Difference between revisions of "Team:HZAU-China/Description"

 
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{{HZAU-China}}
 
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</head>
 
</head>
  
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<body id="jianrong">
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<body>
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   <div class="HZAU_2017_menu">
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   <div class="HZAU_div_main">
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     <img src="https://static.igem.org/mediawiki/2017/8/8e/HZAU_2017_background_1.png" class="beijin">
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     <a class="HZAU_title">Description</a>
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     <ul class="daohang">
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     <a class="zhengwen_disblock">The chromosome replication of bacteria can be divided into three phases: B C and D</a>
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      <li id="HZAU_menu_1">
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         <a class="yinzhu" href="#yinwen_jiaozheng">$^{[1-3]}$</a>
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         <a href="#" id="bianse_1">Background</a>
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        <a class="zhengwen_disblock">, and meanwhile multi-rounds of replication exist simultaneously in one cell</a>
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      </li>
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         <a class="yinzhu" href="#yinwen_jiaozheng">$^{[1]}$</a>
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      <li id="HZAU_menu_2">
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        <a class="zhengwen_disblock">. So both the replication phase and the copy number of chromosome are heterogeneous in a culture.</a>
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         <a href="#item2_1" id="bianse_2">Information</a>
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    <div>
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      </li>
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       <label for="HZAUmenu-toggle" class="zhengwen" style="font-weight:bold;">To know more about replication
−
       <li id="HZAU_menu_3">
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        <span class="caret_black"></span>
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        <a href="#item3_1" id="bianse_3">Why light control</a>
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      </label>
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      </li>
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      <input type="checkbox" id="HZAUmenu-toggle" />
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    </ul>
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       <ul id="HZAUmenu">
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  </div>
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        <a class="zhengwen">The replication process of E. coli can be divided into three phases; phase B, phase C and phase D. Phase B is also called
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  <div class="HZAU_content wrap">
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          pre-replication phase, in which cells are preparing for DNA replication, like G1 phase of eukaryotes. Phase C is also
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    <div class="item" id="item1">
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          called replication phase, in which the genome is under replication, corresponding to phase S in eukaryotic cell cycle.
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       <a class="biaoti">Description</a>
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          The last phase D, of course, is called post-replication phase, in which chromosome separates and one cell divides
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      <a class="zhengwen">In the long history of life evolution, different species living in different environment developed the most adaptive
+
          into two, corresponding to G2 and M phases in eukaryotes. Among the three phases, C and D are relatively constant,
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        surviving mechanism for them under the selection pressure, among which some unmatchable become widly preserved in
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          about 40 min and 20 min separately, so when to initiate a replication determines the whole cell cycle. Recent work
−
        different creatures, and the mechanism of replication is one of them. The majority of prokaryote share the same mechanism
+
          revealed a relationship between replication initiation and cell volume, but many details still remain unknown.
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        of self-replication including DNA replication, chromosome seperation and cell division. These three parts comprised
+
          What we know is that a protein, DnaA, plays an important role in this process. DnaA is a versatile protein possessing
−
        the whole cell cycle, and the main model creature for researching the replication process is E.coli, which at the
+
          many different functions related to cell cycle, among which the most important one is to attach to the OriC,
−
        same time is the main object of our project.</a>
+
          the origins of chromosome replication, and initiates replication. So controlling cell cycle by interrupting the
 +
          attachment of DnaA and the corresponding DNA sequence with dCas9 is an efficient approach.
 +
          <br>
 +
        </a>
 +
        <a  class="zhengwen">The whole cell cycles of eukaryotes and prokaryotes show a certain similarity, but there is difference between them.
 +
          The cell cycle of prokaryotes can overlap, which means the next round of replication initiates before the last
 +
          replication complete, while eukaryotic cell cycle initiates one after another. Experiments have shown that even
 +
          an isogenic bacteria growing in the same culture show differences in both replication phase and genome copy numbers
 +
          and this becomes a huge noise when constructing the 3D genome structure and building up a circuit related to genome
 +
          . Besides, the development of synthetic biology requires a system to control the reproduction of engineered
 +
          organisms. So we believe that our project would be a useful tool no matter in theoretical areas or application
 +
          areas.</a>
 +
      </ul>
 
     </div>
 
     </div>
−
     <img src="https://static.igem.org/mediawiki/2017/b/bc/HZAU_2017_tu1_1.png" class="tu_1">
+
     <img src="https://static.igem.org/mediawiki/2017/4/44/T--HZAU-China--BCDperiod.png" class="tu_1">
−
 
+
     <img src="https://static.igem.org/mediawiki/2017/1/19/T--HZAU-China--description_Figure2.png" class="tu_2">
−
     <div class="item" id="item2">
+
    <a class="zhengwen_disblock">Our project is inspired by the research about constructing 4D genomes of eukaryotes. We wonder why there isn’t a
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       <div id="item2_1" class="jiaozheng"></div>
+
       4D genome project of prokaryote. After investigation we find that due to the complicated mechanisms of bacteria chromosome replication, there will be a huge noise while detecting its chromosome structure, which hinders the research on prokaryotic 4D genome
−
      <a class="zhengwen">The replication process of E.coli replication can be devided into phase B,C and D, three phases. Phase B, also called
+
    </a>
−
        pre-replication phase, is for DNA replication proparation similar as G1 phase in eukaryote cell cycle. Phase C is
+
    <a class="yinzhu" href="#yinwen_jiaozheng">$^{[4]}$</a>
−
        regarded as replication phase during which the chromosome is replicating corespond to the S phase in eukaryote. The
+
    <a class="zhengwen_disblock">. </a>
−
        last phase, phase D, is called post-replication phase, in which the behave of chromosome seperation and cell division
+
    <a class="zhengwen_disblock">Besides, the heterogenicity of cells are gathering more and more attentions in different fields, like industrial fermentation,
−
        happend just like what happened in G2 and M phase of eukaryote cells. the time of C phase and D phase in a generation
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      antidrug resistance research and synthetic biology</a>
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        is relative constant, so what actually determines the cell cycle is the initiation of genome replication. We know
+
    <a class="yinzhu" href="#yinwen_jiaozheng">$^{[5-7]}$</a>
−
        that cell have to garantee that each cell should have at least one chormosome, and this requires a highly coordination
+
    <a class="zhengwen_disblock">.</a>
−
        between DNA replication and cell divsion. Though the delicate mechanism of the corrdination is still a puzzle, it
+
    <img src="https://static.igem.org/mediawiki/2017/a/a6/T--HZAU-China--computorHand.png" class="tu_3">
−
        is clear that DnaA protein plays a significant role in this event. DnaA is a versatile protein, it can not only behave
+
    <a class="zhengwen">Therefore, we begin to think if there could be a method to eliminate the heterogeneity. When thinking deeper into this
−
        like a helicase opening the duble-helix of replication initiation site, OriC, while have the function of raising
+
      problem, it becomes interesting that what would happen if all the cells are synchronized, will there be a new phenomenon
−
        other proteins forming into the replisome to prolong the replication, but also can anchor the replicationg choromosome
+
      that can change the traditional opinions?
−
        on the cell membrane leading the following seperation of chromosome. But what makes it the linker between replication
+
      In our mind, the ideal synchronization methods should not only simply inhibit the cell cycle but at the same time
−
        and division is that its concentration determines the initiation volume of replication. So according to these information,
+
      can free the inhibition according to our requirements. As we all know, the manipulation of machine is much more accurate
−
        we think that regulating the combination of DNA and DnaA protein will be an efficient method to regulate cell replication.
+
      than living beings, and there is a trend to let machine help us to control the organisms, so we want our synchronization
−
        <a href="">For more information please click here.</a>
+
      system can also be controlled by machine and program.</a>   
−
       </a>
+
    <a class="zhengwen">
 +
      <br>
 +
    </a>
 +
    <div>
 +
      <div id="yinwen_jiaozheng" class="jiaozheng">
 +
       </div>
 
     </div>
 
     </div>
−
     <img src="https://static.igem.org/mediawiki/2017/5/51/HZAU_2017_tu2_1.png" class="tu_2">
+
     <a class="biaoti">References</a>
−
 
+
     <a class="yinwen">1. Helmstetter CE. DNA synthesis during the division cycle of rapidly growing Escherichia coli B/r. J Mol Biol. 1968
−
     <div class="item" id="item3">
+
       Feb;31(3) 507-518. doi:10.1016/0022-2836(68)90424-5.</a>
−
       <div id="item3_1" class="jiaozheng"></div>
+
    <a class="yinwen">2. Skarstad K, Steen HB, Boye E. Cell cycle parameters of slowly growing Escherichia coli B/r studied by flow cytometry.
−
      <a class="zhengwen">There will be about 1h for an entire genome replication, but cell division can reach about 20min per generation. this
+
      J Bacteriol. 1983 May;154(2) 656-662.</a>
−
        reflects the multi-copy number of bacterial genome and only with this mechanism can E.coli reproduce in such a high
+
    <a class="yinwen">3. Umbarger, M. A., Toro, E., Wright, M. A., Porreca, G. J., Bau, D., Hong, S. H., . . . Church, G. M. (2011). The three-dimensional
−
        speed. what's worse is that even isogenic cells grow in the same culture have a scattering distribution not only
+
      architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell, 44(2), 252-264.
−
        in phase but also in genome copy number. the strong heterogenic in cell cycle and genome copy number hinds the 3D
+
    </a>
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        genome research and may be a potential noise on genome gene expression. At the same time, the developing synthetic
+
    <a class="yinwen">4. Paalme, T., Tiisma, K., Kahru, A., Vanatalu, K. & Vilu, R. Glucose-limited fed-batch cultivation of Escherichia coli
−
        biology requires an approach that can control cell reproduction and can be easily incorporated into circuits, so
+
      with computer-controlled fixed growth rate. Biotechnol. Bioeng. 35, 312–319 (1990).</a>
−
        that the whole system can be more safe and controlable. taking these into consider, we decided to use CRISPRi to
+
     <a class="yinwen">5. Baumgart, Leo & Mather, William & Hasty, Jeff. (2017). Synchronized DNA cycling across a bacterial population. Nature
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        inhibit its cell cycle, for more details please see design.</a>
+
      Genetics. 49. . 10.1038/ng.3915.</a>
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        <br>
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  </div>
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      <a class="zhengwen">But barely pause the replication in some circumstance can't satisfy our needs, and long time inhibition will prolong
+
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        its length, so there is a need to totally control its replication, not only block but also open. with that purpose
+
−
        we decided to use optogentic to control this system, and the operablity of light to computer makes our system programable,
+
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        which can be called 4C.</a>
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Latest revision as of 12:27, 28 November 2017

Description The chromosome replication of bacteria can be divided into three phases: B C and D $^{[1-3]}$ , and meanwhile multi-rounds of replication exist simultaneously in one cell $^{[1]}$ . So both the replication phase and the copy number of chromosome are heterogeneous in a culture.
Our project is inspired by the research about constructing 4D genomes of eukaryotes. We wonder why there isn’t a 4D genome project of prokaryote. After investigation we find that due to the complicated mechanisms of bacteria chromosome replication, there will be a huge noise while detecting its chromosome structure, which hinders the research on prokaryotic 4D genome $^{[4]}$ . Besides, the heterogenicity of cells are gathering more and more attentions in different fields, like industrial fermentation, antidrug resistance research and synthetic biology $^{[5-7]}$ . Therefore, we begin to think if there could be a method to eliminate the heterogeneity. When thinking deeper into this problem, it becomes interesting that what would happen if all the cells are synchronized, will there be a new phenomenon that can change the traditional opinions? In our mind, the ideal synchronization methods should not only simply inhibit the cell cycle but at the same time can free the inhibition according to our requirements. As we all know, the manipulation of machine is much more accurate than living beings, and there is a trend to let machine help us to control the organisms, so we want our synchronization system can also be controlled by machine and program.
References 1. Helmstetter CE. DNA synthesis during the division cycle of rapidly growing Escherichia coli B/r. J Mol Biol. 1968 Feb;31(3) 507-518. doi:10.1016/0022-2836(68)90424-5. 2. Skarstad K, Steen HB, Boye E. Cell cycle parameters of slowly growing Escherichia coli B/r studied by flow cytometry. J Bacteriol. 1983 May;154(2) 656-662. 3. Umbarger, M. A., Toro, E., Wright, M. A., Porreca, G. J., Bau, D., Hong, S. H., . . . Church, G. M. (2011). The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell, 44(2), 252-264. 4. Paalme, T., Tiisma, K., Kahru, A., Vanatalu, K. & Vilu, R. Glucose-limited fed-batch cultivation of Escherichia coli with computer-controlled fixed growth rate. Biotechnol. Bioeng. 35, 312–319 (1990). 5. Baumgart, Leo & Mather, William & Hasty, Jeff. (2017). Synchronized DNA cycling across a bacterial population. Nature Genetics. 49. . 10.1038/ng.3915.