Team:ESBS-Strasbourg/Project/Reference
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HUMAN PRACTICE</a></p> | HUMAN PRACTICE</a></p> | ||
<ul> | <ul> | ||
- | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice | + | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#organisation"> |
Organisation</a></li> | Organisation</a></li> | ||
- | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice | + | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#survey"> |
Survey</a></li> | Survey</a></li> | ||
- | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice | + | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#video"> |
The ClpX video</a></li> | The ClpX video</a></li> | ||
- | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice | + | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#game"> |
The ClpX game</a></li> | The ClpX game</a></li> | ||
- | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/ | + | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#safety"> |
Project Safety</a></li> | Project Safety</a></li> | ||
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<div id="leftmenu"> | <div id="leftmenu"> | ||
<td width="210" rowspan=3 bgcolor="#414141" valign="top"> | <td width="210" rowspan=3 bgcolor="#414141" valign="top"> | ||
- | + | ||
<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). "Versatile modes of | + | <li><p ALIGN="LEFT"> |
- | peptide recognition by the AAA+ adaptor protein SspB." <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). "A tunable synthetic | + | <span>(2009)."Decoding of light signals by plant phytochromes and their interacting proteins." <u>Annu Rev Plant Biol </u><b>59</b>:281-311.</span></p></li> |
- | mammalian oscillator." <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). "Protein degradation and protection | + | <span>(2009)."Engineering synthetic adaptors and substrates for controlled ClpXP |
- | against misfolded or damaged proteins." <u>Nature</u> <b>426</b>(6968): | + | degradation." <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). "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." <u>J Biol Chem</u> <b>278</b>(48): 47449-58.</p></li> | + | "Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a |
- | <li><p ALIGN="LEFT">Grossman, A. D. and K. L. Griffith (2008). "Inducible protein | + | AAA+ protein-unfolding machine." <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." <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). "The N-terminal zinc | + | <span>(2010). |
- | binding domain of ClpX is a dimerization domain that modulates the chaperone | + | "Control of substrate gating and translocation into ClpP by channel residues and |
- | function." <u>J Biol Chem</u> <b>278</b>(49): 48981-90.</p></li> | + | ClpX binding." <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). "Recombinant | + | <li><p ALIGN="LEFT">[5] Baker, |
- | holophytochrome in Escherichia coli." <u>FEBS Lett</u> <b>508</b>(3): | + | T. A., R. T. Sauer, et al. (2005). "Versatile modes of peptide recognition by |
- | 459-62.</p></li> | + | the AAA+ adaptor protein SspB." <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). "Metabolic engineering | + | <li><p ALIGN="LEFT">[6] Baker, |
- | to produce phytochromes with phytochromobilin, phycocyanobilin, or | + | T. A., R. T. Sauer, et al. (2005). "Rebuilt AAA + motors reveal operating |
- | phycoerythrobilin chromophore in Escherichia coli." <u>FEBS Lett</u> <b>580</b>(5): 1333-8.</p></li> | + | principles for ATP-fuelled machines." </span><u> |
- | <li><p ALIGN="LEFT">Maurizi, M. R., R. Grimaud, et al. (1998). "Enzymatic and | + | <span> |
- | structural similarities between the Escherichia coli ATP-dependent proteases, | + | Nature</span></u><span> |
- | ClpXP and ClpAP." <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). "Engineered photoreceptors as | + | [7] Baker, T. A., R. T. Sauer, et al. </span> |
- | novel optogenetic tools." <u>Photochem Photobiol Sci</u> <b>9</b>(10): | + | <span>(2006). |
- | 1286-300.</p></li> | + | "Engineering controllable protein degradation." <u>Mol Cell</u> <b>22</b>(5): |
- | <li><p ALIGN="LEFT">Moroder, L. and C. Renner (2006). "Azobenzene as conformational | + | 701-7.</span></p></li> |
- | switch in model peptides." <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). "ClpXP degrades SsrA-tagged | + | <span>(2007). |
- | proteins in Streptococcus pneumoniae." <u>J Bacteriol</u> < | + | "Altered tethering of the SspB adaptor to the ClpXP protease causes changes in |
- | 191</b>(8): 2894-8.</p></li> | + | substrate delivery." <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). "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." <u>Plant Cell</u> <b>16</b>(11): 3033-44.</p></li> | + | <span>(2006). |
- | <li><p ALIGN="LEFT"> | + | "Channelrhodopsin-2 and optical control of excitable cells." <u>Nat Methods</u> |
- | + | <b>3</b>(10): 785-92.</span></p></li> | |
- | <u> | + | <li><p ALIGN="LEFT">[10] |
- | <li><p ALIGN="LEFT"> | + | Fussenegger, M., M. Tigges, et al. (2009). "A tunable synthetic mammalian |
- | + | oscillator." <u>Nature</u> <b>457</b>(7227): 309-12.</span></p></li> | |
- | <li><p ALIGN="LEFT"> | + | <li><p ALIGN="LEFT">[11] |
- | + | Goldberg, A. L. (2003). "Protein degradation and protection against misfolded or | |
- | + | damaged proteins." </span><u> | |
- | + | <span> | |
- | <li><p ALIGN="LEFT"> | + | Nature</span></u><span> |
- | + | <b>426</b>(6968): 895-9.</span></p></li> | |
- | <u> | + | <li><p ALIGN="LEFT">[12] |
- | <li><p ALIGN="LEFT"> | + | Gregersen, N., C. B. Pedersen, et al.(2003). "Misfolding, degradation, and aggregation of variant proteins. The molecular pathogenesis of short chain acyl-CoA dehydrogenase (SCAD) deficiency." <u>J Biol Chem</u> <b>278</b>(48): 47449-58.</span></p></li> |
- | + | <li><p ALIGN="LEFT">[13] | |
- | <li><p ALIGN="LEFT"> | + | Grossman, A. D. and K. L. Griffith (2008). "Inducible protein degradation in |
- | + | Bacillus subtilis using heterologous peptide tags and adaptor proteins to target | |
- | + | substrates to the protease ClpXP." <u>Mol Microbiol</u> <b>70</b>(4): 1012-25.</span></p></li> | |
- | + | <li><p ALIGN="LEFT">[14] | |
- | <li><p ALIGN="LEFT"> | + | Houry, W. A., U. A. Wojtyra, et al. (2003). "The N-terminal zinc binding domain |
- | + | of ClpX is a dimerization domain that modulates the chaperone function." <u>J | |
- | <u> | + | Biol Chem</u> <b>278</b>(49): 48981-90.</span></p></li> |
- | <li><p ALIGN="LEFT"> | + | <li><p ALIGN="LEFT"> |
- | + | [15] Hughes, J., F. T. Landgraf, et al. </span> | |
- | + | <span>(2001). | |
- | <li><p ALIGN="LEFT">Su, Z., H. Li, et al. (2010). "A protease-based strategy for the | + | "Recombinant holophytochrome in Escherichia coli." <u>FEBS Lett</u> <b>508</b>(3): |
- | controlled release of therapeutic peptides." <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). "Synthetic biology: | + | <li><p ALIGN="LEFT">[16] |
- | engineering Escherichia coli to see light." <u>Nature</u> < | + | Isacoff, E. Y. and P. Gorostiza (2008). "Optical switches for remote and |
- | 438</b>(7067): 441-2.</p></li> | + | noninvasive control of cell signaling." <u>Science</u> <b>322</b>(5900): 395-9.</span></p></li> |
- | <li><p ALIGN="LEFT">Voigt, C. A., A. Levskaya, et al. (2009). "Spatiotemporal | + | <li><p ALIGN="LEFT"> |
- | control of cell | + | [17] Kohchi, T., K. Mukougawa, et al. </span> |
- | <u>Nature</u> <b>461</b>(7266): 997-1001.</p></li> | + | <span>(2006). |
- | <li><p ALIGN="LEFT">Zuber, P. and Y. Zhang (2007). "Requirement of the zinc-binding | + | "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." <u>FEBS |
- | stress on ClpXP activity." <u>J Bacteriol</u> <b>189</b>(21):7669-80.</ | + | Lett</u> <b>580</b>(5): 1333-8.</span></p></li> |
- | + | <li><p ALIGN="LEFT">[18] | |
+ | Sauer, R.T., C.M. Farrell, et al. (2005). "Cytoplasmic degradation of ssrA-tagged proteins." <u>Mol. Microbiol.</u> <b>57</b>(6): 1750-61.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[19] | ||
+ | Lagarias, J. C. and G. A. Gambetta (2001). "Genetic engineering of phytochrome | ||
+ | biosynthesis in bacteria." <u>Proc Natl Acad Sci U S A</u> <b>98</b>(19): | ||
+ | 10566-71.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[20] | ||
+ | Lagarias, J. C., N. C. Rockwell, et al. (2006). "Phytochrome structure and | ||
+ | signaling mechanisms." </span><u> | ||
+ | <span> | ||
+ | Annu Rev Plant Biol</span></u><span> | ||
+ | <b>57</b>: 837-58.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[21] | ||
+ | Lagarias, J.C., M.T. McDowell (2002). "Analysis and reconstitution of | ||
+ | phytochromes." <u>Heme, Chlorophyll, and Bilins: Methods and Protocols</u>, | ||
+ | 293-309</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[22] | ||
+ | Maurizi, M. R., R. Grimaud, et al. (1998). "Enzymatic and structural | ||
+ | similarities between the Escherichia coli ATP-dependent proteases, ClpXP and | ||
+ | ClpAP." <u>J Biol Chem</u> <b>273</b>(20): 12476-81.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[23] | ||
+ | Millar, A. J., O. Sorokina, et al. (2009). "A switchable light-input, | ||
+ | light-output system modelled and constructed in yeast." <u>J Biol Eng</u> <b>3</b>: | ||
+ | 15.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[24] | ||
+ | Moffat, K. and A. Moglich (2010). "Engineered photoreceptors as novel | ||
+ | optogenetic tools." <u>Photochem Photobiol Sci</u> <b>9</b>(10): 1286-300.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[25] | ||
+ | Moffat, K., A. Moglich, et al. (2010). "Structure and function of plant photoreceptors." <u>Annu Rev Plant Biol</u> <b>61</b>: 21-47.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[26] | ||
+ | Moroder, L. and C. Renner (2006). "Azobenzene as conformational switch in model | ||
+ | peptides." <u>Chembiochem</u> <b>7</b>(6): 868-78.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[27] | ||
+ | Morrison, D. A. and S. Ahlawat (2009). "ClpXP degrades SsrA-tagged proteins in | ||
+ | Streptococcus pneumoniae." </span><u> | ||
+ | <span> | ||
+ | J Bacteriol</span></u><span> | ||
+ | <b>191</b>(8): 2894-8.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[28] Muir, | ||
+ | T. W. and A. B. Tyszkiewicz (2008). "Activation of protein splicing with light | ||
+ | in yeast." <u>Nat Methods</u> <b>5</b>(4): 303-5.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[29] | ||
+ | Quail, P. H. (2002). "Phytochrome photosensory signalling networks." <u>Nat Rev | ||
+ | Mol Cell Biol</u> <b>3</b>(2): 85-93.</span></p></li> | ||
+ | <li><p ALIGN="LEFT"> | ||
+ | [30] Quail, P. H., R. Khanna, et al. </span> | ||
+ | <span>(2004). "A | ||
+ | novel molecular recognition motif necessary for targeting photoactivated | ||
+ | phytochrome signaling to specific basic helix-loop-helix transcription factors." | ||
+ | <u>Plant Cell</u> <b>16</b>(11): 3033-44.</span></p></li> | ||
+ | <li><p ALIGN="LEFT"> | ||
+ | [31] Quail, P. H., E. Schafer, et al. </span> | ||
+ | <span>(2006). "Photoactivated | ||
+ | phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated | ||
+ | degradation." </span><u> | ||
+ | <span> | ||
+ | Mol Cell</span></u><span> | ||
+ | <b>23</b>(3): 439-46.</span></p></li> | ||
+ | <li><p ALIGN="LEFT"> | ||
+ | [32] Quail, P. H., S. Shimizu-Sato, et al. </span> | ||
+ | <span>(2002). "A | ||
+ | light-switchable gene promoter system." <u>Nat Biotechnol</u> <b>20</b>(10): | ||
+ | 1041-4.</span></p></li> | ||
+ | <li><p ALIGN="LEFT"> | ||
+ | [33] Quail PH., D. Wagner et al. (1996) "Two small spatially distinct regions of phytochrome B are required for efficient signaling rates." <u>Plant Cell</u> <b>8</b>:859–71.</span></p></li> | ||
+ | <li><p ALIGN="LEFT"> | ||
+ | [34] Park Y., H. Song (2008) "A degradation signal recognition in prokaryotes." <u>J. Synchrotron Rad</u><b>15</b>:246–249.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[35] | ||
+ | Rosen, M. K., D. W. Leung, et al. (2008). "Genetically encoded photoswitching of | ||
+ | actin assembly through the Cdc42-WASP-Arp2/3 complex pathway." <u>Proc Natl Acad | ||
+ | Sci U S A</u> <b>105</b>(35): 12797-802.</span></p></li> | ||
+ | <li><p ALIGN="LEFT"><span>[36] Schafer, E., T. Kunkel, et | ||
+ | al. </span> | ||
+ | <span>(1993). | ||
+ | "In vitro formation of a photoreversible adduct of phycocyanobilin and tobacco | ||
+ | apophytochrome B." <u>Eur J Biochem</u> <b>215</b>(3): 587-94.</span></p></li> | ||
+ | <li><p ALIGN="LEFT"><span>[37] Schaffner, K., C. Hill, et | ||
+ | al. </span> | ||
+ | <span>(1994). | ||
+ | "Expression of phytochrome apoprotein from Avena sativa in Escherichia coli and | ||
+ | formation of photoactive chromoproteins by assembly with phycocyanobilin." <u> | ||
+ | Eur J Biochem</u> <b>223</b>(1): 69-77.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[38] | ||
+ | Sejnowski, T. J. and M. U. Gillette (2005). "Physiology. Biological clocks | ||
+ | coordinately keep life on time." </span><u> | ||
+ | <span> | ||
+ | Science</span></u><span> | ||
+ | <b>309</b>(5738): 1196-8.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[39] | ||
+ | Sharrock, R. A. (2008). "The phytochrome red/far-red photoreceptor superfamily." | ||
+ | <u>Genome Biol</u> <b>9</b>(8): 230.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[40] Su, | ||
+ | Z., H. Li, et al. (2010). "A protease-based strategy for the controlled release | ||
+ | of therapeutic peptides." <u>Angew Chem Int Ed Engl</u> <b>49</b>(29): 4930-3.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[41] | ||
+ | Voigt, C. A., A. Levskaya, et al. (2005). "Synthetic biology: engineering | ||
+ | Escherichia coli to see light." </span><u> | ||
+ | <span> | ||
+ | Nature</span></u><span> | ||
+ | <b>438</b>(7067): 441-2.</span></p></li> | ||
+ | <li><p ALIGN="LEFT"> | ||
+ | [42] Voigt, C. A., A. Levskaya, et al. </span> | ||
+ | <span>(2009). | ||
+ | "Spatiotemporal control of cell signaling using a light-switchable protein | ||
+ | interaction." <u>Nature</u> <b>461</b>(7266): 997-1001.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[43] | ||
+ | Weaver, D. R. and S. M. Reppert (1997). "Forward genetic approach strikes gold: | ||
+ | cloning of a mammalian clock gene." </span><u> | ||
+ | <span> | ||
+ | Cell</span></u><span> | ||
+ | <b>89</b>(4): 487-90.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[44] | ||
+ | </span> | ||
+ | <span>Weitz, C. J., K. F. | ||
+ | Storch, et al. </span> | ||
+ | <span>(2002). | ||
+ | "Extensive and divergent circadian gene expression in liver and heart." <u> | ||
+ | Nature</u> <b>417</b>(6884): 78-83.</span></p></li> | ||
+ | <li><p ALIGN="LEFT"> | ||
+ | [45] Wu SH., JC. Lagarias JC. (2000) "Defining the bilin lyase domain: lessons from the extended phytochrome superfamily." <u>Biochemistry</u><b>39</b>:13487–95.</span></p></li> | ||
+ | <li><p ALIGN="LEFT">[46] | ||
+ | </span> | ||
+ | <span>Zuber, P. and Y. | ||
+ | Zhang (2007). </span> | ||
+ | <span> | ||
+ | "Requirement of the zinc-binding domain of ClpX for Spx proteolysis in Bacillus | ||
+ | subtilis and effects of disulfide stress on ClpXP activity." </span><u> | ||
+ | <span> | ||
+ | J Bacteriol</span></u><span> | ||
+ | <b>189</b>(21): 7669-80.</span></p></li> | ||
+ | </ul> | ||
Latest revision as of 22:56, 27 October 2010
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