Multi-omic analysis showsREVEILLEclock genes are involved in carbohydrate metabolism and proteasome function

Abstract

Plants are able to sense changes in their light environments, such as the onset of day and night, as well as anticipate these changes in order to adapt and survive. Central to this ability is the plant circadian clock, a molecular circuit that precisely orchestrates plant cell processes over the course of a day. REVEILLE proteins (RVEs) are recently discovered members of the plant circadian circuitry that activate the evening complex and PSEUDO-RESPONSE REGULATOR (PRR) genes to maintain regular circadian oscillation. The REVEILLE (RVE) 8 protein and its two homologs, RVE 4 and 6 in Arabidopsis (Arabidopsis thaliana), have been shown to limit the length of the circadian period, with rve 4 6 8 triple-knockout plants possessing an elongated period along with increased leaf surface area, biomass, cell size and delayed flowering relative to wild-type Col-0 plants. Here, using a multi-omics approach consisting of phenomics, transcriptomics, proteomics, and metabolomics we draw new connections between RVE8-like proteins and a number of core plant cell processes. In particular, we reveal that loss of RVE8-like proteins results in altered carbohydrate, organic acid and lipid metabolism, including a starch excess phenotype at dawn. We further demonstrate that rve 4 6 8 plants have lower levels of 20S proteasome subunits and possess significantly reduced proteasome activity, potentially explaining the increase in cell-size observed in RVE8-like mutants. Overall, this robust, multi-omic dataset provides substantial insight into the far-reaching impact RVE8-like proteins have on the diel plant cell environment.

Integrated Systems-Level Proteomics and Metabolomics Reveals the Diel Molecular Landscape of Diverse Kale Cultivars

“…Mechanistically, we observe differences in proteins linked to light perception and the circadian clock (e.g. CRY1), while simultaneously finding group-specific differences in multiple metabolites connected to the circadian clock (Cervela-Cardona et al 2021;Haydon et al 2013;Scandola et al 2022). Overall, our endeavor to define the underlying molecular landscape of diverse, commercially grown kale cultivars has opened up extraordinary opportunities for horticultural production activities moving forward.…”

Submergence Stress Alters the Expression of Clock Genes and Configures New Zeniths and Expression of Outputs in Brachypodium distachyon

“…Another interesting gene is FKF1, a repressor of cellulose synthesis and elongation [55]; its strong up-regulation can indicate that it is a crucial component of the quiescent response under submergence (Figure 4D). Finally, RVE1, a clock component that promotes enzymes for starch degradation and glucose catabolism [56], is more down-regulated in tolerant Bd21-3 and may be associated with the up-regulation of starch metabolism transcripts in sensitive Bd21.…”

Circadian regulation of metabolism across photosynthetic organisms

“…Of particular note are the transcripts encoding GWD and PWD, whose products catalyze early steps of starch degradation (Usadel et al., 2008 ). SEX4 transcripts are expressed at very low levels in the circadian oscillator triple mutant rve468 , leading to an increased starch content phenotype (Scandola et al., 2022 ). This starch excess phenotype also occurs in the prr7 prr9 double mutant (Chew et al., 2022 ; Flis et al., 2019 ).…”