Team:ETH Zurich/Modeling/Parameters

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Contents

Parameters for modeling

Photoinduction

Light sources

Name Description Reference approx. flux at probe Distance source - probe
sun natural sun light ISO 9845-1, ASTMG173 640 W m-2 n/a
room sun*0.3, (UV<350nm)*0.05, (UV>=350nm)*0,90 assumed 210 W m-2 n/a
bulb200W Incandescent light bulb GE200Clear 12 W m-2 1 m

Photoconversion cross section

From Absorption spectrum
Receptor Activation Deactivation References
Quantum yield Ext. coeff. Absorption spectrum Quantum yield Ext. coeff. Absorption spectrum
lov 0.26 1.0655e3 ETH modeling abs lov a.png n/a n/a n/a [Drepper2007]
[Christie1999]
ycgf 0.24 1.13e3 ETH modeling abs ycgf a.png n/a n/a n/a [Tyagi2009]
ccas 0.15 2.7e3 ETH modeling abs ccas a.png 0.12 3.0e3 ETH modeling abs ccas d.png [Hirose2008]
[Hirose2010]
cph1 0.15 8.5e3 ETH modeling abs cph1 a.png 0.12 8.5e3 ETH modeling abs cph1 d.png [VanThor2001]
[Lamparter2002]
From Photon effectiveness
Receptor Activation photon effectiveness Deactivation photon effectiveness References
UVR8 ETH modeling act uvr8 a.png n/a [Brown2009]

UVR8

Parameter Description Value Reference
k_UVR8_hvLight dependent dissociation rate UVR8 dimer s-1from photoinduction model
k_UVR8_decayDimerization rate UVR8 monomer8.4·10-10 nM-1 s-1estimate
KM_TetRTetR repression coefficient 100 nMassumed
n_TetRTetR cooperativity coefficient1[GarciaOjalvo2004]
k_PtetTet promoter expression strength50 nM s-1assumed
ABasal expression fraction0.15assumed
nHill-like pABA cooperativity coefficient1assumed
k_degProtein degradation rate0.03 s-1assumed
KM_PabABPabAB Michaelis constant9.60·105 nM[Roux1992]
k_catPabAB catalysis rate0.65 s-1[Roux1992]
Chor0Intracellular chorismate concentration1.4·105 nMassumed
k_outpABA outflux rate0.01 s-1assumed

UVR8-TetRDBD-LovTAP

Parameter Description Value Reference
k_UVR8_hvLight dependent dissociation rate UVR8 dimer s-1from photoinduction model
k_LOV_hvLight dependent activation rate s-1from photoinduction model
KM_LOVLOV repression coefficient142 nM[Strickland2007]
KM_LacILacI repression coefficient800 nM[Basu2005]
KM_cIcI repression coefficient8 nM[Basu2005]
KM_TetRTetR repression coefficient100 nMassumed
n_LacILacI cooperativity coefficient2[Basu2005]
n_cIcI cooperativity coefficient2[Basu2005]
n_TetRTetR cooperativity coefficient1[GarciaOjalvo2004]
n_LOVLOV cooperativity coefficient1assumed
k_UVR8_decayDimerization rate UVR8 monomer8.4·10-10 nM-1 s-1estimate
k_LOV_decayDark decay rate of active LOV5.8·10-3 s-1[Drepper2007]
k_PtrpTrp promoter expression strength2.34 nM s-1optimized
k_P_RLambda P_R expression strength4.21·10-2 nM s-1optimized
k_P_LLambda P_L expression strength2.1579·10-2 nM s-1optimized
ABasal expression fraction0.15assumed
k_degProtein degradation rate1.9·10-3 s-1assumed


LovTAP-Cph8

Parameter Description Value Reference
k_Cph8_hvLight dependent activation rate s-1from photoinduction model
KM_LOVLOV repression coefficient142 nM[Strickland2007]
KM_Cph8Cph8 activation coefficient1000 nMestimate
KM_LacILacI repression coefficient800 nM[Basu2005]
KM_cIcI repression coefficient8 nM[Basu2005]
KM_TetRTetR repression coefficient100 nMassumed
n_LacILacI cooperativity coefficient2[Basu2005]
n_cIcI cooperativity coefficient2[Basu2005]
n_TetRTetR cooperativity coefficient1[GarciaOjalvo2004]
n_Cph8Cph8 cooperativity coefficient1assumed
n_LOVLOV cooperativity coefficient1assumed
k_LOV_decayDark decay rate of active LOV5.8·10-3 s-1[Drepper2007]
k_Cph8_decayDark decay rate of active Cph85.8·10-3 s-1estimate
k_PtrpTrp promoter expression strength2.23 nM s-1optimized
k_PompCOmpC promoter expression strength3.454·10-1 nM s-1optimized
k_P_RLambda P_R expression strength4.21·10-2 nM s-1optimized
k_P_LLambda P_L expression strength3.0·10-2 nM s-1optimized
ABasal expression fraction0.15assumed
k_degProtein degradation rate1.9·10-3 s-1assumed

Parameters denoted with

  • assumed have been assumed from intuition
  • estimate have been calculated from gels, approximate experimental numbers or other related biological numbers
  • optimized have been adjusted such that the constructs work optimally. These are target constraints that biologists should care for when selecting promoters.


References

  • Brown, B. a, Headland, L. R., & Jenkins, G. I. (2009). UV-B action spectrum for UVR8-mediated HY5 transcript accumulation in Arabidopsis. Photochemistry and photobiology, 85(5), 1147–55.
  • Christie, J. M., Salomon, M., Nozue, K., Wada, M., & Briggs, W. R. (1999): LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): binding sites for the chromophore flavin mononucleotide. Proceedings of the National Academy of Sciences of the United States of America, 96(15), 8779–83.
  • Christie, J. M., Arvai, A. S., Baxter, K. J., Heilmann, M., Pratt, A. J., O’Hara, A., Kelly, S. M., et al. (2012). Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science (New York, N.Y.), 335(6075), 1492–6.
  • Cloix, C., & Jenkins, G. I. (2008). Interaction of the Arabidopsis UV-B-specific signaling component UVR8 with chromatin. Molecular plant, 1(1), 118–28.
  • Cox, R. S., Surette, M. G., & Elowitz, M. B. (2007). Programming gene expression with combinatorial promoters. Molecular systems biology, 3(145), 145. doi:10.1038/msb4100187
  • Drepper, T., Eggert, T., Circolone, F., Heck, A., Krauss, U., Guterl, J.-K., Wendorff, M., et al. (2007). Reporter proteins for in vivo fluorescence without oxygen. Nature biotechnology, 25(4), 443–5
  • Drepper, T., Krauss, U., & Berstenhorst, S. M. zu. (2011). Lights on and action! Controlling microbial gene expression by light. Applied microbiology, 23–40.
  • EuropeanCommission (2006). SCIENTIFIC COMMITTEE ON CONSUMER PRODUCTS SCCP Opinion on Biological effects of ultraviolet radiation relevant to health with particular reference to sunbeds for cosmetic purposes.
  • Elvidge, C. D., Keith, D. M., Tuttle, B. T., & Baugh, K. E. (2010). Spectral identification of lighting type and character. Sensors (Basel, Switzerland), 10(4), 3961–88.
  • GarciaOjalvo, J., Elowitz, M. B., & Strogatz, S. H. (2004). Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proceedings of the National Academy of Sciences of the United States of America, 101(30), 10955–60.
  • Gao Q, Garcia-Pichel F. (2011). Microbial ultraviolet sunscreens. Nat Rev Microbiol. 9(11):791-802.
  • Goosen N, Moolenaar GF. (2008) Repair of UV damage in bacteria. DNA Repair (Amst).7(3):353-79.
  • Heijde, M., & Ulm, R. (2012). UV-B photoreceptor-mediated signalling in plants. Trends in plant science, 17(4), 230–7.
  • Hirose, Y., Narikawa, R., Katayama, M., & Ikeuchi, M. (2010). Cyanobacteriochrome CcaS regulates phycoerythrin accumulation in Nostoc punctiforme, a group II chromatic adapter. Proceedings of the National Academy of Sciences of the United States of America, 107(19), 8854–9.
  • Hirose, Y., Shimada, T., Narikawa, R., Katayama, M., & Ikeuchi, M. (2008). Cyanobacteriochrome CcaS is the green light receptor that induces the expression of phycobilisome linker protein. Proceedings of the National Academy of Sciences of the United States of America, 105(28), 9528–33.
  • Kast, Asif-Ullah & Hilvert (1996) Tetrahedron Lett. 37, 2691 - 2694., Kast, Asif-Ullah, Jiang & Hilvert (1996) Proc. Natl. Acad. Sci. USA 93, 5043 - 5048
  • Kiefer, J., Ebel, N., Schlücker, E., & Leipertz, A. (2010). Characterization of Escherichia coli suspensions using UV/Vis/NIR absorption spectroscopy. Analytical Methods, 9660. doi:10.1039/b9ay00185a
  • Kinkhabwala, A., & Guet, C. C. (2008). Uncovering cis regulatory codes using synthetic promoter shuffling. PloS one, 3(4), e2030.
  • Krebs in Deutschland 2005/2006. Häufigkeiten und Trends. 7. Auflage, 2010, Robert Koch-Institut (Hrsg) und die Gesellschaft der epidemiologischen Krebsregister in Deutschland e. V. (Hrsg). Berlin.
  • Lamparter, T., Michael, N., Mittmann, F., & Esteban, B. (2002). Phytochrome from Agrobacterium tumefaciens has unusual spectral properties and reveals an N-terminal chromophore attachment site. Proceedings of the National Academy of Sciences of the United States of America, 99(18), 11628–33.
  • Levskaya, A. et al (2005). Engineering Escherichia coli to see light. Nature, 438(7067), 442.
  • Mancinelli, A. (1986). Comparison of spectral properties of phytochromes from different preparations. Plant physiology, 82(4), 956–61.
  • Nakasone, Y., Ono, T., Ishii, A., Masuda, S., & Terazima, M. (2007). Transient dimerization and conformational change of a BLUF protein: YcgF. Journal of the American Chemical Society, 129(22), 7028–35.
  • Orth, P., & Schnappinger, D. (2000). Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nature structural biology, 215–219.
  • Parkin, D.M., et al., Global cancer statistics, 2002. CA: a cancer journal for clinicians, 2005. 55(2): p. 74-108.
  • Rajagopal, S., Key, J. M., Purcell, E. B., Boerema, D. J., & Moffat, K. (2004). Purification and initial characterization of a putative blue light-regulated phosphodiesterase from Escherichia coli. Photochemistry and photobiology, 80(3), 542–7.
  • Rizzini, L., Favory, J.-J., Cloix, C., Faggionato, D., O’Hara, A., Kaiserli, E., Baumeister, R., et al. (2011). Perception of UV-B by the Arabidopsis UVR8 protein. Science (New York, N.Y.), 332(6025), 103–6.
  • Roux, B., & Walsh, C. T. (1992). p-aminobenzoate synthesis in Escherichia coli: kinetic and mechanistic characterization of the amidotransferase PabA. Biochemistry, 31(30), 6904–10.
  • Strickland, D. (2008). Light-activated DNA binding in a designed allosteric protein. Proceedings of the National Academy of Sciences of the United States of America, 105(31), 10709–10714.
  • Sinha RP, Häder DP. UV-induced DNA damage and repair: a review. Photochem Photobiol Sci. (2002). 1(4):225-36
  • Sambandan DR, Ratner D. (2011). Sunscreens: an overview and update. J Am Acad Dermatol. 2011 Apr;64(4):748-58.
  • Tabor, J. J., Levskaya, A., & Voigt, C. A. (2011). Multichromatic Control of Gene Expression in Escherichia coli. Journal of Molecular Biology, 405(2), 315–324.
  • Thibodeaux, G., & Cowmeadow, R. (2009). A tetracycline repressor-based mammalian two-hybrid system to detect protein–protein interactions in vivo. Analytical biochemistry, 386(1), 129–131.
  • Tschowri, N., & Busse, S. (2009). The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes & development, 522–534.
  • Tschowri, N., Lindenberg, S., & Hengge, R. (2012). Molecular function and potential evolution of the biofilm-modulating blue light-signalling pathway of Escherichia coli. Molecular microbiology.
  • Tyagi, A. (2009). Photodynamics of a flavin based blue-light regulated phosphodiesterase protein and its photoreceptor BLUF domain.
  • Vainio, H. & Bianchini, F. (2001). IARC Handbooks of Cancer Prevention: Volume 5: Sunscreens. Oxford University Press, USA
  • Quinlivan, Eoin P & Roje, Sanja & Basset, Gilles & Shachar-Hill, Yair & Gregory, Jesse F & Hanson, Andrew D. (2003). The folate precursor p-aminobenzoate is reversibly converted to its glucose ester in the plant cytosol. The Journal of biological chemistry, 278.
  • van Thor, J. J., Borucki, B., Crielaard, W., Otto, H., Lamparter, T., Hughes, J., Hellingwerf, K. J., et al. (2001). Light-induced proton release and proton uptake reactions in the cyanobacterial phytochrome Cph1. Biochemistry, 40(38), 11460–71.
  • Wegkamp A, van Oorschot W, de Vos WM, Smid EJ. (2007 )Characterization of the role of para-aminobenzoic acid biosynthesis in folate production by Lactococcus lactis. Appl Environ Microbiol. Apr;73(8):2673-81.