Comparative proteomics of thylakoids from Arabidopsis grown in laboratory and field conditions

Abstract

Compared to controlled laboratory conditions, plant growth in the field is rarely optimal since it is frequently challenged by large fluctuations in light and temperature which lower the efficiency of photosynthesis and lead to photo‐oxidative stress. Plants grown under natural conditions therefore place an increased onus on the regulatory mechanisms that protect and repair the delicate photosynthetic machinery. Yet, the exact changes in thylakoid proteome composition which allow plants to acclimate to the natural environment remain largely unexplored. Here, we use quantitative label‐free proteomics to demonstrate that field‐grown Arabidopsis plants incorporate aspects of both the low and high light acclimation strategies previously observed in laboratory‐grown plants. Field plants showed increases in the relative abundance of ATP synthase, cytochrome b6f, ferredoxin‐NADP+ reductases (FNR1 and FNR2) and their membrane tethers TIC62 and TROL, thylakoid architecture proteins CURT1A, CURT1B, RIQ1, and RIQ2, the minor monomeric antenna complex CP29.3, rapidly‐relaxing non‐photochemical quenching (qE)‐related proteins PSBS and VDE, the photosystem II (PSII) repair machinery and the cyclic electron transfer complexes NDH, PGRL1B, and PGR5, in addition to decreases in the amounts of LHCII trimers composed of LHCB1.1, LHCB1.2, LHCB1.4, and LHCB2 proteins and CP29.2, all features typical of a laboratory high light acclimation response. Conversely, field plants also showed increases in the abundance of light harvesting proteins LHCB1.3 and CP29.1, zeaxanthin epoxidase (ZEP) and the slowly‐relaxing non‐photochemical quenching (qI)‐related protein LCNP, changes previously associated with a laboratory low light acclimation response. Field plants also showed distinct changes to the proteome including the appearance of stress‐related proteins ELIP1 and ELIP2 and changes to proteins that are largely invariant under laboratory conditions such as state transition related proteins STN7 and TAP38. We discuss the significance of these alterations in the thylakoid proteome considering the unique set of challenges faced by plants growing under natural conditions.

STN7 is not essential for developmental acclimation of Arabidopsis to light intensity

“…To investigate whether these differences in growth and photosynthetic traits were caused by a failure of the stn7 plants to adjust the stoichiometry of the photosynthetic complexes to light intensity, we employed label‐free quantitative (LFQ) mass spectrometry (MS) using a method previously described and validated with orthogonal approaches (Flannery et al., 2021a , b ). Three biological replicate thylakoid membrane preparations from each of the WT, stn7 , and tap38 plants grown under LL, ML, and HL (27 samples in total) were analysed by nanoLC‐MS as three technical repeats in randomised order.…”

“…Building on our earlier characterisation of the proteomic changes associated with developmental acclimation to changes in white light intensity and indoor versus outdoor growth environments (Flannery et al., 2021a , b ), here we addressed the role of STN7 and its cognate phosphatase TAP38 in the LTR. Previous work showed that stn7 plants, unlike the WT, were unable to change their PSI/PSII ratio, LHCII/PSII ratio, or chlorophyll a / b ratio in response to varying spectral quality (Bonardi et al., 2005 ; Pesaresi et al., 2009 ).…”

“…The extent to which the growth and CO 2 assimilation phenotypes in stn7 and tap38 are primarily related to a failure of short-or longterm adaptation strategies remains unclear. In this study we combine label-free quantitative proteomics (Flannery et al, 2021a(Flannery et al, , 2021b with photosynthetic phenotyping using structured illumination microscopy, electron microscopy, chlorophyll fluorescence, and absorption spectroscopy to test the ability of the stn7 and tap38 mutants to acclimate to long-term growth under LL, ML, or HL conditions.…”

Comparative transcriptomics of Hirschfeldia incana and relatives highlights differences in photosynthetic pathways

“…However, this trend of lower or unchanged gene expression was unexpected for genes related to photosynthetic light reactions (included in the “Photosynthesis” pathway, ath00195) and carbon metabolism (included in the homonymous pathway, ath01200). Recent studies of changes in the A. thaliana proteome in response to irradiance increase or switch from controlled to field conditions have highlighted increases in abundance for most proteins involved in light reactions [87, 60]. Furthermore, ample experimental evidence has been collected in the past showing that plants acclimating to high light develop a higher carbon fixation metabolism via increased protein levels [88].…”