SUPPLEMENTARY INFORMATION

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1 An intact light harvesting complex I antenna system is required for complete state transitions in Arabidopsis Samuel L. Benson a+, Pratheesh Maheswaran b++, Maxwell A. Ware b, C. Neil Hunter a, Peter Horton a, Stefan Jansson c, Alexander V. Ruban b and Matthew P. Johnson a* Affiliations: a Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court,Western Bank, Sheffield, S 2TN, United Kingdom. b School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom c Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE Umeå, Sweden. +Present Address: Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom. ++Present Address: Allied Health Sciences Unit, Faculty of Medicine, University of Jaffna, Aadiyapatham Road, Kokuvil East, Kokuvil, Sri Lanka. * Corresponding Author: Matthew P. Johnson (matt.johnson@sheffield.ac.uk). NATURE PLANTS 1

Supplementary Figure 1 Effect of state transitions on phosphorylation state of thylakoid proteins.

or 1 hour of PSII light (I, 30 µmol photons m -2 s -1, 660 nm LEDs).

2 Supplementary Figure 1 Effect of state transitions on phosphorylation state of thylakoid proteins. a, Phosphorylation level of Lhcb1 and 2 Pro-Q/Sypro fluorescence form stained gels b, Anti-phosphothreonine immunodetection of thylakoid proteins. Thylakoids were prepared from plants treated with 1 hour of PSI light (, µmol photons m -2 s -1, 730 nm LEDs) or 1 hour of PSII light (I, 30 µmol photons m -2 s -1, 660 nm LEDs). a Pro-Q Phospho Stain WT ΔLhca1 ΔLhca2 ΔLhca3 Δ pcp43 pd1/d2 plhcii Sypro Ruby protein stain WT ΔLhca1 ΔLhca2 ΔLhca3 Δ b Anti-Phospho Threonine Wild-type ΔLhca1 ΔLhca2 ΔLhca3 Δ pcp43 pd1/d2 plhcii 2 NATURE PLANTS

3 Supplementary Figure 2 Low temperature (77K) fluorescence excitation spectra of wild-type and ΔLhca plants. a, -minus-i excitation (735 nm emission) difference spectrum for wild-type and ΔLhca thylakoids compared to purified LHCII. b, PSII low temperature (77K) fluorescence excitation spectra (705 nm emission, spectra were normalized to the change in the 685/735 nm ratio between and I). shown in blue, I shown in red. a 4 b Fluorescence (Rel.) LHCII trimer WT ΔLhca1 ΔLhca2 ΔLhca3 WT ΔLhca1 ΔLhca2 ΔLhca3 Δ Δ Wavelength (nm) NATURE PLANTS 3

4 Supplementary Figure 3 SYPRO Ruby stained 2D-denaturing PAGE of BN- PAGE. (a) Wild-type, (b) ΔLhca1, (c) ΔLhca3, (d) ΔLhca2, (e) Δ. Supplemental Figure 3. a# b# WT WT I ΔLhca1 ΔLhca1 I c# ΔLhca3 ΔLhca3 I d# ΔLhca2 ΔLhca2 I Lhca3 Lhca2 e# Δ Δ I 4 NATURE PLANTS

5 Supplementary Table 1 Percentage distribution and chlorophyll a/b ratios of thylakoids solubilised with 1% digitonin derived from wild-type Arabidopsis leaves treated for 1 hour with (730 nm) or I (660 nm) light. P700 + formation kinetics (830-8 nm) were measured on isolated thylakoid membranes, membrane fragments or purified PSI-LHCI complexes in the presence of 30 µm DCMU, 0 µm methyl viologen and 0 µm sodium ascorbate (and 0.01% n-dodecyl- α -d-maltoside for PSI-LHCI) to create a donor-limited situation. Traces were fitted with a single exponential functions and the tabulated data is the average of 4 traces per sample. The light intensity was 29 µmol photons m -2 s -1. PSI Antenna size calculated as: (PSI- LHCI t½ sample t½) 0% expressed as a percentage of PSI-LHCI antenna size. Fraction I I I a/b ratio a/b ratio % chlorophyll % chlorophyll P700 + (t½, ms)/ P700 + (t½, ms)/ distribution distribution Calculated PSI Calculated PSI antenna size antenna size % of PSI-LHCI % of PSI-LHCI Whole thylakoids 2.8 ± ± 0.1 0% 0% 179 ± ± 8 111% ± 3 142% ± 3 Grana (40000 x g pellet) 2.2 ± ± ± 3 % 46 ± 5 % 172 ± 8 116% ± ± 11 7% ± 8 Stromal Lamellae ( x g pellet) 4.5 ± ± ± 2 % 12 ± 3 % 185 ± 5 7% ± ± 6 116% ± 3 Supernatant 3.2 ± ± ± 3% 32 ± 4 % - - Purified PSI-LHCI.8 ± ± 12-0% NATURE PLANTS 5

A previously found thylakoid membrane protein of 14 kda (TMP14) is a novel subunit of plant photosystem I and is designated PSI-P

FEBS Letters 579 (2005) 4808 4812 FEBS 29860 A previously found thylakoid membrane protein of 14 kda (TMP14) is a novel subunit of plant photosystem I and is designated PSI-P Anastassia Khrouchtchova a,