. As shown in Extended Data Fig. 1a, an ECS signal is visible in P.tricornutum, the characteristics of which depend on the physiological conditions. Deconvolution of the ECS decay-associated spectra (DAS) (see Supplementary Information and Extended Data Fig. 1b,c) explains these observations by revealing the existence of two ECS components (Fig. 1a), respectively characterized by linear and quadratic responses to the ΔΨ (Fig. 1b). The existence of a quadratic ECS, predicted by theory 7 but observed to date only in green algae mutants (Fig. 1c), but was also suppressed by anaerobiosis or by pharmacological inhibition of mitochondrial activity (Fig. 1d, e). This suggests that the PMF is generated in the dark by the plastidial ATPase, which hydrolyses ATP of mitochondrial origin, as previously suggested in green algae 9 .In Viridiplantae (including green algae and higher plants), the AEPs generating additional ATP in the light comprise cyclic electron flow (CEF) around PS1 10 and the water-to-water cycles (WWC). uptake (U 0 ) increased with light, being ~2.5-fold higher at saturating light intensities than in the dark (Extended Data Fig. 2b, d). We further found that the light-stimulated consumption of oxygen was blocked by DCMU (Extended Data Fig. 2c, d), indicating that it was fed by electrons derived from PS2.Moreover, U 0 linearly increased with O 2 evolution, in agreement with earlier findings in the diatom Thalassiosira pseudonana 15, with a slope indicating that ~10% of the electron flow from PSII participate in WWC, regardless of light intensity (Fig 2b). These results indicate that WWC produces a constant extra ATP per photosynthetically-generated NADPH. This is expected for an AEP that contributes to optimizing CO 2 assimilation at any light intensity, and is not the case for CEF, which is completely insensitive to changes in the photosynthetic flux (LEF, Fig 2a).If this WWC is due to the export of photosynthetic products towards the mitochondrial oxidases, then any mitochondrial dysfunction should negatively affect photosynthetic electron transfer rates (ETR PSII ) and light-dependent growth. Mitochondrial respiration comprises a cyanidesensitive pathway (involving Complex III) and an insensitive pathway involving the alternative oxidase (AOX). We therefore modulated mitochondrial activity by adding increasing amounts of Antimycin A (AA) or myxothiazol (Mx), inhibitors of Complex III, in conditions where the AOX was inhibited by SHAM (see legend to Fig. 2d). Both the ΔΨ d and ETR PSII followed respiration linearly (Fig. 2c, d and Extended Data Fig. 3). The almost complete shut-down of respiration resulted in a decrease of photosynthesis which was independent of light intensity (Fig. 3b).Overall we found that in the dark a PMF is generated in the plastid by hydrolysis of ATP produced in mitochondria (Fig 1d,e and Fig. 2c). Conversely, in the light, respiration increases linearly with photosynthesis (Fig. 2b), and vice versa (Fig. 2d). This tight energetic coupling is likely instrumental for adjusting ...

BackgroundNucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing for several major and deep-branching eukaryotic groups, such as the Stramenopiles, which include the diatoms. Diatoms are highly diverse and ubiquitous species of phytoplankton that play a key role in global biogeochemical cycles. Dissecting chromatin-mediated regulation of genes in diatoms will help understand the ecological success of these organisms in contemporary oceans.ResultsHere, we use high resolution mass spectrometry to identify a full repertoire of post-translational modifications on histones of the marine diatom Phaeodactylum tricornutum, including eight novel modifications. We map five histone marks coupled with expression data and show that P. tricornutum displays both unique and broadly conserved chromatin features, reflecting the chimeric nature of its genome. Combinatorial analysis of histone marks and DNA methylation demonstrates the presence of an epigenetic code defining activating or repressive chromatin states. We further profile three specific histone marks under conditions of nitrate depletion and show that the histone code is dynamic and targets specific sets of genes.ConclusionsThis study is the first genome-wide characterization of the histone code from a stramenopile and a marine phytoplankton. The work represents an important initial step for understanding the evolutionary history of chromatin and how epigenetic modifications affect gene expression in response to environmental cues in marine environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0671-8) contains supplementary material, which is available to authorized users.