Role of ubiquitin in cellular regulation

Group leader : Pascal GENSCHIK

Research area

The ubiquitin-proteasome system (UPS) was discovered as a central player for rapid and selective proteolysis in the nucleus and the cytosol. This pathway is also involved in the degradation of short-lived and key regulatory proteins that control a variety of cellular processes, such as the cell cycle and various developmental and hormonal signalling cascades. Degradation via this pathway is a two-step process in which the protein is first tagged by covalent attachment of ubiquitin, and subsequently degraded by the 26S proteasome. Notably some ubiquitylated proteins can also be degraded by selective autophagy. The transfer of ubiquitin to the target proteins requires ubiquitin protein-ligases (E3s), which are the key components in the pathway, as these enzymes determine the specificity of the ubiquitylation reaction.

Recent results have shown that plants make extensive use of regulated proteolysis by the UPS to modulate signal transduction pathways, in particular phytohormones, light signalling and stress responses. On the basis of the Arabidopsis and rice genome sequences, it is predicted more than 1000 E3 ubiquitin protein-ligases. So far, biological functions have only been assigned to a limited number of them. Therefore a better understanding of their function and the identification of their substrates is essential at the fundamental level, but will also be of great value for biotechnology and agriculture.

Our laboratory works on a selected set of Arabidopsis thaliana E3 ubiquitin protein-ligases involved in the cell cycle control, phytohormone signalling and post-transcriptional gene silencing. To unravel their cellular functions, we use a multidisciplinary approach combining, genetics, molecular and cell biology, physiology, biochemistry and structural biology.

Projects

Mechanisms of Argonaute proteins degradation

Project manager: Pascal GENSCHIK

Argonaute proteins are core components of the RNA-induced silencing complex (RISC). These proteins have undergone a high degree of gene duplication in metazoans and plants. Strikingly, molecular mechanisms regulating Argonaute proteins turnover in both metazoans and plants are poorly understood. Here we focus on post-translational regulations of AGO1, one of the 10 Arabidopsis Argonaute proteins, that plays a central role in both miRNA and si-mediated RNA silencing. Recently, we have shown that AGO1 is degraded by a mechanism of selective autophagy (Derrien et al., 2012). The present project aims to unravel the molecular components and machineries triggering AGO1 degradation and, most importantly, to determine their physiological functions.

Molecular mechanisms of E3 ubiquitin protein-ligases in the control of the cell cycle

Project manager: Sandra NOIR

Plant growth and development result from a fine-tuning of cell cycle progression. Especially, the transition from G1 to S phase (i.e. DNA synthesis) as well as the progression and exit from mitosis are key steps that need multiple levels of control, one of which being assumed by the ubiquitin proteasome system (UPS). Our project aims to characterize Arabidopsis E3s involved in plant cell cycle control and subsequently, to identify their substrates. Most importantly, we wish to elucidate how these cell cycle-related UPS players are regulated by endogenous (e.g. hormone signalling) and/or exogenous (e.g. drought stress) plant signals.

The EBF1&2/EIN3 module in ethylene signalling

Project manager: Thomas POTUSCHAK

Ethylene gas is one of the major plant hormones, which regulates key developmental processes, growth and stress responses. We and others have previously shown that in the absence of ethylene, the transcription factor EIN3 that is necessary to control the expression of ethylene-responsive genes, is ubiquitylated and targeted for proteasomal degradation by the SCFEBF1/2 (EBF1 and EBF2 are F-box proteins that interact with EIN3). However, in presence of ethylene, EIN3 protein accumulates and triggers the hormonal response. Our project aims to clarify at the molecular level how the EIN3 transcription factor is stabilized in presence of ethylene and further characterize the EBF1&2/EIN3 module in stress responses.

Modulation of ABA signalling by CUL3-BPM E3 ligases

Project manager: Esther LECHNER

The Arabidopsis genome encodes six members of the evolutionarily conserved MATH-BTB protein family (called BPM1-6), which are adaptor proteins of CRL3 ubiquitin ligases. In a search to identify putative protein targets of BPMs, we recently found that all six members of this BTB protein family interact with transcription factors forming a subclade of the class I homeobox-leucine zipper (HD-ZIP), including ATHB6 and ATHB5, both involved in ABA signalling. Our project aims to better determine the function of ATHB6 in plant responses to ABA and drought. Moreover, several lines of evidence indicate that ATHB6 is subject to different post-translational modifications, including phosphorylation, ubiquitylation and SUMOylation. We wish to characterize these modifications and their crosstalk in order to determine how they affect ATHB6 function in ABA signalling.

Functional characterization of Arabidopsis MSI proteins, potential DCAF receptors for the CRL4-E3 ligase

Project manager: Marie-Claire CRIQUI

The MSI (Multicopy Suppressor of IRA3) protein family harbours a conserved motif called DWxR and could therefore function as substrate receptors or DCAF for the CRL4 complex. Arabidopsis encodes 5 MSI proteins that seem to have evolved functional diversification. Thus MSI1 and MSI4(FVE)/MSI5 are involved respectively in epigenetic maintenance of reproductive development and flowering time control through the autonomous pathway. Our project aims to characterize the function of Arabidopsis MSI2/3 in the light of potential protein interactors recently identified and to establish if the MSI2/3 function is linked to CRL4.

Members

Selected publications

  • GENTRIC N., MASOUD K., JOURNOT R.P., COGNAT V., CHABOUTÉ M.E., NOIR S. and GENSCHIK P.

    The F-box-like protein FBL17 is a regulator of DNA-damage response and co-localizes with RETINOBLASTOMA RELATED 1 at DNA lesion sites

    Plant Physiology, :20.00188, 2020. | DOI : DOI:10.1104/pp.20.00188DOI logo

  • DERRIEN B., CLAVEL M., BAUMBERGER N., IKI T., SARAZIN A., HACQUARD T., ZIEGLER-GRAFF V., VAUCHERET H., MICOL J.L., VOINNET O. and GENSCHIK P.

    A Suppressor Screen for AGO1 Degradation by the Viral F-Box P0 Protein Uncovers a Role for AGO DUF1785 in sRNA Duplex Unwinding.

    Plant Cell, :1353-1374., 2018. | DOI : 10.1105/tpc.18.00111DOI logo

  • CLAVEL M., MICHAELI S. and GENSCHIK P.

    Autophagy: A Double-Edged Sword to Fight Plant Viruses.

    Trends in Plant Science, :646-648, 2017. | DOI : 10.1016/j.tplants.2017.06.007DOI logo

  • NOIR S., MARROCCO K., HLEIBIEH K., THOMANN A., GUSTI A., BITRIAN M., SCHNITTGER A. and GENSCHIK P.

    The Control of Arabidopsis thaliana Growth by Cell Proliferation and Endoreplication Requires the F-Box Protein FBL17.

    Plant Cell, 27:1461-1476, 2015. | DOI : 10.1105/tpc.114.135301DOI logo

  • DERRIEN B., BAUMBERGER N., SCHEPETILNIKOV M., VIOTTI C., DE CILLIA J., ZIEGLER-GRAFF V., ISONO E., SCHUMACHER K. and GENSCHIK P.

    Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway

    Proceedings of the National Academy of Sciences of the United States of America, 109(39):15942-15946, 2012. | DOI : 10.1073/pnas.1209487109DOI logo