From Computational Biology Group
Being sessile organisms, plants posses various mechanisms to react to different and changing environmental stimuli. One of these mechanisms allows plants to adjust their growth direction to the direction of incoming blue light. This phototropic response involves sensing of light by photoreceptors, here mainly the membrane-associated proteins phot1 and phot2 , redirection of the flux of the hormone auxin [1, 3, 5, 10, 11], as well as other downstream signaling events [2, 4, 6, 7, 9, 12]. Although these key players in phototropism in Arabidopsis thaliana are known, detailed means of interaction remain hidden.
The current view on phototropism can be summarized as follows: phototropism is a blue light- initiated process with its response being fluence rate dependent. For simplicity, here only low fluence rates of maximally 0.1 μmol m-2s -1 are considered—a scenario in which the phototropic response depends mostly on the activity of the photo receptor phot1. Under these fluence conditions, the second receptor of the same family, phot2, can be neglected. In addition, the two cryptochromes cry1 and cry2 have a mild effect on phototropism  but are not further considered here.
Considering the fact that during phototropism a lateral auxin gradient with its maximum on the shaded side is formed, the question arises how it is possible that such a gradient is established. Here, it is of special interest why the maximum of the gradient is located on the shaded side since the original blue light stimulus is applied to the opposite side and photo-activation seems to be positively fluence correlated. Still, one can argue that the light absorption of a tissue like a dark grown hypocotyl (with a diameter of about 250μm) hardly absorbs any light but then one would need to question why a gradient is formed at all.
In the course of this project, it is planned to investigate this gradient formation relying on both, experimental techniques as well as computational modeling, collaborating with the groups of Richard Smith and Christian Fankhauser as part of the Plant Growth project from SystemsX.ch.
-  J. J. Blakeslee, A. Bandyopadhyay, W. A. Peer ans S. N. Makam, and A. S. Murphy. Relocalization of the PIN1 Auxin Efflux Facilitator Plays a Role in Phototropic Responses. Plant Physiol, 134(1):28–31, 2004.
-  M.deCarbonnel,P.Davis,M.R.G.Roelfsema,S.Inoue,I.Schepens,P.Lariguet,M.Geisler,K.Shimazaki,R.Hangarter, and C. Fankhauser. The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 Protein Is a Phototropin Signaling Element That Regulates Leaf Flattening and Leaf Postitioning. Plant Physiol, 152(3):1391–1405, 2010.
-  C. A. Esmon, A. G. Tinsley, K. Ljung, G. Sandberg, L. B. Hearne, and E. Liscum. A gradient of auxin and auxin- dependent transcription precedes tropic growth responses. P Natl Acad Sci USA, 103(1):236–241, 2006.
-  K. M. Folta, E. J. Lieg, T. Durham, and E. P. Spalding. Primary Inhibition of Hypocotyl Growth and Phototropism Depend Differently on Phototropin-Mediated Increases in Cytoplasmic Calcium Induced by Blue Light. Plant Physiol, 133(4):1464–1470, 2003.
-  J. Friml, J. Wiśniewska, E. Benková, K. Mendgen, and K. Palme. Lateral relocation of auxin efflux regulator PIN3 mediates tropism in Arabidopsis. Nature, 415(6873):806–809, 2002.
-  A.HaradaandK.Shimazaki.PhototropinsandBlueLight-dependentCalciumSignalinginHigherPlants.Photochem Photobiol, 83(1):102–111, 2007.
-  S. Inoue, T. Kinoshita, M. Matsumoto, K. I. Nakayama, M. Doi, and K. Shimazaki. Blue light-induced autophospho- rylation of phototropin is a primary step for signaling. P Natl Acad Sci USA, 105(14):5626–5631, 2008.
-  M. Kimura and T. Kagawa. Phototropin and light-signaling in phototropism. Curr Opin Plant Biol, 9(5):503–508, 2006.
-  P. Lariguet, I Schepens, D. Hodgson, U. V. Pedmale, M. Trevisan, C. Kami, M. de Carbonnel, J. M. Alonso, J. R. Ecker, E. Liscum, and C. Fankhauser. PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism. P Natl Acad Sci USA, 103(26):10134–10139, 2006.
-  B. Noh, A. Bandyopadhyay, W. A. Peer, E. P. Spalding, and A. S. Murphy. Enhanced gravi- and phototropism in plant mdr mutants mislocalizing the auxin efflux protein PIN1. Nature, 423(6943):999–1002, 2003.
-  W. A. Peer, A. Bandyopadhyay, J. J. Blakeslee, S. N. Makam, R. J. Chen, P. H. Masson, and A. S. Murphy. Variation in Expression and Protein Localization of the PIN Family Auxin Efflux Facilitator Proteins in Flavonoid Mutants with Altered Auxin Transport in Arabidopsis thaliana. Plant Cell, 16(7):1898–1911, 2004.
-  Y.-L. Wan, W. Eisinger, D. Ehrhardt, U. Kubitscheck, F. Baluska, and W. Briggs. The Subcellular Localization and Blue-Light-Induced Movement of Phototropin 1-GFP in Etiolated Seedlings of Arabidopsis thaliana. Mol Plant, 1 (1):103–117, 2008.