Team:EPF-Lausanne/References

1. Purcell EB, Crosson S. Photoregulation in prokaryotes. Curr Opin Microbiol. 2008 Apr;11(2):168-78. Epub 2008 Apr 8. Review. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18400553 Link]
2. Strickland et al. Light-activated DNA binding in a designed allosteric protein. Proceedings of the National Academy of Sciences (2008) vol. 105 (31) pp. 10709 Article
3. Ávila-Pérez et al. Blue Light Activates the σB-Dependent Stress Response of Bacillus subtilis via YtvA. Journal of bacteriology (2006) Article
4. Jaubert et al. Light and redox control of photosynthesis gene expression in Bradyrhizobium: dual roles of two PpsR. Journal of Biological Chemistry (2004) Article
5. Lawson et al. E. coli trp repressor forms a domain-swapped array in aqueous alcohol. Structure (2004) vol. 12 (6) pp. 1099-1108 [http://www.ncbi.nlm.nih.gov/pubmed/15274929?dopt=Abstract Link]
6. Cusanovich and Meyer.Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism. Biochemistry, 42, 4759-4770. (2003) [http://pubs.acs.org/doi/abs/10.1021/bi020690e Link]
7. Harper et al. Structural basis of a phototropin light switch. Science (2003) [http://www.sciencemag.org/cgi/content/abstract/301/5639/1541 Link]
8. Baliga et al. Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proceedings of the National Academy of Sciences (2002) vol. 99 (23) pp. 14913-14918 Article [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=137519&blobname=pnas_192558999_index.html Supporting information]
9. Baliga et al. Genomic and genetic dissection of an archaeal regulon. Proceedings of the National Academy of Sciences (2001) vol. 98 (5) pp. 2521 Article
10. Reedstrom et al. Affinity and specificity of trp repressor-DNA interactions studied with fluorescent oligonucleotides. Journal of Molecular Biology (1997) vol. 273 (3) pp. 572-585
11. Gropp and Betlach. The bat gene of Halobacterium halobium encodes a trans-acting oxygen inducibility factor. Proceedings of the National Academy of Sciences (1994) Article
12. Shand and Betlach. Expression of the bop gene cluster of Halobacterium halobium is induced by low oxygen tension and by light. Journal of bacteriology (1991) Article
13. Bass et al. Mutant Trp repressors with new DNA-binding specificities. Science (1988) vol. 242 (4876) pp. 240-245, find here [http://www.jstor.org/stable/i298930]
14. Bass et al. DNA specificity determinants of Escherichia coli tryptophan repressor binding. Genes & Development (1987) vol. 1 (6) pp. 565-572
15. Giraud et al. Bacteriophytochrome and regulation of the synthesis of the photosynthetic apparatus in Rhodopseudomonas palustris: pitfalls of using laboratory strainsPhotochem.Photobiol.Sci., 2004, 3, 587-591.
16. Allen Introduction to Molecular Dynamics Simulation published in Computational Soft Matter: From Synthetic Polymers to Proteins, Lecture Notes, Norbert Attig, Kurt Binder, Helmut Grubmüller, Kurt Kremer(Eds.), John von Neumann Institute for Computing, Jülich, NIC Series, Vol. 23, ISBN3-00-012641-4, pp. 1-28, 2004. Article
17. Koyama et al. Different role of the Ja Helix in the light-induced activation of the LOV2 domains in various phototropins Biochemistry 2009, 48, 7621-7628 7621.

Media we used

An interesting course on TrpR and Trp operon: [http://www2.hawaii.edu/~scallaha/SMCsite/475%20Lectures/475Lecture34.pdf TrpR]

Biobricks

Characterizes E.Coli Trp repressor, and the Trp operon sequence :
Summary of what characterizes E.Coli Trp repressor : The tryptophan biosynthetic pathway
One good article : RNA-based regulation of genes of tryptophan synthesis and degradation
Protein sequence from NCBI here‎‎