Phytochrome-based modules – function and applications
Main funder
Funder's project number: 330678
Funds granted by main funder (€)
- 438 874,00
Funding program
Project timetable
Project start date: 01/09/2020
Project end date: 31/08/2025
Summary
Proteins in nature are modular, consisting of a set of domains with a unique mode of function. The function and interplay of these different domains are challenging to study and control. Phytochromes are excellent model proteins to study these properties. They are modular, red light-sensing photoreceptors found in plants and bacteria. I have revealed structurally how incident light induces of a hierarchy of structural changes that lead to a large opening of the phytochrome photosensory module. This movement changes the activity of the effector module and its interactions with a response regulator protein. However, the structural details of these changes still remain unknown.
Optogenetics is a field of research where protein complexes, and hence cellular processes, are controlled with light. For this, photoreceptor proteins are rationally engineered as optogenetic tools. Currently most of these tools are limited because they sense blue light, are nonreversible, or require external chromophores. Bacterial phytochromes offers a solution for these limitations as they sense red light, are reversible, and use a chromophore native to mammalian cells. These unique properties make them excellent optogenetic tools.
The project will develop new structural understanding of phytochrome signaling and subunit interplay. For detecting initial states of its photoactivation Serial Femtosecond Crystallography will be used. The project will uncover new phytochrome interactions and effector combinations, which will serve as novel ways to apply phytochromes for optogenetics. This information will be used in developing two optogenetic gene regulator tools: a red light-regulated CRISPR-Cas9 and a bacterial pREDusk system. These tools allow non-invasive gene editing in living organisms with spatial and temporal precision, which has enormous advances in bioengineering, biological research, and gene therapy.
The project includes a variation of methods from structural biology and biochemistry to cell biology. It seamlessly combines structural and functional studies on photoreceptors and the generation of new applications. I have a strong background in phytochrome research (e.g. Takala et al. Nature 2014), and this first-hand knowledge will provide an excellent match with the proposed project. The project allows the establishment of a research group in Finland that lies at the interface of structural and cell biology, with a special focus on engineering optogenetic proteins.
Optogenetics is a field of research where protein complexes, and hence cellular processes, are controlled with light. For this, photoreceptor proteins are rationally engineered as optogenetic tools. Currently most of these tools are limited because they sense blue light, are nonreversible, or require external chromophores. Bacterial phytochromes offers a solution for these limitations as they sense red light, are reversible, and use a chromophore native to mammalian cells. These unique properties make them excellent optogenetic tools.
The project will develop new structural understanding of phytochrome signaling and subunit interplay. For detecting initial states of its photoactivation Serial Femtosecond Crystallography will be used. The project will uncover new phytochrome interactions and effector combinations, which will serve as novel ways to apply phytochromes for optogenetics. This information will be used in developing two optogenetic gene regulator tools: a red light-regulated CRISPR-Cas9 and a bacterial pREDusk system. These tools allow non-invasive gene editing in living organisms with spatial and temporal precision, which has enormous advances in bioengineering, biological research, and gene therapy.
The project includes a variation of methods from structural biology and biochemistry to cell biology. It seamlessly combines structural and functional studies on photoreceptors and the generation of new applications. I have a strong background in phytochrome research (e.g. Takala et al. Nature 2014), and this first-hand knowledge will provide an excellent match with the proposed project. The project allows the establishment of a research group in Finland that lies at the interface of structural and cell biology, with a special focus on engineering optogenetic proteins.
Principal Investigator
Primary responsible unit
Related publications and other outputs
- Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome (2022) Lehtivuori, Heli; et al.; A1; OA
- Optogenetic Control of Bacterial Expression by Red Light (2022) Multamäki, Elina; et al.; A1; OA
- Red Light Optogenetics in Neuroscience (2022) Lehtinen, Kimmo; et al.; A2; OA
- Structural mechanism of signal transduction in a phytochrome histidine kinase (2022) Wahlgren, Weixiao Yuan; et al.; A1; OA
- The structural effect between the output module and chromophore-binding domain is a two-way street via the hairpin extension (2022) Kurttila, Moona; et al.; A1; OA
- Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling (2021) Multamäki, Elina; et al.; A1; OA
- Site-by-site tracking of signal transduction in an azidophenylalanine-labeled bacteriophytochrome with step-scan FTIR spectroscopy (2021) Kurttila, Moona; et al.; A1; OA
- The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome : a UV–vis absorption spectroscopy study (2021) Rumfeldt, Jessica; et al.; A1; OA
- The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature (2021) Cellini, Andrea; et al.; A1; OA
