Team:ESBS-Strasbourg/Project/Reference

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HUMAN PRACTICE</a></p>
HUMAN PRACTICE</a></p>
                         <ul>
                         <ul>
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<li><a href="http://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice/organisation">
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<li><a href="http://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#organisation">
Organisation</a></li>
Organisation</a></li>
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<li><a href="http://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice/survey">
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<li><a href="http://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#survey">
Survey</a></li>
Survey</a></li>
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                                 <li><a href="http://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice/video">
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                                 <li><a href="http://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#video">
The ClpX video</a></li>
The ClpX video</a></li>
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                                 <li><a href="http://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice/game">
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                                 <li><a href="http://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#game">
The ClpX game</a></li>
The ClpX game</a></li>
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<li><a href="http://2010.igem.org/Team:ESBS-Strasbourg/Notebook/safety">
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<li><a href="http://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#safety">
Project Safety</a></li>
Project Safety</a></li>
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<div class="heading">References</div>
<div class="heading">References</div>
<div class="desc">
<div class="desc">
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<ul>
<ul>
<font>
<font>
-
<li><p ALIGN="LEFT">Baker, T. A., R. T. Sauer, et al. (2005). &quot;Versatile modes of  
+
<li><p ALIGN="LEFT">
-
peptide recognition by the AAA+ adaptor protein SspB.&quot; <u>Nat Struct Mol Biol</u> <b>12</b>(6): 520-5.</p></li>
+
[1] Bae, G., G. Choi </span>
-
<li><p ALIGN="LEFT">Fussenegger, M., M. Tigges, et al. (2009). &quot;A tunable synthetic  
+
<span>(2009).&quot;Decoding of light signals by plant phytochromes and their interacting proteins.&quot; <u>Annu Rev Plant Biol </u><b>59</b>:281-311.</span></p></li>
-
mammalian oscillator.&quot; <u>Nature</u> <b>457</b>(7227):  
+
<li><p ALIGN="LEFT">
-
309-12.</p></li>
+
[2] Baker, T. A., R. T. Sauer, et al. </span>
-
<li><p ALIGN="LEFT">Goldberg, A. L. (2003). &quot;Protein degradation and protection  
+
<span>(2009).&quot;Engineering synthetic adaptors and substrates for controlled ClpXP
-
against misfolded or damaged proteins.&quot; <u>Nature</u> <b>426</b>(6968):  
+
degradation.&quot; <u>J Biol Chem </u><b>284</b>(33): 21848-55.</span></p></li>
-
895-9.</p></li>
+
<li><p ALIGN="LEFT">
-
<li><p ALIGN="LEFT">Gregersen, N., C. B. Pedersen, et al. (2003). &quot;Misfolding,  
+
[3] Baker, T. A., R. T. Sauer, et al. </span>
-
degradation, and aggregation of variant proteins. The molecular pathogenesis of  
+
<span>(2009).
-
short chain acyl-CoA dehydrogenase (SCAD) deficiency.&quot; <u>J Biol Chem</u> <b>278</b>(48): 47449-58.</p></li>
+
&quot;Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a
-
<li><p ALIGN="LEFT">Grossman, A. D. and K. L. Griffith (2008). &quot;Inducible protein  
+
AAA+ protein-unfolding machine.&quot; <u>Cell</u> <b>139</b>(4): 744-56.</span></p></li>
-
degradation in Bacillus subtilis using heterologous peptide tags and adaptor  
+
<li><p ALIGN="LEFT">
-
proteins to target substrates to the protease ClpXP.&quot; <u>Mol Microbiol</u> <b>70</b>(4): 1012-25.</p></li>
+
[4] Baker, T. A., R. T. Sauer, et al. </span>
-
<li><p ALIGN="LEFT">Houry, W. A., U. A. Wojtyra, et al. (2003). &quot;The N-terminal zinc  
+
<span>(2010).
-
binding domain of ClpX is a dimerization domain that modulates the chaperone  
+
&quot;Control of substrate gating and translocation into ClpP by channel residues and
-
function.&quot; <u>J Biol Chem</u> <b>278</b>(49): 48981-90.</p></li>
+
ClpX binding.&quot; <u>J Mol Biol</u> <b>399</b>(5): 707-18.</span></p></li>
-
<li><p ALIGN="LEFT">Hughes, J., F. T. Landgraf, et al. (2001). &quot;Recombinant  
+
<li><p ALIGN="LEFT">[5] Baker,
-
holophytochrome in Escherichia coli.&quot; <u>FEBS Lett</u> <b>508</b>(3):  
+
T. A., R. T. Sauer, et al. (2005). &quot;Versatile modes of peptide recognition by  
-
459-62.</p></li>
+
the AAA+ adaptor protein SspB.&quot; <u>Nat Struct Mol Biol</u> <b>12</b>(6): 520-5.</span></p></li>
-
<li><p ALIGN="LEFT">Kohchi, T., K. Mukougawa, et al. (2006). &quot;Metabolic engineering  
+
<li><p ALIGN="LEFT">[6] Baker,
-
to produce phytochromes with phytochromobilin, phycocyanobilin, or  
+
T. A., R. T. Sauer, et al. (2005). &quot;Rebuilt AAA + motors reveal operating
-
phycoerythrobilin chromophore in Escherichia coli.&quot; <u>FEBS Lett</u> <b>580</b>(5): 1333-8.</p></li>
+
principles for ATP-fuelled machines.&quot; </span><u>
-
<li><p ALIGN="LEFT">Maurizi, M. R., R. Grimaud, et al. (1998). &quot;Enzymatic and  
+
<span>
-
structural similarities between the Escherichia coli ATP-dependent proteases,  
+
Nature</span></u><span>
-
ClpXP and ClpAP.&quot; <u>J Biol Chem</u> <b>273</b>(20):  
+
<b>437</b>(7062): 1115-20.</span></p></li>
-
12476-81.</p></li>
+
<li><p ALIGN="LEFT">
-
<li><p ALIGN="LEFT">Moffat, K. and A. Moglich (2010). &quot;Engineered photoreceptors as  
+
[7] Baker, T. A., R. T. Sauer, et al. </span>
-
novel optogenetic tools.&quot; <u>Photochem Photobiol Sci</u> <b>9</b>(10):  
+
<span>(2006).
-
1286-300.</p></li>
+
&quot;Engineering controllable protein degradation.&quot; <u>Mol Cell</u> <b>22</b>(5):
-
<li><p ALIGN="LEFT">Moroder, L. and C. Renner (2006). &quot;Azobenzene as conformational  
+
701-7.</span></p></li>
-
switch in model peptides.&quot; <u>Chembiochem</u> <b>7</b>(6):  
+
<li><p ALIGN="LEFT">
-
868-78.</p></li>
+
[8] Baker, T. A., R. T. Sauer, et al. </span>
-
<li><p ALIGN="LEFT">Morrison, D. A. and S. Ahlawat (2009). &quot;ClpXP degrades SsrA-tagged  
+
<span>(2007).
-
proteins in Streptococcus pneumoniae.&quot; <u>J Bacteriol</u> <b>
+
&quot;Altered tethering of the SspB adaptor to the ClpXP protease causes changes in
-
191</b>(8): 2894-8.</p></li>
+
substrate delivery.&quot; <u>J Biol Chem</u> <b>282</b>(15): 11465-73.</span></p></li>
-
<li><p ALIGN="LEFT">Quail, P. H., R. Khanna, et al. (2004). &quot;A novel molecular  
+
<li><p ALIGN="LEFT">
-
recognition motif necessary for targeting photoactivated phytochrome signaling  
+
[9] Deisseroth, K., F. Zhang, et al. </span>
-
to specific basic helix-loop-helix transcription factors.&quot; <u>Plant Cell</u> <b>16</b>(11): 3033-44.</p></li>
+
<span>(2006).
-
<li><p ALIGN="LEFT">Rosen, M. K., D. W. Leung, et al. (2008). &quot;Genetically encoded
+
&quot;Channelrhodopsin-2 and optical control of excitable cells.&quot; <u>Nat Methods</u>
-
photoswitching of assembly through the Cdc42-WASP-Arp2/3 complex pathway.&quot;  
+
<b>3</b>(10): 785-92.</span></p></li>
-
<u>Proc Natl Acad Sci U S A</u> <b>105</b>(35): 12797-802.</p></li>
+
<li><p ALIGN="LEFT">[10]
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2009). &quot;Engineering synthetic
+
Fussenegger, M., M. Tigges, et al. (2009). &quot;A tunable synthetic mammalian  
-
adaptors and substrates for controlled ClpXP degradation.&quot; <u>J Biol Chem</u> <b>284</b>(33): 21848-55.</p></li>
+
oscillator.&quot; <u>Nature</u> <b>457</b>(7227): 309-12.</span></p></li>
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2009). &quot;Structures of  
+
<li><p ALIGN="LEFT">[11]
-
asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+
+
Goldberg, A. L. (2003). &quot;Protein degradation and protection against misfolded or  
-
protein-unfolding machine.&quot; <u>Cell</u> <b>139</b>(4):  
+
damaged proteins.&quot; </span><u>
-
744-56.</p></li>
+
<span>
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2010). &quot;Control of substrate
+
Nature</span></u><span>
-
gating and translocation into ClpP by channel residues and ClpX binding.&quot;  
+
<b>426</b>(6968): 895-9.</span></p></li>
-
<u>J Mol Biol</u> <b>39 </b>(5): 707-18.</p></li>
+
<li><p ALIGN="LEFT">[12]
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2005). &quot;Rebuilt AAA + motors
+
Gregersen, N., C. B. Pedersen, et al.(2003). &quot;Misfolding, degradation, and aggregation of variant proteins. The molecular pathogenesis of short chain acyl-CoA dehydrogenase (SCAD) deficiency.&quot; <u>J Biol Chem</u> <b>278</b>(48): 47449-58.</span></p></li>
-
reveal operating principles for ATP-fuelled machines.&quot; <u>Nature</u> <b>437</b>(7062): 1115-20.</p></li>
+
<li><p ALIGN="LEFT">[13]
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2006). &quot;Engineering
+
Grossman, A. D. and K. L. Griffith (2008). &quot;Inducible protein degradation in  
-
controllable protein degradation.&quot; <u>Mol Cell</u> <b>22</b>(5):  
+
Bacillus subtilis using heterologous peptide tags and adaptor proteins to target  
-
701-7.</font></p></li>
+
substrates to the protease ClpXP.&quot; <u>Mol Microbiol</u> <b>70</b>(4): 1012-25.</span></p></li>
-
<font>
+
<li><p ALIGN="LEFT">[14]
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2007). &quot;Altered tethering of
+
Houry, W. A., U. A. Wojtyra, et al. (2003). &quot;The N-terminal zinc binding domain  
-
the SspB adaptor to the ClpXP protease causes changes in substrate delivery.&quot;  
+
of ClpX is a dimerization domain that modulates the chaperone function.&quot; <u>J  
-
<u>J Biol Chem</u> <b>282</b>(15): 11465-73.</p></li>
+
Biol Chem</u> <b>278</b>(49): 48981-90.</span></p></li>
-
<li><p ALIGN="LEFT">Schafer, E., T. Kunkel, et al. (1993). &quot;In vitro formation of a
+
<li><p ALIGN="LEFT">
-
photoreversible adduct of phycocyanobilin and tobacco apophytochrome B.&quot; <u>Eur J
+
[15] Hughes, J., F. T. Landgraf, et al. </span>
-
Biochem</u> <b>215</b>(3): 587-94. </p></li>
+
<span>(2001).  
-
<li><p ALIGN="LEFT">Su, Z., H. Li, et al. (2010). &quot;A protease-based strategy for the  
+
&quot;Recombinant holophytochrome in Escherichia coli.&quot; <u>FEBS Lett</u> <b>508</b>(3):  
-
controlled release of therapeutic peptides.&quot; <u>Angew Chem Int Ed Engl</u> <b>49</b>(29): 4930-3.</p></li>
+
459-62.</span></p></li>
-
<li><p ALIGN="LEFT">Voigt, C. A., A. Levskaya, et al. (2005). &quot;Synthetic biology:  
+
<li><p ALIGN="LEFT">[16]
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engineering Escherichia coli to see light.&quot; <u>Nature</u> <b>
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Isacoff, E. Y. and P. Gorostiza (2008). &quot;Optical switches for remote and
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438</b>(7067): 441-2.</p></li>
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noninvasive control of cell signaling.&quot; <u>Science</u> <b>322</b>(5900): 395-9.</span></p></li>
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<li><p ALIGN="LEFT">Voigt, C. A., A. Levskaya, et al. (2009). &quot;Spatiotemporal  
+
<li><p ALIGN="LEFT">
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control of cell signalling using a light-switchable protein interaction.&quot;  
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[17] Kohchi, T., K. Mukougawa, et al. </span>
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<u>Nature</u> <b>461</b>(7266): 997-1001.</p></li>
+
<span>(2006).  
-
<li><p ALIGN="LEFT">Zuber, P. and Y. Zhang (2007). &quot;Requirement of the zinc-binding  
+
&quot;Metabolic engineering to produce phytochromes with phytochromobilin,  
-
domain of ClpX for Spx proteolysis in Bacillus subtilis and effects of disulfide  
+
phycocyanobilin, or phycoerythrobilin chromophore in Escherichia coli.&quot; <u>FEBS  
-
stress on ClpXP activity.&quot; <u>J Bacteriol</u> <b>189</b>(21):7669-80.</p></li>
+
Lett</u> <b>580</b>(5): 1333-8.</span></p></li>
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</font></p></li></ul>
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Sauer, R.T., C.M. Farrell, et al. (2005). &quot;Cytoplasmic degradation of ssrA-tagged proteins.&quot; <u>Mol. Microbiol.</u> <b>57</b>(6): 1750-61.</span></p></li>
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Lagarias, J. C. and G. A. Gambetta (2001). &quot;Genetic engineering of phytochrome
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biosynthesis in bacteria.&quot; <u>Proc Natl Acad Sci U S A</u> <b>98</b>(19):
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Lagarias, J. C., N. C. Rockwell, et al. (2006). &quot;Phytochrome structure and
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&nbsp;signaling mechanisms.&quot; </span><u>
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<b>57</b>: 837-58.</span></p></li>
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Lagarias, J.C., M.T. McDowell (2002). &quot;Analysis and reconstitution of
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phytochromes.&quot; <u>Heme, Chlorophyll, and Bilins: Methods and Protocols</u>,
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Maurizi, M. R., R. Grimaud, et al. (1998). &quot;Enzymatic and structural  
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similarities between the Escherichia coli ATP-dependent proteases, ClpXP and  
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ClpAP.&quot; <u>J Biol Chem</u> <b>273</b>(20): 12476-81.</span></p></li>
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Millar, A. J., O. Sorokina, et al. (2009). &quot;A switchable light-input,
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Moffat, K. and A. Moglich (2010). &quot;Engineered photoreceptors as novel  
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optogenetic tools.&quot; <u>Photochem Photobiol Sci</u> <b>9</b>(10): 1286-300.</span></p></li>
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Moffat, K., A. Moglich, et al. (2010). &quot;Structure and function of plant photoreceptors.&quot; <u>Annu Rev Plant Biol</u> <b>61</b>: 21-47.</span></p></li>
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Moroder, L. and C. Renner (2006). &quot;Azobenzene as conformational switch in model  
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peptides.&quot; <u>Chembiochem</u> <b>7</b>(6): 868-78.</span></p></li>
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Morrison, D. A. and S. Ahlawat (2009). &quot;ClpXP degrades SsrA-tagged proteins in  
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Streptococcus pneumoniae.&quot; </span><u>
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<span>
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J Bacteriol</span></u><span>
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<b>191</b>(8): 2894-8.</span></p></li>
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novel molecular recognition motif necessary for targeting photoactivated  
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phytochrome signaling to specific basic helix-loop-helix transcription factors.&quot;
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Rosen, M. K., D. W. Leung, et al. (2008). &quot;Genetically encoded photoswitching of  
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actin assembly through the Cdc42-WASP-Arp2/3 complex pathway.&quot; <u>Proc Natl Acad
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Sci U S A</u> <b>105</b>(35): 12797-802.</span></p></li>
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al. </span>
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&quot;In vitro formation of a photoreversible adduct of phycocyanobilin and tobacco
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apophytochrome B.&quot; <u>Eur J Biochem</u> <b>215</b>(3): 587-94.</span></p></li>
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Z., H. Li, et al. (2010). &quot;A protease-based strategy for the controlled release  
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Voigt, C. A., A. Levskaya, et al. (2005). &quot;Synthetic biology: engineering  
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Escherichia coli to see light.&quot; </span><u>
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<span>(2009).  
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&quot;Spatiotemporal control of cell signaling using a light-switchable protein  
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interaction.&quot; <u>Nature</u> <b>461</b>(7266): 997-1001.</span></p></li>
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</span>
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<span>Zuber, P. and Y.  
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Zhang (2007). </span>
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<span>
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&quot;Requirement of the zinc-binding domain of ClpX for Spx proteolysis in Bacillus  
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subtilis and effects of disulfide stress on ClpXP activity.&quot; </span><u>
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<span>
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J Bacteriol</span></u><span>
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<b>189</b>(21): 7669-80.</span></p></li>
 +
</ul>

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References

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