Abstract
Mathematical models are important tools in helping us to understand complex biological systems. Models of phytochrome-regulated systems in Arabidopsis thaliana have shown the importance of dimerization, nuclear transport, and thermal/dark reversion in mediating phytochrome activity and plant development. Here we go through the steps required to calculate the steady-state amounts of phytochrome subspecies relative to the total phytochrome molecule population. Starting from a simplified two-state system we expand and apply the technique to the extended phytochrome dimer model. Additionally, we provide a Python package that can automatically calculate the proportion of phytochrome B in a particular state given specific experimental conditions.
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22 June 2021
In the original version of this book, Chapter 9 was inadvertently published with few errors in Table 2 data. This has now been rectified in this revised version of the book.
References
Rüdiger W, Thümmler F, Cmiel E et al (1983) Chromophore structure of the physiologically active form (Pfr) of phytochrome. Proc Natl Acad Sci U S A 80:6244–6248
Li L, Lagarias JC (1992) Phytochrome assembly. J Biol Chem 267:19204–19210
Rausenberger J, Hussong A, Kircher S et al (2010) An integrative model for phytochrome B mediated photomorphogenesis: from protein dynamics to physiology. PLoS One 5:e10721
Chen M, Schwab R, Chory J (2003) Characterization of the requirements for localization of phytochrome B to nuclear bodies. Proc Natl Acad Sci U S A 100:14493–14498
Tepperman JM, Hudson ME, Khanna R et al (2004) Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J 38:725–739
Al-Sady B, Kikis EA, Monte E et al (2008) Mechanistic duality of transcription factor function in phytochrome signaling. Proc Natl Acad Sci U S A 105:2232–2237
Park E, Park J, Kim J et al (2012) Phytochrome B inhibits binding of phytochrome-interacting factors to their target promoters. Plant J 72:537–546
Pfeiffer A, Nagel MK, Popp C et al (2012) Interaction with plant transcription factors can mediate nuclear import of phytochrome B. Proc Natl Acad Sci U S A 109:5892–5897
Schäfer E, Schmidt W (1974) Temperature dependence of phytochrome dark reactions. Planta 116:257–266
Medzihradszky M, Bindics J, Ádám É et al (2013) Phosphorylation of phytochrome B inhibits light-induced signaling via accelerated dark reversion in Arabidopsis. Plant Cell 25:535–544
Burgie ES, Bussell AN, Walker JM et al (2014) Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Proc Natl Acad Sci U S A 111:10179–10184
Klose C, Venezia F, Hussong A et al (2015) Systematic analysis of how phytochrome B dimerization determines its specificity. Nat Plants 1:15090
Mancinelli AL (1994) The physiology of phytochrome action. In: Kendrick RE, Kronenberg GMH (eds) Photomorphogenesis in plants. Kluwer Academic Publishers, Dordrecht
Rausenberger J, Tscheuschler A, Nordmeier W et al (2011) Photoconversion and nuclear trafficking cycles determine phytochrome A’s response profile to far-red light. Cell 146:813–825
Hennig L, Büche C, Schäfer E (2000) Degradation of phytochrome A and the high irradiance response in Arabidopsis: a kinetic analysis. Plant Cell Environ 23:727–734
Smith RW, Helwig B, Westphal AH et al (2016) Unearthing the transition rates between photoreceptor conformers. BMC Syst Biol 10:110
Smith RW, Helwig B, Westphal AH et al (2017) Interactions between phyB and PIF proteins alter thermal reversion reactions in vitro. Photochem Photobiol 93:1525–1531
Li H, Zhang J, Vierstra RD et al (2010) Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy. Proc Natl Acad Sci U S A 107:10872–10877
Acknowledgments
We would like to thank Andreas Hiltbrunner and Rik van Rosmalen for testing the tool and for providing valuable feedback as to its usage and how it can be made easier for users. RWS is funded by FP7 Marie Curie Initial Training Network grant agreement number 316723 and EU Horizon 2020 grant agreement number 634942. CF is funded by HFSP Research grant RGP0025/2013.
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Smith, R.W., Fleck, C. (2019). Basic Phytochrome B Calculations. In: Hiltbrunner, A. (eds) Phytochromes. Methods in Molecular Biology, vol 2026. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9612-4_9
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DOI: https://doi.org/10.1007/978-1-4939-9612-4_9
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