Difference between revisions of "Team:Jilin China/Background"

 
(36 intermediate revisions by 5 users not shown)
Line 6: Line 6:
 
<style>
 
<style>
 
.s1{
 
.s1{
−
  background: url(https://static.igem.org/mediawiki/2018/f/f3/T--Jilin_China--Description--Banner.jpeg) no-repeat top left;
+
  background: url(https://static.igem.org/mediawiki/2018/a/a4/T--Jilin_China--Background--Banner.jpeg) no-repeat top left;
 
  background-size: cover;
 
  background-size: cover;
 
}
 
}
Line 54: Line 54:
 
   <table>
 
   <table>
 
   <tr>
 
   <tr>
−
     <td><a href="#pragraph_1" class="clickwave">Promoters</a></td>
+
     <td><a href="#pragraph_1" class="clickwave">Temperature Sensing</a></td>
 +
    <td><a href="#pragraph_1" class="clickwave">Biological Systems</a></td>
 
   </tr>
 
   </tr>
 
   </table>
 
   </table>
Line 64: Line 65:
 
   <!--<section class="s0"></section>-->
 
   <!--<section class="s0"></section>-->
 
   <ul class="sidenav">
 
   <ul class="sidenav">
−
   <li><a href="#pragraph_1">Temperature Sensing</a></li>
+
   <li><a href="#paragraph_1">Temperature Sensing</a></li>
−
   <li><a href="#pragraph_1"></a>Transduction Systems</li>
+
   <li><a href="#paragraph_2">Biological Systems</a></li>
 
   </ul>
 
   </ul>
 
   <section class="s2">
 
   <section class="s2">
 
   <ul>
 
   <ul>
−
     <li class="pragraph_1 start" id="pragraph_1">
+
     <li class="paragraph_1 start" id="paragraph_1">
 
     <div>
 
     <div>
−
       <h2>Sensing and responding to temperature is essential for bacterial survival</h2>
+
       <h2>Sensing and responding to temperature are essential for bacterial survival</h2>
−
       <p>There are always challenges for bacterial survival, especially to keep suitable living status facing fluctuations of chemical and physical parameters. The common chemical perturbations include sudden deprivation of nutrients or key metabolites and changes in surrounding pH. And the most representative physical deviation is temperature shift. But in most cases, the ambient temperature change is more essential for bacterial life cycle than chemical parameters, due to the efficiency of all cellular processes is temperature dependent, especially the expression of any given gene. Therefore, it’s indispensable for bacteria to evolve effective strategies , which can respond to temperature forwardly before the damages such as unfolded proteins or membrane rigidification occur.</p>
+
       <p>There are always challenges for bacterial survival, especially to keep suitable living status facing fluctuations of chemical and physical parameters<sup>[1]</sup>. The common chemical perturbations include sudden deprivation of nutrients or key metabolites and changes in surrounding pH，and the most representative physical deviation is temperature shift. But in most cases, the ambient temperature change is more essential for bacterial life cycle than chemical parameters, since the efficiency of all cellular processes is temperature dependent, especially the expression of any given gene<sup>[2,3]</sup>. Therefore, it is indispensable for bacteria to evolve more sensitive and more effective abilities, which can respond to temperature forwardly before the damages such as unfolded proteins or membrane rigidification occur<sup>[4]</sup> (figure 1).</p>
−
       <img src="https://static.igem.org/mediawiki/2018/a/a7/T--Jilin_China--Background--Physical_Chemical_Factor.svg" />
+
       <center><img src="https://static.igem.org/mediawiki/2018/a/a7/T--Jilin_China--Background--Physical_Chemical_Factor.svg" width="70%" /></center>
 +
      <p class="figure">Figure 1. To survival in the change of many physical and chemical parameters, bacteria have evolved many kinds of biosensors to respond to its surroundings.</p>
 
     </div>
 
     </div>
 
     </li>
 
     </li>
−
     <li class="pragraph_2" id="pragraph_2">
+
     <li class="paragraph_2" id="paragraph_2">
 
     <div>
 
     <div>
−
       <h2>Biological signal transduction systems that detect temperature shifts</h2>
+
       <h2>Biological signal transduction systems that sense temperature shifts</h2>
−
       <p>When it comes to the biological behavior of temperature sensing, it’s very important to elicit a proper response that could coordinate the expression of temperature-relevant genes. The common detecting systems in bacterial cells are based on three manners as following:</p>
+
       <p>When it comes to the biological behavior of temperature sensing, it is crucial to elicit a proper response that could coordinate the expression of temperature-relevant genes. The common detecting systems in bacterial cells are based on three manners as following:</p>
 
       <h3>1.Transcriptional level</h3>
 
       <h3>1.Transcriptional level</h3>
−
       <p>Temperature sensing through DNA involves local DNA topological change followed by transcriptional event. For example, the thesis of transcription factorσ32 in E.Coli increases rapidly when temperature upshift, which could mediate the transcription of genes that haveσ32 -recognizing promoters. But this regulatory pathway takes some time to come into effect because the thermosensing proteins required time for upregulation.</p>
+
       <p>Temperature sensing in this level involves local DNA topological change followed by transcriptional events. For example, the expression of transcription factor σ<sup>32</sup> in bacteria <i>E.coli</i> increases rapidly when temperature upshifts, which could mediate the transcription of genes including σ<sup>32</sup> -recognizing promoters<sup>[5]</sup>(figure 2). But this regulatory pathway takes some time to come into effect because the thermosensing proteins require time for upregulation<sup>[1]</sup>.</p>
−
       <center><img src="https://static.igem.org/mediawiki/2018/3/3c/T--Jilin_China--Background--Transcription.svg" /></center>
+
       <center><img src="https://static.igem.org/mediawiki/2018/3/3c/T--Jilin_China--Background--Transcription.svg" width="70%"/></center>
 +
      <p class="figure">Figure 2. The example of transcriptonal thermoregulation (1) Heat-induced up-regulation of transcription factor σ32. (2) σ32  recognizes the specific promoters and recruits the core enzyme of  RNA polymerase. (3) RNA polymerase consisting of core enzyme and  σ32  promotes the transcriptional initiation and elongation. (4) The heat-induced chaperones or proteases  are expressed increasingly.</p>
 
       <h3>2.Translational level</h3>
 
       <h3>2.Translational level</h3>
−
       <p>Temperature sensing also bases on many types of thermoregulatory RNA elements, also known for RNA-based thermosensors(RTSs), which are located in the 5’ untranslated region(5’ UTR) of mRNA. The 5’ UTR is a part of bacterial transcript of gene, which would not be translated into peptide. Therefore, RTSs are none-coding RNA elements. These types of thermoregulation respond to temperature and modulate the translation of already existing or nascent mRNAs, which could induce altered mRNA stability and ribosome accessibility of ribosome binding site(RBS) thereby controlling the translation efficiency.</p>
+
       <p>Temperature sensing also bases on many types of thermoregulatory RNA elements, also known for RNA-based thermosensors (RTs), which are located in the 5’ untranslated region (5’ UTR) of mRNA<sup>[6]</sup>. The 5’ UTR is a part of bacterial transcript of gene, which would not be translated into peptide. Therefore, RTs are none-coding RNA elements. These types of thermoregulation respond to temperature and modulate the translation of already existing or nascent mRNAs, which could induce altered mRNA stability and ribosome accessibility of ribosome binding site (RBS) thereby controlling the translation efficiency (figure 3).</p>
−
       <center><img src="https://static.igem.org/mediawiki/2018/a/a5/T--Jilin_China--Background--Translation.svg" /></center>
+
      <center><a href="https://2018.igem.org/Team:Jilin_China/Background2"><font size="4.5">>See more details about RTs，which are we focus on this year</font>.<</a></center>
 +
      <br>
 +
      <br>
 +
       <center><img src="https://static.igem.org/mediawiki/2018/a/a5/T--Jilin_China--Background--Translation.svg" width="70%" /></center>
 +
      <p class="figure">Figure 3. The example of translational thermoregulation (A) At low temperatures, the stem-loop in 5’- UTR of mRNA hides the SD sequence by base-paring with vicinal anti-SD sequence. Ribosome could not bind to RBS and the translation switches off.  (B) At high temperatures, the stem-loop melts, resulting the full liberation of the SD sequence and start codon. This conformational change promotes the entire ribosome accessibility of RBS. The translation switches on.</p>
 
       <h3>3.Post-translational level</h3>
 
       <h3>3.Post-translational level</h3>
−
       <p>Unfolded or incorrect protein conformation is the most example of the consequences of temperature-induced damages. When temperature upshifts, chaperone proteins that are overexpressed can promote nascent polypeptide chains to fold into correct conformation, which is known as post-translational thermoregulation. But this process is more similar to lock the barn door after the horse was stolen, meaning cellular processes have already been altered due to temperature shifts.</p>
+
       <p>Unfolded or misfolded protein conformations are the most common example of the consequences of temperature-induced damages. When temperature upshifts, chaperone proteins that are overexpressed can promote nascent polypeptide chains to fold into correct conformation, which is known as post-translational thermoregulation<sup>[7,8]</sup>(figure 4). But this process is more like to lock the barn door after the horse was stolen, which means cellular processes have already been altered due to temperature shifts.</p>
−
       <center><img src="https://static.igem.org/mediawiki/2018/c/c0/T--Jilin_China--Background--Post_Translation.svg" /></center>
+
       <center><img src="https://static.igem.org/mediawiki/2018/d/d3/T--Jilin_China--BG-fig4.svg" width="60%" /></center>
 +
      <p class="figure">Figure 4. The example of post-translational thermoregulation. (1) Heat-induced unfolding or misfolding of protein. (2) Heat-induced up-regulation of chaperones. (3) The increased chaperones bind to peptides. (4) Chaperones help peptides fold into correct conformations. </p>
 +
    </div>
 +
    </li>
 +
    <li class="reference" id="paragraph_3">
 +
    <div>
 +
      <h2>References</h2>
 +
      <ul>
 +
      <li>[1]Kortmann J, Narberhaus F. Bacterial RNA thermometers: molecular zippers and switches.[J]. Nature Reviews Microbiology, 2012, 10(4):255-65.</li>
 +
      <li>[2]Abduljalil J M. Bacterial riboswitches and RNA thermometers: Nature and contributions to pathogenesis[J]. Non-coding RNA Research, 2018, 3(2):54-63.</li>
 +
      <li>[3]Angel E. Garcia,† and, Dietmar Paschek‡. Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin[J]. Journal of the American Chemical Society, 2008, 130(3):815-7.</li>
 +
      <li>[4]Inaba M, Suzuki I, Szalontai B, et al. Gene-engineered Rigidification of Membrane Lipids Enhances the Cold Inducibility of Gene Expression in Synechocystis[J]. Journal of Biological Chemistry, 2003, 278(14):12191.</li>
 +
      <li>[5]Guisbert E, Yura T, Rhodius V A, et al. Convergence of molecular, modeling, and systems approaches for an understanding of the <i>Escherichia coli</i> heat shock response.[J]. Microbiology & Molecular Biology Reviews Mmbr, 2008, 72(3):545-54.</li>
 +
      <li>[6]Grosso-Becera M V, Servín-González L, Soberón-Chávez G. RNA structures are involved in the thermoregulation of bacterial virulence-associated traits[J]. Trends in Microbiology, 2015, 23(8):509-518.</li>
 +
      <li>[7]Tomoyasu T, Ogura T, Tatsuta T, et al. Levels of DnaK and DnaJ provide tight control of heat shock gene expression and protein repair in <i>Escherichia coli</i>[J]. Molecular Microbiology, 2010, 30(3):567-581.</li>
 +
      <li>[8]Langer T, Lu C, Echols H, et al. Successive action of DnaK, DnaJ and GroEL along the pathway of chaperone-mediated protein folding.[J]. Nature, 1992, 356(6371):683-689.</li>
 +
      </ul>
 
     </div>
 
     </div>
 
     </li>
 
     </li>

Latest revision as of 20:13, 17 October 2018

BACKGROUND
Thermoregulation


Temperature Sensing Biological Systems

Overview

  • Sensing and responding to temperature are essential for bacterial survival

    There are always challenges for bacterial survival, especially to keep suitable living status facing fluctuations of chemical and physical parameters[1]. The common chemical perturbations include sudden deprivation of nutrients or key metabolites and changes in surrounding pH，and the most representative physical deviation is temperature shift. But in most cases, the ambient temperature change is more essential for bacterial life cycle than chemical parameters, since the efficiency of all cellular processes is temperature dependent, especially the expression of any given gene[2,3]. Therefore, it is indispensable for bacteria to evolve more sensitive and more effective abilities, which can respond to temperature forwardly before the damages such as unfolded proteins or membrane rigidification occur[4] (figure 1).

    Figure 1. To survival in the change of many physical and chemical parameters, bacteria have evolved many kinds of biosensors to respond to its surroundings.

  • Biological signal transduction systems that sense temperature shifts

    When it comes to the biological behavior of temperature sensing, it is crucial to elicit a proper response that could coordinate the expression of temperature-relevant genes. The common detecting systems in bacterial cells are based on three manners as following:

    1.Transcriptional level

    Temperature sensing in this level involves local DNA topological change followed by transcriptional events. For example, the expression of transcription factor σ32 in bacteria E.coli increases rapidly when temperature upshifts, which could mediate the transcription of genes including σ32 -recognizing promoters[5](figure 2). But this regulatory pathway takes some time to come into effect because the thermosensing proteins require time for upregulation[1].

    Figure 2. The example of transcriptonal thermoregulation (1) Heat-induced up-regulation of transcription factor σ32. (2) σ32 recognizes the specific promoters and recruits the core enzyme of RNA polymerase. (3) RNA polymerase consisting of core enzyme and σ32 promotes the transcriptional initiation and elongation. (4) The heat-induced chaperones or proteases are expressed increasingly.

    2.Translational level

    Temperature sensing also bases on many types of thermoregulatory RNA elements, also known for RNA-based thermosensors (RTs), which are located in the 5’ untranslated region (5’ UTR) of mRNA[6]. The 5’ UTR is a part of bacterial transcript of gene, which would not be translated into peptide. Therefore, RTs are none-coding RNA elements. These types of thermoregulation respond to temperature and modulate the translation of already existing or nascent mRNAs, which could induce altered mRNA stability and ribosome accessibility of ribosome binding site (RBS) thereby controlling the translation efficiency (figure 3).

    >See more details about RTs，which are we focus on this year.<


    Figure 3. The example of translational thermoregulation (A) At low temperatures, the stem-loop in 5’- UTR of mRNA hides the SD sequence by base-paring with vicinal anti-SD sequence. Ribosome could not bind to RBS and the translation switches off. (B) At high temperatures, the stem-loop melts, resulting the full liberation of the SD sequence and start codon. This conformational change promotes the entire ribosome accessibility of RBS. The translation switches on.

    3.Post-translational level

    Unfolded or misfolded protein conformations are the most common example of the consequences of temperature-induced damages. When temperature upshifts, chaperone proteins that are overexpressed can promote nascent polypeptide chains to fold into correct conformation, which is known as post-translational thermoregulation[7,8](figure 4). But this process is more like to lock the barn door after the horse was stolen, which means cellular processes have already been altered due to temperature shifts.

    Figure 4. The example of post-translational thermoregulation. (1) Heat-induced unfolding or misfolding of protein. (2) Heat-induced up-regulation of chaperones. (3) The increased chaperones bind to peptides. (4) Chaperones help peptides fold into correct conformations.

  • References

    • [1]Kortmann J, Narberhaus F. Bacterial RNA thermometers: molecular zippers and switches.[J]. Nature Reviews Microbiology, 2012, 10(4):255-65.
    • [2]Abduljalil J M. Bacterial riboswitches and RNA thermometers: Nature and contributions to pathogenesis[J]. Non-coding RNA Research, 2018, 3(2):54-63.
    • [3]Angel E. Garcia,† and, Dietmar Paschek‡. Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin[J]. Journal of the American Chemical Society, 2008, 130(3):815-7.
    • [4]Inaba M, Suzuki I, Szalontai B, et al. Gene-engineered Rigidification of Membrane Lipids Enhances the Cold Inducibility of Gene Expression in Synechocystis[J]. Journal of Biological Chemistry, 2003, 278(14):12191.
    • [5]Guisbert E, Yura T, Rhodius V A, et al. Convergence of molecular, modeling, and systems approaches for an understanding of the Escherichia coli heat shock response.[J]. Microbiology & Molecular Biology Reviews Mmbr, 2008, 72(3):545-54.
    • [6]Grosso-Becera M V, Servín-González L, Soberón-Chávez G. RNA structures are involved in the thermoregulation of bacterial virulence-associated traits[J]. Trends in Microbiology, 2015, 23(8):509-518.
    • [7]Tomoyasu T, Ogura T, Tatsuta T, et al. Levels of DnaK and DnaJ provide tight control of heat shock gene expression and protein repair in Escherichia coli[J]. Molecular Microbiology, 2010, 30(3):567-581.
    • [8]Langer T, Lu C, Echols H, et al. Successive action of DnaK, DnaJ and GroEL along the pathway of chaperone-mediated protein folding.[J]. Nature, 1992, 356(6371):683-689.