Team:ESBS-Strasbourg/Project/Reference

[1] Bae, G., G. Choi (2009)."Decoding of light signals by plant phytochromes and their interacting proteins." Annu Rev Plant Biol 59:281-311.

[2] Baker, T. A., R. T. Sauer, et al. (2009)."Engineering synthetic adaptors and substrates for controlled ClpXP degradation." J Biol Chem 284(33): 21848-55.

[3] Baker, T. A., R. T. Sauer, et al. (2009). "Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine." Cell 139(4): 744-56.

[4] Baker, T. A., R. T. Sauer, et al. (2010). "Control of substrate gating and translocation into ClpP by channel residues and ClpX binding." J Mol Biol 399(5): 707-18.

[5] Baker, T. A., R. T. Sauer, et al. (2005). "Versatile modes of peptide recognition by the AAA+ adaptor protein SspB." Nat Struct Mol Biol 12(6): 520-5.

[6] Baker, T. A., R. T. Sauer, et al. (2005). "Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines." Nature 437(7062): 1115-20.

[7] Baker, T. A., R. T. Sauer, et al. (2006). "Engineering controllable protein degradation." Mol Cell 22(5): 701-7.

[8] Baker, T. A., R. T. Sauer, et al. (2007). "Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery." J Biol Chem 282(15): 11465-73.

[9] Deisseroth, K., F. Zhang, et al. (2006). "Channelrhodopsin-2 and optical control of excitable cells." Nat Methods 3(10): 785-92.

[10] Fussenegger, M., M. Tigges, et al. (2009). "A tunable synthetic mammalian oscillator." Nature 457(7227): 309-12.

[11] Goldberg, A. L. (2003). "Protein degradation and protection against misfolded or damaged proteins." Nature 426(6968): 895-9.

[12] 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." J Biol Chem 278(48): 47449-58.

[13] 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." Mol Microbiol 70(4): 1012-25.

[14] 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." J Biol Chem 278(49): 48981-90.

[15] Hughes, J., F. T. Landgraf, et al. (2001). "Recombinant holophytochrome in Escherichia coli." FEBS Lett 508(3): 459-62.

[16] Isacoff, E. Y. and P. Gorostiza (2008). "Optical switches for remote and noninvasive control of cell signaling." Science 322(5900): 395-9.

[17] Kohchi, T., K. Mukougawa, et al. (2006). "Metabolic engineering to produce phytochromes with phytochromobilin, phycocyanobilin, or phycoerythrobilin chromophore in Escherichia coli." FEBS Lett 580(5): 1333-8.

[18] Kohchi, T., K. Mukougawa, et al. (2006). "Metabolic engineering to produce phytochromes with phytochromobilin, phycocyanobilin, or phycoerythrobilin chromophore in Escherichia coli." FEBS Lett 580(5): 1333-8.

[19] Lagarias, J. C. and G. A. Gambetta (2001). "Genetic engineering of phytochrome biosynthesis in bacteria." Proc Natl Acad Sci U S A 98(19): 10566-71.

[20] Lagarias, J. C., N. C. Rockwell, et al. (2006). "Phytochrome structure and  signaling mechanisms." Annu Rev Plant Biol 57: 837-58.

[21] Lagarias, J.C., M.T. McDowell (2002). "Analysis and reconstitution of phytochromes." Heme, Chlorophyll, and Bilins: Methods and Protocols, 293-309

[22] Maurizi, M. R., R. Grimaud, et al. (1998). "Enzymatic and structural similarities between the Escherichia coli ATP-dependent proteases, ClpXP and ClpAP." J Biol Chem 273(20): 12476-81.

[23] Millar, A. J., O. Sorokina, et al. (2009). "A switchable light-input, light-output system modelled and constructed in yeast." J Biol Eng 3: 15.

[24] Moffat, K. and A. Moglich (2010). "Engineered photoreceptors as novel optogenetic tools." Photochem Photobiol Sci 9(10): 1286-300.

[25] Moffat, K., A. Moglich, et al. (2010). "Structure and function of plant photoreceptors." Annu Rev Plant Biol 61: 21-47.

[26] Moroder, L. and C. Renner (2006). "Azobenzene as conformational switch in model peptides." Chembiochem 7(6): 868-78.

[27] Morrison, D. A. and S. Ahlawat (2009). "ClpXP degrades SsrA-tagged proteins in Streptococcus pneumoniae." J Bacteriol 191(8): 2894-8.

[28] Muir, T. W. and A. B. Tyszkiewicz (2008). "Activation of protein splicing with light in yeast." Nat Methods 5(4): 303-5.

[29] Quail, P. H. (2002). "Phytochrome photosensory signalling networks." Nat Rev Mol Cell Biol 3(2): 85-93.

[30] Quail, P. H., R. Khanna, et al. (2004). "A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors." Plant Cell 16(11): 3033-44.

[31] Quail, P. H., E. Schafer, et al. (2006). "Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated degradation." Mol Cell 23(3): 439-46.

[32] Quail, P. H., S. Shimizu-Sato, et al. (2002). "A light-switchable gene promoter system." Nat Biotechnol 20(10): 1041-4.

[33] Quail PH., D. Wagner et al. (1996) "Two small spatially distinct regions of phytochrome B are required for efficient signaling rates." Plant Cell 8:859–71.

[34] Park Y., H. Song (2008) "A degradation signal recognition in prokaryotes." J. Synchrotron Rad15:246–249.

[35] Rosen, M. K., D. W. Leung, et al. (2008). "Genetically encoded photoswitching of actin assembly through the Cdc42-WASP-Arp2/3 complex pathway." Proc Natl Acad Sci U S A 105(35): 12797-802.

[36] Schafer, E., T. Kunkel, et al. (1993). "In vitro formation of a photoreversible adduct of phycocyanobilin and tobacco apophytochrome B." Eur J Biochem 215(3): 587-94.

[37] Schaffner, K., C. Hill, et al. (1994). "Expression of phytochrome apoprotein from Avena sativa in Escherichia coli and formation of photoactive chromoproteins by assembly with phycocyanobilin." Eur J Biochem 223(1): 69-77.

[38] Sejnowski, T. J. and M. U. Gillette (2005). "Physiology. Biological clocks coordinately keep life on time." Science 309(5738): 1196-8.

[39] Sharrock, R. A. (2008). "The phytochrome red/far-red photoreceptor superfamily." Genome Biol 9(8): 230.

[40] Su, Z., H. Li, et al. (2010). "A protease-based strategy for the controlled release of therapeutic peptides." Angew Chem Int Ed Engl 49(29): 4930-3.

[41] Voigt, C. A., A. Levskaya, et al. (2005). "Synthetic biology: engineering Escherichia coli to see light." Nature 438(7067): 441-2.

[42] Voigt, C. A., A. Levskaya, et al. (2009). "Spatiotemporal control of cell signaling using a light-switchable protein interaction." Nature 461(7266): 997-1001.

[43] Weaver, D. R. and S. M. Reppert (1997). "Forward genetic approach strikes gold: cloning of a mammalian clock gene." Cell 89(4): 487-90.

[44] Weitz, C. J., K. F. Storch, et al. (2002). "Extensive and divergent circadian gene expression in liver and heart." Nature 417(6884): 78-83.

[45] Wu SH., JC. Lagarias JC. (2000) "Defining the bilin lyase domain: lessons from the extended phytochrome superfamily." Biochemistry39:13487–95.

[46] Zuber, P. and Y. Zhang (2007). "Requirement of the zinc-binding domain of ClpX for Spx proteolysis in Bacillus subtilis and effects of disulfide stress on ClpXP activity." J Bacteriol 189(21): 7669-80.