Template:Team:Bonn:NetworkData
From 2013.igem.org
(Difference between revisions)
Line 239: | Line 239: | ||
content.childs=[]; | content.childs=[]; | ||
content.titleShort = "Other systems"; | content.titleShort = "Other systems"; | ||
- | content.titleLong = " | + | content.titleLong = "Other systems"; |
content.summary= "More systems"; | content.summary= "More systems"; | ||
content.text= "More systems"; | content.text= "More systems"; | ||
Line 264: | Line 264: | ||
content.parents=[17]; | content.parents=[17]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort="Chemical"; | + | content.titleShort="Chemical Induction"; |
- | content.titleLong="Chemical | + | content.titleLong="Chemical Induction"; |
content.summary= "A review on chemical induction and its advantages and disadvantages"; | content.summary= "A review on chemical induction and its advantages and disadvantages"; | ||
content.text= "Chemical induction can be used to provide both expressional and structural changes in proteins.<sup><a href=#321>32.1</a></sup><sup><a href=#322>32.2</a></sup> As an advantage it is highly reliable and tunable which renders it very useful for ensuring constant expression levels.<sup><a href=#321>32.1</a></sup> Several promoters such as pBad which is inducible with arabinose or pLac which is inducible with IPTG are frequently used for such purpose.<sup><a href=#326>32.6</a></sup> Yet changes in protein expression require large timescales i.e. tens of minutes to hours, whereas structural changes such as dimerization (for example rapamycin induced dimerization of FRB and FKBP12<sup><a href=#324>32.4</a></sup>) occur much faster i.e. seconds to minutes.<sup><a href=#322>32.2</a></sup> <div class='content-image' align='center'><a href='https://static.igem.org/mediawiki/2013/8/8c/BonnRapamycin3D.jpg'><img src='https://static.igem.org/mediawiki/2013/8/8c/BonnRapamycin3D.jpg' height=260 width=260></a></br><i>A 3D Structure of a Rapamycin induced FKBP-FRB heteromer<sup><a href='#327'>32.7</a></sup></i></div> However compared to other methods of induction such temporal resolution is inferior. Additionally there are several problems arising from the use of chemical agents. Firstly to come into effect any molecule has to penetrate the cell membrane thus either being actively ingested by the cell or diffusing passively through it, which becomes a severe hindrance when none of these requirements are met.<sup><a href=#324>32.4</a></sup> Secondly any chemical can be bioactive and hence interfere with the cells metabolism or other substances.<sup><a href=#321>32.1</a></sup> Also specificity can be a problem especially in vivo, where often several cell types in multicellular organisms are effected. <sup><a href=#325>32.5</a></sup> Sub cellular spatial resolution can be difficult to achieve since molecules are subject to diffusion. It can be concluded that spatiotemporal resolution is low in chemically induced systems. <div class='content-image' align='center'><a href=https://static.igem.org/mediawiki/2013/0/0f/BonnLacOperon.jpg><img src='https://static.igem.org/mediawiki/2013/0/0f/BonnLacOperon.jpg' height=260 width=260></a></br><i>The Lac Operon: Origin of the Lac1 Promoter</i></div> <h2>References:</h2> <p><a name=321>32.1</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16554/'>J. Keith Joung, Elizabeth I. Ramm, and Carl O. Pabo: <i>A bacterial two-hybrid selection system for studying protein–DNA and protein–protein interactions.</i> "PNAS" (June 2000)</a></p> <p><a name=322>32.2</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368803/'>Takafumi Miyamoto, Robert DeRose, Allison Suarez, Tasuku Ueno, Melinda Chen, Tai-ping Sun, Michael J. Wolfgang, Chandrani Mukherjee, David J. Meyers, and Takanari Inoue: <i>Rapid and Orthogonal Logic Gating with a Gibberellin-induced Dimerization System. </i>"Nature chemical biology" 8, 465–470 (2012) </a></p> <p><a name=323>32.3</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724991/'>Adilson José da Silva, Antonio Carlos Luperni Horta, Ana Maria Velez, Mônica Rosas C Iemma, Cíntia Regina Sargo, Raquel LC Giordano, Maria Teresa M Novo, Roberto C Giordano, and Teresa Cristina Zangirolami: <i>Non-conventional induction strategies for production of subunit swine erysipelas vaccine antigen in rE. coli fed-batch cultures</i> "Springerplus"2, 322 (2013)</a></p> <p><a name=324>32.4</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133816/'>Andrei V. Karginov, Yan Zou, David Shirvanyants, Pradeep Kota, Nikolay V. Dokholyan, Douglas D. Young, Klaus M. Hahn, and Alexander Deiters: <i>Light-regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP </i>"Journal of the American Chemical Society" 133(3) 420-423 (2011)</a></p> <p><a name=325>32.5</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529099/'>Yuan Mei and Feng Zhang:<i>Molecular Tools and Approaches for Optogenetics</i> "Biological Psychatry"(2012)</a></p> <p><a name=326>32.6</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711423/'>Jarno Mäkelä, Meenakshisundaram Kandhavelu, Samuel M. D. Oliveira, Jerome G. Chandraseelan, Jason Lloyd-Price, Juha Peltonen, Olli Yli-Harja and Andre S. Ribeiro:<i> In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter</i> "Nucleic Acids Research" (2013) </a></p><p><a name='327'>32.7</a><a href='http://www.ncbi.nlm.nih.gov/pubmed/10089303'>Liang J, Choi J, Clardy J.:Refined structure of the FKBP12-rapamycin-FRB ternary complex at 2.2 A resolution."Acta crystallographica"(1999)</a></p>"; | content.text= "Chemical induction can be used to provide both expressional and structural changes in proteins.<sup><a href=#321>32.1</a></sup><sup><a href=#322>32.2</a></sup> As an advantage it is highly reliable and tunable which renders it very useful for ensuring constant expression levels.<sup><a href=#321>32.1</a></sup> Several promoters such as pBad which is inducible with arabinose or pLac which is inducible with IPTG are frequently used for such purpose.<sup><a href=#326>32.6</a></sup> Yet changes in protein expression require large timescales i.e. tens of minutes to hours, whereas structural changes such as dimerization (for example rapamycin induced dimerization of FRB and FKBP12<sup><a href=#324>32.4</a></sup>) occur much faster i.e. seconds to minutes.<sup><a href=#322>32.2</a></sup> <div class='content-image' align='center'><a href='https://static.igem.org/mediawiki/2013/8/8c/BonnRapamycin3D.jpg'><img src='https://static.igem.org/mediawiki/2013/8/8c/BonnRapamycin3D.jpg' height=260 width=260></a></br><i>A 3D Structure of a Rapamycin induced FKBP-FRB heteromer<sup><a href='#327'>32.7</a></sup></i></div> However compared to other methods of induction such temporal resolution is inferior. Additionally there are several problems arising from the use of chemical agents. Firstly to come into effect any molecule has to penetrate the cell membrane thus either being actively ingested by the cell or diffusing passively through it, which becomes a severe hindrance when none of these requirements are met.<sup><a href=#324>32.4</a></sup> Secondly any chemical can be bioactive and hence interfere with the cells metabolism or other substances.<sup><a href=#321>32.1</a></sup> Also specificity can be a problem especially in vivo, where often several cell types in multicellular organisms are effected. <sup><a href=#325>32.5</a></sup> Sub cellular spatial resolution can be difficult to achieve since molecules are subject to diffusion. It can be concluded that spatiotemporal resolution is low in chemically induced systems. <div class='content-image' align='center'><a href=https://static.igem.org/mediawiki/2013/0/0f/BonnLacOperon.jpg><img src='https://static.igem.org/mediawiki/2013/0/0f/BonnLacOperon.jpg' height=260 width=260></a></br><i>The Lac Operon: Origin of the Lac1 Promoter</i></div> <h2>References:</h2> <p><a name=321>32.1</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16554/'>J. Keith Joung, Elizabeth I. Ramm, and Carl O. Pabo: <i>A bacterial two-hybrid selection system for studying protein–DNA and protein–protein interactions.</i> "PNAS" (June 2000)</a></p> <p><a name=322>32.2</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368803/'>Takafumi Miyamoto, Robert DeRose, Allison Suarez, Tasuku Ueno, Melinda Chen, Tai-ping Sun, Michael J. Wolfgang, Chandrani Mukherjee, David J. Meyers, and Takanari Inoue: <i>Rapid and Orthogonal Logic Gating with a Gibberellin-induced Dimerization System. </i>"Nature chemical biology" 8, 465–470 (2012) </a></p> <p><a name=323>32.3</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724991/'>Adilson José da Silva, Antonio Carlos Luperni Horta, Ana Maria Velez, Mônica Rosas C Iemma, Cíntia Regina Sargo, Raquel LC Giordano, Maria Teresa M Novo, Roberto C Giordano, and Teresa Cristina Zangirolami: <i>Non-conventional induction strategies for production of subunit swine erysipelas vaccine antigen in rE. coli fed-batch cultures</i> "Springerplus"2, 322 (2013)</a></p> <p><a name=324>32.4</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133816/'>Andrei V. Karginov, Yan Zou, David Shirvanyants, Pradeep Kota, Nikolay V. Dokholyan, Douglas D. Young, Klaus M. Hahn, and Alexander Deiters: <i>Light-regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP </i>"Journal of the American Chemical Society" 133(3) 420-423 (2011)</a></p> <p><a name=325>32.5</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529099/'>Yuan Mei and Feng Zhang:<i>Molecular Tools and Approaches for Optogenetics</i> "Biological Psychatry"(2012)</a></p> <p><a name=326>32.6</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711423/'>Jarno Mäkelä, Meenakshisundaram Kandhavelu, Samuel M. D. Oliveira, Jerome G. Chandraseelan, Jason Lloyd-Price, Juha Peltonen, Olli Yli-Harja and Andre S. Ribeiro:<i> In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter</i> "Nucleic Acids Research" (2013) </a></p><p><a name='327'>32.7</a><a href='http://www.ncbi.nlm.nih.gov/pubmed/10089303'>Liang J, Choi J, Clardy J.:Refined structure of the FKBP12-rapamycin-FRB ternary complex at 2.2 A resolution."Acta crystallographica"(1999)</a></p>"; | ||
Line 291: | Line 291: | ||
content.parents=[17]; | content.parents=[17]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = "Electrical"; | + | content.titleShort = "Electrical Induction"; |
content.titleLong = "Electrical Induction"; | content.titleLong = "Electrical Induction"; | ||
content.summary= "A review on chemical induction and its advantages and disadvantages"; | content.summary= "A review on chemical induction and its advantages and disadvantages"; | ||
Line 376: | Line 376: | ||
content.parents=[74]; | content.parents=[74]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = " | + | content.titleShort = "SspBα"; |
content.titleLong = "C. crescentus sspBα"; | content.titleLong = "C. crescentus sspBα"; | ||
content.summary= "This article deals with the structure of sspBα and conformational details of its binding to ssrA and ClpXP during tethering."; | content.summary= "This article deals with the structure of sspBα and conformational details of its binding to ssrA and ClpXP during tethering."; | ||
Line 401: | Line 401: | ||
content.parents=[74]; | content.parents=[74]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = " | + | content.titleShort = "SsrA"; |
content.titleLong = "C. crescentus ssrA and its application in E. coli"; | content.titleLong = "C. crescentus ssrA and its application in E. coli"; | ||
content.summary= "Proteins that need to be degraded by the ClpXP protease have to be tagged with the ssrA peptide previosly. Here is some information on the structure of ssrA."; | content.summary= "Proteins that need to be degraded by the ClpXP protease have to be tagged with the ssrA peptide previosly. Here is some information on the structure of ssrA."; | ||
Line 427: | Line 427: | ||
content.parents=[45]; | content.parents=[45]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = " | + | content.titleShort = "Speed"; |
- | content.titleLong = " | + | content.titleLong = "Speed"; |
content.summary= "Due to the use of the protease system protein regulation is fast"; | content.summary= "Due to the use of the protease system protein regulation is fast"; | ||
content.text= ""; | content.text= ""; | ||
Line 440: | Line 440: | ||
content.parents=[45]; | content.parents=[45]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = " | + | content.titleShort = "General applicability"; |
- | content.titleLong = " | + | content.titleLong = "General applicability"; |
content.summary= "Since the system is commonly used and reliable its easily applicable to a wide variety of proteins"; | content.summary= "Since the system is commonly used and reliable its easily applicable to a wide variety of proteins"; | ||
content.text= ""; | content.text= ""; | ||
Line 453: | Line 453: | ||
content.parents=[45]; | content.parents=[45]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = " | + | content.titleShort = "Low influence"; |
- | content.titleLong = " | + | content.titleLong = "Low influence on proteins"; |
content.summary= "Fusing only a 15Aa small tag to the desired protein leads to low influence on its native function"; | content.summary= "Fusing only a 15Aa small tag to the desired protein leads to low influence on its native function"; | ||
content.text= ""; | content.text= ""; | ||
Line 466: | Line 466: | ||
content.parents=[45]; | content.parents=[45]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = " | + | content.titleShort = "Temporal control"; |
- | content.titleLong = " | + | content.titleLong = "Temporal control"; |
content.summary= "Using light easily makes a temporal specific control of activation possible"; | content.summary= "Using light easily makes a temporal specific control of activation possible"; | ||
content.text= ""; | content.text= ""; | ||
Line 479: | Line 479: | ||
content.parents=[45]; | content.parents=[45]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = " | + | content.titleShort = "Spatial control"; |
- | content.titleLong = " | + | content.titleLong = "Spatial control"; |
content.summary= "High spatial control can be achieved easily by local irradation with light"; | content.summary= "High spatial control can be achieved easily by local irradation with light"; | ||
content.text= ""; | content.text= ""; | ||
Line 491: | Line 491: | ||
content.parents=[45]; | content.parents=[45]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = " | + | content.titleShort = "Great activity difference"; |
- | content.titleLong = " | + | content.titleLong = "Great activity difference"; |
content.summary= "Degradation of the protein leads to a great difference of activity"; | content.summary= "Degradation of the protein leads to a great difference of activity"; | ||
content.text= ""; | content.text= ""; | ||
Line 637: | Line 637: | ||
content.parents=[37]; | content.parents=[37]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = " | + | content.titleShort = "Generated plasmids"; |
- | content.titleLong = " | + | content.titleLong = "Generated plasmids"; |
content.summary= ""; | content.summary= ""; | ||
content.text=""; | content.text=""; | ||
Line 674: | Line 674: | ||
content.childs=[]; | content.childs=[]; | ||
content.titleShort = "ccdA/ccdB"; | content.titleShort = "ccdA/ccdB"; | ||
- | content.titleLong = " | + | content.titleLong = "The ccd toxin-antitoxin system"; |
content.summary= "this is a summary6"; | content.summary= "this is a summary6"; | ||
content.text= "The ccd module is a toxin-antitoxin (TA) system similar to the mazE/mazF system. The module is located on the F Plasmid in Escherichia coli bacteria and essential for their survival. Normally the toxin ccdB is inactivated by the presence of the antitoxin ccdA in the form of a ccdAB complex. If ccdA is no longer available, ccdB inhibits DNA gyrase which leads to cell death. Gyrase is a type IIA topoisomerase and is able to produce negative DNA supercoiling by making a double-strand break in the DNA and religating it. The gyrase enzyme consists of two subunits: the C-terminal GyrA domain that wraps around the DNA strand and the N-terminal GyrB domain that catalyses the ATP-dependant supercoiling of the DNA. CcdB stabilizes the gyrase cleavage complex by binding to the GyrA domain and thus blocks the catalytic function of the gyrase. That means that the gyrase remains bound to the DNA and the cleaved DNA is not religated. DNA- and RNA polymerases can’t copy the DNA anymore and cell proliferation as well as protein biosynthesis is stopped. The double-stranded breaks in the DNA initiate cell death.<p>Because gyrases are specific to bacteria such as E. coli it is also a target for some anti-bacterial medications e.g. ciprofloxacin (CFX). As can be seen in the data below, CcdB proves to be as effective as CFX at inducing DNA cleavage <sup><a href=#681>68.1</a></sup><sup> <a href=#682>68.2</a></sup></p><div class='content-image'align='center'><img src='https://static.igem.org/mediawiki/2013/2/2f/Sspb_CFX_compared.jpg' width='300'>Comparison of the effect of CcdB and CFX on gyrase activity. N: negatively supercoiled DNA, L: linear DNA, SC: supercoiled DNA. A higher concentration of CcdB/CFX leads to more cleaved (linear) DNA<sup><a href= http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635281/figure/fig2/>[source]</a></sup></div><div class='content-image' align='center'><img src='https://static.igem.org/mediawiki/2013/e/e4/Bonn_Ccdb_and_ccda.jpg' width='300'> A higher concentration of ccdB leads to blocking of gyrase and positively supercoiled DNA is cleaved to linear DNA instead of being processed to negatively supercoiled DNA. <sup><a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460896/figure/pone-0046499-g003/>[source]</a></sup></div><p>We used this system to build a light-induced kill-switch. Therefore we added the ssrA tag to the antitoxin ccdA. When the bacteria a emitted to light, ccdA is degraded and ccdB is set free and can bind to the gyrase. and cell death is initiated. Like in most TA systems, the toxin ccdB is relatively stable, while the antitoxin ccdA is vulnerable to degradation.</p><h2>References</h2><p><a name=681>68.1</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635281/'>A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site, Andrew B. Smith and Anthony Maxwell, Nucleic Acids Res. 2006 October; 34(17): 4667–4676, PMC 1635281</a></p><p><a name=682>68.2</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460896/'> A Common Origin for the Bacterial Toxin-Antitoxin Systems parD and ccd, Suggested by Analyses of Toxin/Target and Toxin/Antitoxin Interactions, Andew B. Smith et al, PLoS One. 2012; 7(9): e46499, PMCID: PMC3460896</a></p>"; | content.text= "The ccd module is a toxin-antitoxin (TA) system similar to the mazE/mazF system. The module is located on the F Plasmid in Escherichia coli bacteria and essential for their survival. Normally the toxin ccdB is inactivated by the presence of the antitoxin ccdA in the form of a ccdAB complex. If ccdA is no longer available, ccdB inhibits DNA gyrase which leads to cell death. Gyrase is a type IIA topoisomerase and is able to produce negative DNA supercoiling by making a double-strand break in the DNA and religating it. The gyrase enzyme consists of two subunits: the C-terminal GyrA domain that wraps around the DNA strand and the N-terminal GyrB domain that catalyses the ATP-dependant supercoiling of the DNA. CcdB stabilizes the gyrase cleavage complex by binding to the GyrA domain and thus blocks the catalytic function of the gyrase. That means that the gyrase remains bound to the DNA and the cleaved DNA is not religated. DNA- and RNA polymerases can’t copy the DNA anymore and cell proliferation as well as protein biosynthesis is stopped. The double-stranded breaks in the DNA initiate cell death.<p>Because gyrases are specific to bacteria such as E. coli it is also a target for some anti-bacterial medications e.g. ciprofloxacin (CFX). As can be seen in the data below, CcdB proves to be as effective as CFX at inducing DNA cleavage <sup><a href=#681>68.1</a></sup><sup> <a href=#682>68.2</a></sup></p><div class='content-image'align='center'><img src='https://static.igem.org/mediawiki/2013/2/2f/Sspb_CFX_compared.jpg' width='300'>Comparison of the effect of CcdB and CFX on gyrase activity. N: negatively supercoiled DNA, L: linear DNA, SC: supercoiled DNA. A higher concentration of CcdB/CFX leads to more cleaved (linear) DNA<sup><a href= http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635281/figure/fig2/>[source]</a></sup></div><div class='content-image' align='center'><img src='https://static.igem.org/mediawiki/2013/e/e4/Bonn_Ccdb_and_ccda.jpg' width='300'> A higher concentration of ccdB leads to blocking of gyrase and positively supercoiled DNA is cleaved to linear DNA instead of being processed to negatively supercoiled DNA. <sup><a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460896/figure/pone-0046499-g003/>[source]</a></sup></div><p>We used this system to build a light-induced kill-switch. Therefore we added the ssrA tag to the antitoxin ccdA. When the bacteria a emitted to light, ccdA is degraded and ccdB is set free and can bind to the gyrase. and cell death is initiated. Like in most TA systems, the toxin ccdB is relatively stable, while the antitoxin ccdA is vulnerable to degradation.</p><h2>References</h2><p><a name=681>68.1</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635281/'>A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site, Andrew B. Smith and Anthony Maxwell, Nucleic Acids Res. 2006 October; 34(17): 4667–4676, PMC 1635281</a></p><p><a name=682>68.2</a> <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460896/'> A Common Origin for the Bacterial Toxin-Antitoxin Systems parD and ccd, Suggested by Analyses of Toxin/Target and Toxin/Antitoxin Interactions, Andew B. Smith et al, PLoS One. 2012; 7(9): e46499, PMCID: PMC3460896</a></p>"; | ||
Line 744: | Line 744: | ||
content.parents=[40]; | content.parents=[40]; | ||
content.childs=[42,44]; | content.childs=[42,44]; | ||
- | content.titleShort = "ssrA and | + | content.titleShort = "ssrA and SspBα"; |
- | content.titleLong = "Introduction to C. crescentus ssrA and | + | content.titleLong = "Introduction to C. crescentus ssrA and SspBα"; |
content.summary= "This article gives a brief overview of the roles of ssrA and sspBα for specific function of the ClpXP protease system in C. crescentus."; | content.summary= "This article gives a brief overview of the roles of ssrA and sspBα for specific function of the ClpXP protease system in C. crescentus."; | ||
content.text= "ssrA and sspB are peptides that mediate proteolysis via the ClpXP protease system in bacteria. In this article and the related articles, focus is laid on their orthologs in C. crescentus, being referred to as <sup>Cc</sup>ssrA and <sup>Cc</sup>sspBα, respectively, omitting <sup>Cc</sup> when obvious out of context. The ClpXP protease has an important function in regulation of the cell division cycle by effective proteolysis of short-lived regulatory proteins.</br>A protein which needs to be degraded will be tagged with the amino acid peptide <sup>Cc</sup>ssrA, which is added at its C-terminus during translation. <sup><a href=#741>74.1</a>, <a href=#742>74.2</a></sup> The ClpX subunit of the ClpXP protease recognizes the ssrA tag by specific binding and unfolds the tagged protein, in which ATP is hydrolyzed. In C. crescentus, the ssrA tag has a length of 14 amino acids, while the E. coli ortholog is only eleven amino acids long. </br>sspBα is a dimeric protein that serves as a tether which brings the ssrA-tagged protein and the ClpXP protease together and therefore accelerates protein degradation. It simultaneously binds to both the ssrA tag and the ClpX subunit and in this way brings the tagged protein in close contact with the protease. </br></br><h2>References</h2></br><a name=741>74.1</a> <a href='http://www.ncbi.nlm.nih.gov/pubmed/11535833'>Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis, Flynn et al., Proceedings of the National Academy of Sciences of the United States of America, 2001, PMID: 11535833</a></br><a name=742>74.2</a> <a href='http://www.ncbi.nlm.nih.gov/pubmed/17937918'> Structure and substrate specificity of an SspB ortholog: design implications for AAA+ adaptors, Chien et al., Cell Press, 2007, PMID: 17937918</a>"; | content.text= "ssrA and sspB are peptides that mediate proteolysis via the ClpXP protease system in bacteria. In this article and the related articles, focus is laid on their orthologs in C. crescentus, being referred to as <sup>Cc</sup>ssrA and <sup>Cc</sup>sspBα, respectively, omitting <sup>Cc</sup> when obvious out of context. The ClpXP protease has an important function in regulation of the cell division cycle by effective proteolysis of short-lived regulatory proteins.</br>A protein which needs to be degraded will be tagged with the amino acid peptide <sup>Cc</sup>ssrA, which is added at its C-terminus during translation. <sup><a href=#741>74.1</a>, <a href=#742>74.2</a></sup> The ClpX subunit of the ClpXP protease recognizes the ssrA tag by specific binding and unfolds the tagged protein, in which ATP is hydrolyzed. In C. crescentus, the ssrA tag has a length of 14 amino acids, while the E. coli ortholog is only eleven amino acids long. </br>sspBα is a dimeric protein that serves as a tether which brings the ssrA-tagged protein and the ClpXP protease together and therefore accelerates protein degradation. It simultaneously binds to both the ssrA tag and the ClpX subunit and in this way brings the tagged protein in close contact with the protease. </br></br><h2>References</h2></br><a name=741>74.1</a> <a href='http://www.ncbi.nlm.nih.gov/pubmed/11535833'>Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis, Flynn et al., Proceedings of the National Academy of Sciences of the United States of America, 2001, PMID: 11535833</a></br><a name=742>74.2</a> <a href='http://www.ncbi.nlm.nih.gov/pubmed/17937918'> Structure and substrate specificity of an SspB ortholog: design implications for AAA+ adaptors, Chien et al., Cell Press, 2007, PMID: 17937918</a>"; | ||
Line 788: | Line 788: | ||
content.parents=[101]; | content.parents=[101]; | ||
content.childs=[]; | content.childs=[]; | ||
- | content.titleShort = " | + | content.titleShort = "Biocom congress Berlin"; |
- | content.titleLong = " | + | content.titleLong = "Biocom congress Berlin"; |
content.summary= "our day in Berlin. We met important people and other iGEM teams"; | content.summary= "our day in Berlin. We met important people and other iGEM teams"; | ||
- | content.text= "iGEM Bonn 2013 was invited to join the Biocom AG | + | content.text= "iGEM Bonn 2013 was invited to join the Biocom AG congress "Biotechnologie 2020+" (biotechnology 2020+) in Berlin on June 27th. We gladly accepted this invitation, as it presented us with a chance to get in touch with all the other german iGEM teams and gain from the feedback the professional audience could give us on our ideas.</br></br>Among the attendees were directors and leading scientists of Max-Planck and Fraunhofer institutes, and also government representatives. Their response not only to our ideas but also to the design of our poster was very positive, with some criticism regarding the lack of self-gathered data confirming the functionality of the system. Some of the more applianceoriented scientists pointed our thinkings about possible applications towards new directions such as pro-drug design and specific location targeting.</br></br>At least as rewarding was the chance to talk to members of other iGEM teams. Was it a talk with the more experienced to learn about new techniques, or a chat with the less experienced during which we could share our own knowledge, one could always either give or gain valuable knowledge. In the end, we believe most iGEM teams, us very much included, found the meeting to have been an inspiring and fun possibility to improve on their own projects. <table><tr><th><div class='content-image'><img src='https://2013.igem.org/File:Bonn_Berlin_Niklas.JPG'>Niklas (left) in a discussion with a member of team Darmstadt</div></th><th><div class='content-image'><img src='https://2013.igem.org/File:Bonn_Poster_Berlin.JPG'>Our Poster for the congress</th><th><div class='content-image'><img src='https://2013.igem.org/File:Bonn_Berlin_Poster_Media.JPG'>Our Poster in place</div></th></tr><tr><th><div class='content-image'><img src='https://2013.igem.org/File:Bonn_Berlin_Poster_explanation_Max.JPG'></th><div class='content-image'><img src='https://2013.igem.org/File:Bonn_Berlin_all_the_iGEMs.JPG'></tr></table>"; |
content.type="Human Practice"; | content.type="Human Practice"; | ||
break; | break; |
Revision as of 01:28, 5 October 2013