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| - | + | <a href="https://2009.igem.org/Team:EPF-Lausanne/LOVTAP" | |
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| + | <br> | ||
| + | ---- | ||
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| + | <font size="12" color="#007CBC">References</font> | ||
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| + | ---- | ||
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| + | # 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] | ||
# 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 [[Media:Light-activated.pdf | Article]] | # 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 [[Media:Light-activated.pdf | Article]] | ||
# Ávila-Pérez et al. '''Blue Light Activates the σB-Dependent Stress Response of Bacillus subtilis via YtvA.''' Journal of bacteriology (2006) [[Media:Blue-light_in_b.subtilis.pdf | Article]] | # Ávila-Pérez et al. '''Blue Light Activates the σB-Dependent Stress Response of Bacillus subtilis via YtvA.''' Journal of bacteriology (2006) [[Media:Blue-light_in_b.subtilis.pdf | Article]] | ||
# Jaubert et al. '''Light and redox control of photosynthesis gene expression in Bradyrhizobium: dual roles of two PpsR.''' Journal of Biological Chemistry (2004) [[Media:Light_and_Redox_Control_of_Photosynthesis_Gene_Expression.pdf | Article]] | # Jaubert et al. '''Light and redox control of photosynthesis gene expression in Bradyrhizobium: dual roles of two PpsR.''' Journal of Biological Chemistry (2004) [[Media:Light_and_Redox_Control_of_Photosynthesis_Gene_Expression.pdf | Article]] | ||
| - | # 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 | + | # 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] |
| - | # 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 | + | # 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] |
| - | # Harper et al. '''Structural basis of a phototropin light switch.''' Science (2003) [http://www.sciencemag.org/cgi/content/abstract/301/5639/1541 | + | # Harper et al. '''Structural basis of a phototropin light switch.''' Science (2003) [http://www.sciencemag.org/cgi/content/abstract/301/5639/1541 Link] |
| - | # 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 [ | + | # 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 [[Media:Coordinate_regulation_of_energy_transduction_modules.pdf | Article]] [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=137519&blobname=pnas_192558999_index.html Supporting information] |
| - | # Baliga et al. '''Genomic and genetic dissection of an archaeal regulon.''' Proceedings of the National Academy of Sciences (2001) vol. 98 (5) pp. 2521 | + | # Baliga et al. '''Genomic and genetic dissection of an archaeal regulon.''' Proceedings of the National Academy of Sciences (2001) vol. 98 (5) pp. 2521 [[Media: Genomic_and_genetic_dissection_of_an_archaeal_regulon.pdf | Article]] |
# 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 | # 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 | ||
| - | # Gropp and Betlach. '''The bat gene of Halobacterium halobium encodes a trans-acting oxygen inducibility factor.''' Proceedings of the National Academy of Sciences (1994) | + | # Gropp and Betlach. '''The bat gene of Halobacterium halobium encodes a trans-acting oxygen inducibility factor.''' Proceedings of the National Academy of Sciences (1994) [[Media:The_bat_gene_of_Halobacterium_halobium.pdf | Article]] |
| - | # Shand and Betlach. '''Expression of the bop gene cluster of Halobacterium halobium is induced by low oxygen tension and by | + | # 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) [[Media:Expression_of_the_bop_Gene_Cluster.pdf | Article]] |
# 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] | # 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] | ||
# Bass et al. '''DNA specificity determinants of Escherichia coli tryptophan repressor binding.''' Genes & Development (1987) vol. 1 (6) pp. 565-572 | # Bass et al. '''DNA specificity determinants of Escherichia coli tryptophan repressor binding.''' Genes & Development (1987) vol. 1 (6) pp. 565-572 | ||
| + | # Giraud et al. '''Bacteriophytochrome and regulation of the synthesis of the photosynthetic apparatus in Rhodopseudomonas palustris: pitfalls of using laboratory strains'''Photochem.Photobiol.Sci., 2004, 3, 587-591. | ||
| + | # 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. [[Media:Introduction_to_molecular_Dynamics_Simulation.pdf | Article]] | ||
| + | # 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. | ||
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| - | | | + | ==Media we used== |
| + | An interesting course on TrpR and Trp operon: [http://www2.hawaii.edu/~scallaha/SMCsite/475%20Lectures/475Lecture34.pdf TrpR] | ||
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| + | '''Biobricks''' | ||
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| + | Characterizes E.Coli Trp repressor, and the Trp operon sequence : | ||
| + | <br> Summary of what characterizes E.Coli Trp repressor : [[Media:The_tryptophan_biosynthetic_pathway.pdf|The tryptophan biosynthetic pathway]] | ||
| + | <br> One good article : [[Media:RNA-based_regulation_of_genes_of_tryptophan_synthesis_an_degradation.pdf|RNA-based regulation of genes of tryptophan synthesis and degradation]] | ||
| + | <br> Protein sequence from NCBI [[Media:Sequence_du_Trp_repressor.txt|here]] | ||
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Latest revision as of 16:55, 21 October 2009
Contents |
- Purcell EB, Crosson S. Photoregulation in prokaryotes. Curr Opin Microbiol. 2008 Apr;11(2):168-78. Epub 2008 Apr 8. Review. Link
- 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
- Ávila-Pérez et al. Blue Light Activates the σB-Dependent Stress Response of Bacillus subtilis via YtvA. Journal of bacteriology (2006) Article
- Jaubert et al. Light and redox control of photosynthesis gene expression in Bradyrhizobium: dual roles of two PpsR. Journal of Biological Chemistry (2004) Article
- Lawson et al. E. coli trp repressor forms a domain-swapped array in aqueous alcohol. Structure (2004) vol. 12 (6) pp. 1099-1108 Link
- Cusanovich and Meyer.Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism. Biochemistry, 42, 4759-4770. (2003) Link
- Harper et al. Structural basis of a phototropin light switch. Science (2003) Link
- 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 Supporting information
- 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
- 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
- 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
- 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
- Bass et al. Mutant Trp repressors with new DNA-binding specificities. Science (1988) vol. 242 (4876) pp. 240-245, find here [1]
- Bass et al. DNA specificity determinants of Escherichia coli tryptophan repressor binding. Genes & Development (1987) vol. 1 (6) pp. 565-572
- 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.
- 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
- 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: 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
