Plant Light Perception and Utilization Research Unit

Research

Research projects of Plant Photo- and Chronobiology Group

Three main research programs are run in the Plant Photo- and Chronobiology Group.

During these programs we want to understand:

I, the molecular mechanism of plant light sensing.

II, the regulation of plant circadian clock.

III, the mechanism and function of different quality control systems in plants.
 

I. Molecular mechanism of plant light regulation

 I/1. Phytochrome signal transduction

Phytochrome photoreceptors play critical role in red and far-red light sensing in plants. In the dicot model organism Arabidopsis thaliana five partially redundant phytochromes have been described. Although phytochrome signaling has been intensively studied, the role of individual phytochromes especially the minor phytochromes (phytochrome C, D and E), their connections and the fine tuning of phytochrome responses are not well understood. In a long term program, we have elaborated an experimental system that allows us to study the function of each phytochrome separately or in different combinations. Detailed description of each phytochrome mediated signal transduction pathways allows us to incorporate the components of each pathway into different organisms thereby activity of transgenes could be precisely regulated by proper light treatments.

I/2. The role of post-translational modifications of photoreceptors in light responses

Plant light regulation is controlled at many different levels. Our group has been studying for a long time the role of post-translational modifications (PTM) of photoreceptors in light regulation. We have shown that both phosphorylation and SUMOylation of the major phytochrome PHYB play critical role in proper red light responses. We have also identified many PTMs (1) on the far-red sensitive phytochrome PHYA photoreceptor, (2) on the UV-B sensitive UVR8 photoreceptor and (3) on the PIF3 major light signal component. During this program the biological relevance of these PTMs are experimentally tested, the given genes are inactivated, and then complementation assays are conducted with mutated genes in which the PTMs are altered. The success of the project could significantly contribute to our knowledge about plant light regulation.

II. Novel regulatory mechanisms of the plant circadian clock

Eukaryotic circadian clocks are oscillating gene networks, where the primary rhythm is generated at the level of transcription and is then adjusted by several additional mechanisms in order to keep the app. 24 h period. The proper pace/speed of the clock is essential to maintain synchrony with the environment. After performing a successful mutant screen in Arabidopsis thaliana, we identified mutations in two proteins pointing to novel regulatory modes of the plant circadian clock. The first protein is an ubiquitin protease (UBP12) removing ubiquitin moieties from proteins, including clock proteins. Analysis of the specific mutation that we identified revealed that the protease activity, and so the stabilization function of UBP12 towards clock proteins, is inhibited by phosphorylation.  Orthologues of UBP12 are present in many eukaryotic organisms ranging from yeast to humans, in some cases the circadian clock-related function of the orthologue has also been demonstrated. Intriguingly, the particular residue that is potentially phosphorylated in UBP12 is strongly conserved in virtually all of the UBP12-like proteins from other hosts. Thus we aim at testing if phosphorylation at the identified specific amino acid is a general mode of tuning UBP12 activities, including circadian functions, in distantly related organisms.

The other protein (UHD1) has a well-known general protein interacting domain at the N-terminal part, whereas the mutation we identified marks a plant specific domain at the C-terminus with a yet unknown function. We showed recently that UHD1 physically interacts with the TOC1 protein, a central component of the plant circadian oscillator. Moreover, comparison of transcriptomic datasets from uhd1 mutants and TOC1 over-expressor lines revealed a large group of differentially expressed genes that are present in both backgrounds. This suggests that UHD1 probably attenuates the function of TOC1 via direct binding. Thus, our current research focuses on the molecular details and mechanisms of the discovered UHD1-TOC1 physical/functional interaction.

This research program will reveal significant novel details of the molecular structure of the plant clock, but also could contribute to a better understanding of the evolution of circadian regulation.

III. Mechanism and regulation of plant quality control systems

Most of the quality control systems function during translation. We study two translation coupled RNA quality control systems in plant: the Nonsense-mediated mRNA decay (NMD) system (III/1), which degrades premature termination codon containing aberrant transcripts, and the No-go decay (NGD) system (III/2), which eliminates faulty transcripts harboring elongation blocking sequences. Moreover, we want to unravel how these systems cooperate with other quality control systems and their role in stress responses.

III/1. The role of NMD in plant stress responses and how it functions in haploid algae

Translation of premature termination codon (PTC) containing aberrant mRNAs could lead to the generation of detrimental, potentially dominant negative truncated proteins, thus elimination of these faulty transcripts is important in eukaryotes. Previously we have identified the cis and trans factors of plant NMD and revealed how it is autoregulated. During this project we want to analyze the role of NMD in heat stress responses (in collaboration with the Plant Stress Biology Group of MATE). We hypothesize that heat stress leads to enhanced production of faulty mRNAs including PTC containing aberrant transcripts and that NMD mediated degradation of these aberrant transcripts plays an important role in adaptive heat stress response. Indeed, we have found that NMD mutants are heat sensitive and that in heat response NMD cooperates with TFIIS mediated transcriptional quality control system.

NMD has been studied only in diploid (or polyploid) organisms. In these organisms the advantage of efficient NMD is obvious, if a mutant allele, which encodes PTC containing aberrant mRNAs, is present in heterozygous form, NMD mediated decay of the aberrant transcripts allows that only perfect transcripts generated from the normal allele can be translated.  However, it is not clear whether in a haploid organism like in Chlamydomonas green alga NMD is advantageous, maybe translation of truncated proteins from the PTC containing transcript is better than no protein production. Our goal is to clarify whether NMD functions in Chlamydomonas. We identified the potential NMD components in Chlamydomonas and tested whether transcripts, which are targeted in plants by NMD, accumulate in green alga or not. Surprisingly our results suggest that in Chlamydomonas, like in plants, expression of PTC containing mRNAs are repressed, however in the haploid green alga it occurs in NMD independent manner.

III/2 The plant NGD system and its connection with a translation coupled protein quality control system

Previously we have shown that in plants NGD degrades aberrant transcripts containing elongation inhibiting sequences. We proved that A-stretch leads to ribosome stalling, which then results in NGD mediated mRNA cleavage and rapid decay of cleaved transcript. During this program we have unraveled that NGD is linked to the Ribosome associated Quality Control (RQC) protein quality control system in plants. We try to study the biological role of NGD-RQC systems during abiotic stress conditions.

Description of mechanisms of plant quality control systems could significantly contribute to our knowledge how plants maintain mRNA and protein homeostasis during stress conditions. Moreover, understanding the quality control systems might help breeders to accelerate stress resistance breeding.