that the cyclization happens. It is thought that the ribozyme site of the splicing is far from the reactive site, and it lowers the probability. So we’ll design complemental sequence near the ribozyme site and the reactive site of splicing to make them accessible to each other, and raise the probability of the cyclization in the theme.</p>
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| − | | + | <p> In last year, we succeeded in designing the sequence which synthesizes circular mRNA and long chain protein in <i>Escherichia coli</i>. In this year, we had 2 purposes in our study.</p> |
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| − | <h4> <font size="5" face="Century"> ABSTRACT </font> </h4>
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| − | <p> In last year, we succeeded in designing the sequence which synthesizes circular mRNA and long chain protein in <i>Escherichia coli</i>.In this year, we had 2 purposes in our study.</p> | + | |
| | <p> One was an efficiency of the circularization. The efficiency was lower in our previous study. This was why the splicing was hard to happen because two sequences to act as ribozyme for splicing were far each other. So we incorporated complementary sequences around the ribozyme regions. We thought that the treatment brought two regions close and the efficiency of the circularization improved.</p> | | <p> One was an efficiency of the circularization. The efficiency was lower in our previous study. This was why the splicing was hard to happen because two sequences to act as ribozyme for splicing were far each other. So we incorporated complementary sequences around the ribozyme regions. We thought that the treatment brought two regions close and the efficiency of the circularization improved.</p> |
| | <p> The other was to synthesize useful proteins. In our previous study, synthesized long-chain proteins lose their function because the folding of the proteins was broken. So we incorporated linker sequences into circular mRNA to synthesize the functional long-chain protein.</p> | | <p> The other was to synthesize useful proteins. In our previous study, synthesized long-chain proteins lose their function because the folding of the proteins was broken. So we incorporated linker sequences into circular mRNA to synthesize the functional long-chain protein.</p> |
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| | <li><a href="#descri" style="text-decoration:none;" >DESCRIPTION </a></li> | | <li><a href="#descri" style="text-decoration:none;" >DESCRIPTION </a></li> |
| − | <li><a href="#abst"style="text-decoration:none;" >ABSTRACT </a></li>
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| | <li><a href="#ASS"style="text-decoration:none;" >About Self-Splicing </a></li> | | <li><a href="#ASS"style="text-decoration:none;" >About Self-Splicing </a></li> |
| | <li><a href="#PIE_M"style="text-decoration:none;" >PIE Method </a></li> | | <li><a href="#PIE_M"style="text-decoration:none;" >PIE Method </a></li> |
| | <li><a href="#experiments"style="text-decoration:none;" >Experiments </a></li> | | <li><a href="#experiments"style="text-decoration:none;" >Experiments </a></li> |
| − | <li><a href="#results"style="text-decoration:none;" >Results&Data analysis </a></li> | + | <li><a href="#results"style="text-decoration:none;" >RESULT& </a></li> |
| | + | <li><a href="#Mod"style="text-decoration:none;" >MODELING </a></li> |
| | <li><a href="#futurework"style="text-decoration:none;" >Future Works </a></li> | | <li><a href="#futurework"style="text-decoration:none;" >Future Works </a></li> |
| | <li><a href="#conclusions"style="text-decoration:none;" >Conclusions </a></li> | | <li><a href="#conclusions"style="text-decoration:none;" >Conclusions </a></li> |
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PROJECT
DESCRIPTION
This year, the theme of iGEM Gifu is to synthesize a long chain protein with circular mRNA. It is a sequel to our theme of the last year.
Here, we explain our theme of the last year.
The circular mRNA is expressed in E. coli by using a mechanism of self-splicing.
In td gene of T4 phage, there is the group 1 intron. A part of the RNA transcribed from the group 1 intron is a ribozyme which catalyzes a splicing reaction, and this RNA splices itself.
The circular mRNA can be expressed in E. coli by cloning a domain which functions as ribozyme for splicing of the td gene, and putting it in the plasmid. This method is called “PIE method.”
In last year, we succeeded in designing the sequence which synthesizes circular mRNA and long chain protein in Escherichia coli. In this year, we had 2 purposes in our study.
One was an efficiency of the circularization. The efficiency was lower in our previous study. This was why the splicing was hard to happen because two sequences to act as ribozyme for splicing were far each other. So we incorporated complementary sequences around the ribozyme regions. We thought that the treatment brought two regions close and the efficiency of the circularization improved.
The other was to synthesize useful proteins. In our previous study, synthesized long-chain proteins lose their function because the folding of the proteins was broken. So we incorporated linker sequences into circular mRNA to synthesize the functional long-chain protein.
About Self-Splicing
The group I intron in td gene of T4 phage has self-splicing mechanism. The self-splicing is a mechanism that circularizes the intron and connects exons. This is catalyzed by several base sequences of the ends of the introns as a ribozyme. We permuted exons and introns with the mechanism and attempted an exon circularization. So we constructed mRNA circularization devices in last year.
We explain the circularization mechanism of group I intron with td gene of T4 phage as an example. Td gene consists of an upstream exon, an upstream intron, an ORF, a downstream intron and a downstream exon. This mechanism is divided into 3 steps. As the first step, a nucleophilic attack by a guanosine separates the upstream exon from the upstream intron and then the guanosine bonds to the 5’ end of the upstream intron.
As the second step, the downstream exon is separated from the downstream intron by a nucleophilic attack. The nucleophilic attack takes place by a hydroxy group at the 3’ end of the upstream exon. (Figure 1)
Fig.2 Self-splicing in T4 phage: the first and second step (Blue: intron, Orange: exon)
As the third step, the upstream intron bonds to the downstream intron by an attack on an adenine of the upstream intron. The attack takes place by a hydroxyl group of an end of the downstream intron. And then a circular intron is formed.(Figure 2)
Fig.3 Self-splicing in T4 phage: the third step (Blue: intron, Orange: exon)
PIE Method
The PIE method is shown below(Figure 5). First, we picked out the intron and splice sites in the exon from td gene in T4 phage. Second, sandwich the sequence that you want to circularize between preceding fragments.
Fig.5 PIE method
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