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Light-induced structural changes in a full-length cyanobacterial phytochrome probed by time-resolved X-ray scattering
Abstract
Phytochromes are photoreceptor proteins that transmit a light signal from a photosensory region to an output domain. Photoconversion involves protein conformational changes whose nature is not fully understood. Here, we use time-resolved X-ray scattering and optical spectroscopy to study the kinetics of structural changes in a full-length cyanobacterial phytochrome and in a truncated form with no output domain. X-ray and spectroscopic signals on the µs/ms timescale are largely independent of the presence of the output domain. On longer time-scales, large differences between the full-length and truncated proteins indicate the timeframe during which the structural transition is transmitted from the photosensory region to the output domain and represent a large quaternary motion. The suggested independence of the photosensory-region dynamics on the µs/ms timescale defines a time window in which the photoreaction can be characterized (e.g. for optogenetic design) independently of the nature of the engineered output domain.
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Aging is manifested as a progressive functional decline leading to exponentially increasing prevalence and incidence of chronic age-related diseases and disease-specific mortality.
“Aging is manifested as a progressive functional decline leading to exponentially increasing prevalence1,2 and incidence of chronic age-related diseases (e.g., cancers, diabetes, cardiovascular diseases, etc.3–5) and disease-specific mortality6.”
From Longitudinal Analysis of Blood Markers Reveals Progressive Loss of Resilience and Predicts Human Lifespan Limit (2021) · cites this paper as [3]
The Discussion and Results passages concern light-induced structural changes in a cyanobacterial phytochrome, not human aging or chronic disease. Searches for progressive functional decline, age-related disease prevalence and incidence, and disease-specific mortality found no passage addressing the claim. Page numbers are unavailable in our copy. (LLM, conf=0.78)
Experimental — accuracy not yet measuredAll-cause mortality in humans and the incidence of chronic age-related diseases increase exponentially and double every 8 years.
“All-cause mortality in humans17,18 and the incidence of chronic age-related diseases increase exponentially and double every 8 years3.”
From Longitudinal Analysis of Blood Markers Reveals Progressive Loss of Resilience and Predicts Human Lifespan Limit (2021) · cites this paper as [3]
Citation 3 is attached to the claim about chronic age-related disease incidence. The Results sections on time-resolved X-ray scattering and transient absorption spectroscopy report millisecond-scale changes in a cyanobacterial phytochrome, not human disease incidence. Searches for age-related disease incidence and eight-year doubling found no passage addressing that claim; the mortality clause carries separate citations. (LLM, conf=0.78)
Experimental — accuracy not yet measuredThe assumption that all chronic diseases and death originate from single protective barrier crossings could naturally explain why mortality and the incidence of major age-related diseases increase exponentially with age at approximately the same rate.
“This is, of course, a simplification and yet the assumption could naturally explain why mortality and the incidence of major age-related diseases increase exponentially with age at approximately the same rate3.”
From Longitudinal Analysis of Blood Markers Reveals Progressive Loss of Resilience and Predicts Human Lifespan Limit (2021) · cites this paper as [3]
The Results (Time-resolved X-ray scattering; page unavailable) describe exponential lifetimes for light-induced changes in a cyanobacterial phytochrome, not age-related mortality or disease incidence. Searches for mortality, age-related disease, and protective barrier crossings found no passage in our copy addressing the claim. (LLM, conf=0.77)
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Research works printed but not linked: 22
- Nagy, F. & Schäfer, E. Phytochromes control photomorphogenesis by differentially regulated, interacting signaling pathways in higher plants. Annu. Rev. Plant. Biol. 53, 329–355 (2002). · DOI
- Rockwell, N. C. & Clark Lagarias, J. A Brief History of Phytochromes. Chemphyschem 11, 1172–1180 (2010). · DOI
- Chernov, K. G., Redchuk, T. A., Omelina, E. S. & Verkhusha, V. V. Near-infrared fluorescent proteins, biosensors, and optogenetic tools engineered from phytochromes. Chem. Rev. 117, 6423–6446 (2017). · DOI
- Burgie, E. S., Walker, J. M., Phillips, G. N., Jr. & Vierstra, R. D. Crystal structure of the blue-light absorbing form of the Thermosynechococcus elongatus PixJ GAF-domain. Struct. Summ. https://www.ncbi.nlm.nih.gov/Structure/pdb/4FOF (2013). · DOI
- Cornilescu, C. C. et al. Dynamic structural changes underpin photoconversion of a blue/green cyanobacteriochrome between its dark and photoactivated states. J. Biol. Chem. 289, 3055–3065 (2014). · DOI
- von Stetten, D. et al. Highly conserved residues Asp-197 and His-250 in Agp1 phytochrome control the proton affinity of the chromophore and Pfr formation. J. Biol. Chem. 282, 2116–2123 (2007). · DOI
- Heyes, D. J. et al. Ultrafast red light activation of Synechocystis phytochrome Cph1 triggers major structural change to form the Pfr signalling-competent state. PLoS ONE 7, e52418 (2012). · DOI
- Björling, A. et al. Structural photoactivation of a full-length bacterial phytochrome. Sci. Adv. 2, e1600920 (2016). · DOI
- Takala, H. et al. Signal amplification and transduction in phytochrome photosensors. Nature 509, 245–248 (2014). · DOI
- Burgie, E. S., Zhang, J. & Vierstra, R. D. Crystal structure of Deinococcus phytochrome in the photoactivated state reveals a cascade of structural rearrangements during photoconversion. Structure 24, 448–457 (2016). · DOI
- Takala, H. et al. Light-induced structural changes in a monomeric bacteriophytochrome. Struct. Dyn. 3, 054701 (2016). · DOI
- Hirai, M., Iwase, H., Hayakawa, T., Miura, K. & Inoue, K. Structural hierarchy of several proteins observed by wide-angle solution scattering. J. Synchrotron Radiat. 9, 202–205 (2002). · DOI
- Cammarata, M. et al. Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering. Nat. Methods 5, 881–886 (2008). · DOI
- Remberg, A. et al. Raman spectroscopic and light-induced kinetic characterization of a recombinant phytochrome of the cyanobacterium Synechocystis. Biochemistry 36, 13389–13395 (1997). · DOI
- van Thor, J. J. et al. Light-induced proton release and proton uptake reactions in the cyanobacterial phytochrome Cph1. Biochemistry 40, 11460–11471 (2001). · DOI
- Essen, L.-O., Mailliet, J. & Hughes, J. The structure of a complete phytochrome sensory module in the Pr ground state. Proc. Natl Acad. Sci. USA 105, 14709–14714 (2008). · DOI
- Takala, H., Björling, A., Linna, M., Westenhoff, S. & Ihalainen, J. A. Light-induced changes in the dimerization interface of bacteriophytochromes. J. Biol. Chem. 290, 16383–16392 (2015). · DOI
- Choudry, U. et al. Photochemical mechanism of an atypical algal phytochrome. ChemBioChem. 19, 1036-1043 (2018). · DOI
- Gourinchas, G. et al. Long-range allosteric signaling in red light-regulated diguanylyl cyclases. Sci. Adv. 3, e1602498 (2017). · DOI
- Etzl, S., Lindner, R., Nelson, M. D. & Winkler, A. Structure-guided design and functional characterization of an artificial red light-regulated guanylate/adenylate cyclase for optogenetic applications. J. Biol. Chem. 293, 9078–9089 (2018). · DOI
- Henry, E. R. & Hofrichter, J. [8] Singular value decomposition: application to analysis of experimental data. Methods Enzymol. 210, 129–192 (1992). · DOI
- Franke, D. et al. a comprehensive data analysis suite for small-angle scattering from macromolecular solutions. J. Appl. Crystallogr. 50, 1212–1225 (2017). · DOI
Cited by
Sorted by citations
Pyrkov, T. V., Avchaciov, K., Tarkhov, A. E., Menshikov, L. I., Gudkov, A. V., & Fedichev, P. O. (2021) · Nature Communications · doi:10.1038/s41467-021-23014-1 · Cited by 139
Metadata
- Authors
- Heyes, D. J., Hardman, S. J. O., Pedersen, M. N., Woodhouse, J., De La Mora, E., Wulff, M., Weik, M., Cammarata, M., Scrutton, N. S., & Schirò, G.
- Venue
- Communications Biology
- Published
- 2019-01-03
- Volume
- 2
- Issue
- 1
- ISSN
- 2399-3642
- PMC
- PMC6318211
- Cited by
- 132
- References
- 0
- Language
- en
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