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Structural insights into photoactivation and signalling in plant phytochromes

Abstract

Plant phytochromes are red/far-red photochromic photoreceptors that act as master regulators of development, controlling the expression of thousands of genes. Here, we describe the crystal structures of four plant phytochrome sensory modules, three at about 2 Å resolution or better, including the first of an A-type phytochrome. Together with extensive spectral data, these structures provide detailed insight into the structure and function of plant phytochromes. In the Pr state, the substitution of phycocyanobilin and phytochromobilin cofactors has no structural effect, nor does the amino-terminal extension play a significant functional role. Our data suggest that the chromophore propionates and especially the phytochrome-specific domain tongue act differently in plant and prokaryotic phytochromes. We find that the photoproduct in period–ARNT–single-minded (PAS)–cGMP-specific phosphodiesterase–adenylyl cyclase–FhlA (GAF) bidomains might represent a novel intermediate between MetaRc and Pfr. We also discuss the possible role of a likely nuclear localization signal specific to and conserved in the phytochrome A lineage.

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Fig. 1: UV–vis absorbance and CD spectra of the seven plant phytochrome constructs investigated.
Fig. 2: Sb.phyB(PG)–PCB 1.8 Å structure (PDB 6TBY).
Fig. 3: Gm.phyB(PGP)–PCB 2.9 Å structure (PDB 6TL4).
Fig. 4: Gm.phyA(PG)–PCB 2.1 Å structure (PDB 6TC7).

Data availability

The three-dimensional structural data that support the findings of this study have been deposited in wwPDB with the accession codes 6TBY, 6TC5, 6TL4 and 6TC7. The authors declare that all other data supporting the findings of this study are available within the paper and its Supplementary Information files.

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Acknowledgements

We thank SFB 1078 for funding (subprojects B6 to P.H. and B8 to J.H.). The X-ray diffraction measurements were carried out at BL14.1 at BESSY II (Helmholtz-Zentrum Berlin für Materialien und Energie (HZB)) and at ID30-A3 at ESRF with support from CALIPSOplus (Grant Agreement 730872 of the EU Framework Programme HORIZON 2020) and HZB. We thank L.-O. Essen (University of Marburg) for collaboration in the early stages of the project, W. Wende (Giessen) for cooperation in measuring the CD spectra and C. Lang (Giessen) for expert technical assistance. We dedicate this paper to the memory of Winslow Briggs.

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S.N., G.K. and S.M.S. designed, cloned, expressed, purified and crystallized the holophytochrome constructs. S.N. solved the structures with suggestions from C.F. and M.W. S.N. and J.H. interpreted the structures. A.K., D.B. and P.H. measured and interpreted the vibrational spectra. J.H. wrote the manuscript with the participation of P.H. and in discussion with all authors. J.H. devised and co-ordinated the project.

Corresponding author

Correspondence to Jon Hughes.

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Extended data

Extended Data Fig. 1 RR and IR difference spectra of phyA and phyB constructs.

Left, Sorghum bicolor; Right Glycine max. Above: RR spectra of the Pr states (blue traces) and their photoconversion products (red traces) obtained upon 670 and 750 nm irradiation at ambient temperature. All spectra were measured at 90 K with 1064 nm excitation. The spectral regions labelled are indicative of (i) the methine bridge configurations and conformations (C=C stretching modes of the A-B and C-D methine bridges at ca. 1600–1650 cm−1), (ii) pyrrole nitrogen protonation state (N-H in-plane bending modes of rings B and C at ca. 1550 – 1580 cm−1) and (iii) the C-D methine bridge torsion (hydrogen-out-of-plane [HOOP] mode at ca. 795 - 825 cm−1). The broad feature at ca. 1460 cm−1 is largely due to non-resonant Raman bands of the protein. The high intensity of this feature relative to the RR bands of the chromophore indicates that the latter experience a low resonance enhancement. Below: IR “photoproduct minus Pr” difference spectra obtained upon irradiation with 670 and 750 nm at ambient temperature. The positive signals indicated by black lines and labels refer to the photoproduct, whereas the grey lines and labels mark the signals of the Pr state. Representative spectra based on at least two samples are shown. Spectra for each sample were measured several times. Each spectrum is based on 1000 separate FT scans.

Extended Data Fig. 2 Sb.phyB(PG)-PCB and -PΦB structures are almost identical.

Above: Superimposition of peptide chains with chromophores. The N- and C-termini, the two unresolved loops and the somewhat deviant R234-D236 regions are labelled. Inset: superimposition of the PCB (cyan) and P(B (green) D rings. Below: Chemical structures of PCB, PΦB, and the incorrect model used in 4OUR (PDB cofactor codes CYC, O6E and 2VO, respectively). Note that the uncharged structures are shown, whereas in both Pr and Pfr holoprotein states all four cofactor nitrogens are protonated.

Extended Data Fig. 3 Gm.phyA(PG)-PCB 2.1 Å structure (PDB 6TC7) of subunit B.

PCB (cyan), PAS (slate), GAF (gold), PCB (cyan), waters (red spheres). PW, pyrrole water. Subunit A (grey) is superimposed.

Extended Data Fig. 4 Gm.phyA(PG)-PCB 2.1 Å structure (PDB 6TC7) of subunit B including side chains and hydrogen bonding network.

Note that the weak (3.1 Å) D-ring carbonyl – H370 hydrogen bond in subunit B is somewhat stronger (3.0 Å) in subunit A. PCB (cyan), PAS (slate), GAF (gold), PCB (cyan), waters (red spheres). PW, pyrrole water.

Extended Data Fig. 5 Putative Class I NLS specific to A-type plant phytochromes.

Above. Superimposition of Gm.phyA(PG)-PCB subunit B (GAF domain, gold) with subunit A (grey) superimposed. Although the more mobile N-terminal section of the “380s” loop is missing (gold dashes), the final triad of the putative NLS (R360-R362) is resolved. Below. Alignment of the “380s” loop region in plant phytochromes (from Mathews et al. 47). sm, Selaginella martensii; cp, Ceratodon purpureus; ac, Adiantum caperis-veneris; atA-D, Arabidopsis thaliana PHYA-D; cpA, Curcurbita pepo PHYA; psA, Pisum sativum PHYA; stA/B, Solanum tuberosum PHYA/B, asA-D, Avena sativa PHYA; osA/B, Oryza sativa PHYA/B; zmA, Zea mais PHYA. The K(R/K)K(R/K) consensus is boxed red.

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Supplementary Figs. 1–3, Tables 1 and 2, and references.

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Nagano, S., Guan, K., Shenkutie, S.M. et al. Structural insights into photoactivation and signalling in plant phytochromes. Nat. Plants 6, 581–588 (2020). https://doi.org/10.1038/s41477-020-0638-y

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