Interdependent iron and phosphorus availability controls photosynthesis through retrograde signaling

International audienceAbstract Iron deficiency hampers photosynthesis and is associated with chlorosis. We recently showed that iron deficiency-induced chlorosis depends on phosphorus availability. How plants integrate these cues to control chlorophyll accumulation is unknown. Here, we show that iron limitation downregulates photosynthesis genes in a phosphorus-dependent manner. Using transcriptomics and genome-wide association analysis, we identify two genes, PHT4;4 encoding a chloroplastic ascorbate transporter and bZIP58 , encoding a nuclear transcription factor, which prevent the downregulation of photosynthesis genes leading to the stay-green phenotype under iron-phosphorus deficiency. Joint limitation of these nutrients induces ascorbate accumulation by activating expression of an ascorbate biosynthesis gene, VTC4 , which requires bZIP58. Furthermore, we demonstrate that chloroplastic ascorbate transport prevents the downregulation of photosynthesis genes under iron-phosphorus combined deficiency through modulation of ROS homeostasis. Our study uncovers a ROS-mediated chloroplastic retrograde signaling pathway to adapt photosynthesis to nutrient availability

Additional file 1: of Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction

Tables S1, S3 and S4 list the candidate transcriptional regulators predicted in Arabidopsis, fruit fly, and human, respectively. Table S2 shows the number of families predicted from the genome by each criterion and the enrichment fold yield by each criteria towards the identification of regulators in Arabidopsis, fruit fly and human. Table S5 lists the physical interactions between predicted regulators and proteins involved in transcription available in the BioGRID database [108] and determined in this study. Table S6 shows the results of the segregation analysis of chiq1–1 phenotype (dwarfism) in the F2 populations of chiq1–1 x Col-0 (wild type) crosses. Table S7 shows the results of the linkage analysis of chiq1–1 phenotype (dwarfism) and genotype in the F2 populations of chiq1–1 x Col-0 (wild type) crosses. Table S8 lists the proteins that co-immunoprecipitated (Co-IP/MS) with CHIQ1-GFP in vivo. Table S9 lists the physical interactions among nine CHIQ proteins. Figure S1 illustrates the pipeline workflow and the number of predictions in yeast, fruit fly and human. Figure S2 shows the proportion of unknown genes in families with less than three or more than two members in Arabidopsis, yeast, fruit fly and human and the proportion of the predictions among the unknown families with more than two members. Figure S3 shows the precision, recall and F1 score of TF predictions in Arabidopsis. Figure S4 shows the maximum number of aspartic acid, glutamic acid, asparagine, glutamine, serine, proline and acidic amino acids in all proteins, TFs and the predicted regulators in Arabidopsis, fruit fly and human. Figure S5 shows the GUS activity of the negative controls for the in planta transactivation assay. Figure S6 shows the number of leaves at different ages and the age of bolting in wild type (Col-0), chiq1–1 and B12 (complemented line). (DOCX 1780 kb

Poly(A)-binding protein is an ataxin-2 chaperone that emulsifies biomolecular condensates

Biomolecular condensation underlies the biogenesis of an expanding array of membraneless assemblies, including stress granules (SGs) which form under a variety of cellular stresses. Advances have been made in understanding the molecular grammar that dictates the behavior of a few key scaffold proteins that make up these phases but how the partitioning of hundreds of other SG proteins is regulated remains largely unresolved. While investigating the rules that govern the condensation of ataxin-2, a SG protein implicated in neurodegenerative disease, we unexpectedly identified a short 14aa sequence that acts as an ataxin-2 condensation switch and is conserved across the eukaryote lineage. We identify poly(A)-binding proteins as unconventional RNA-dependent chaperones that control this regulatory switch. Our results uncover a hierarchy of cis and trans interactions that fine-tune ataxin-2 condensation and reveal a new molecular function for ancient poly(A)-binding proteins as emulsifiers of biomolecular condensate proteins. These findings may inspire novel approaches to therapeutically target aberrant phases in disease

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation

Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change. [Abstract copyright: Copyright © 2021 Elsevier Inc. All rights reserved.