Ndathe, R. | Search bioRxiv

bioRxiv2021

A dynamic model of the ABA Signaling pathway with its core components: translation rate of PP2C determines the kinetics of ABA-induced gene expression

The abscisic acid (ABA) signaling pathway is the key defense mechanism against drought stress in plants, yet the connectivity of cellular molecules related to gene expression in response to ABA is little understood. A dynamic model of the core components of the ABA signaling pathway was built using ordinary differential equations to understand the connectivity. Parameter values of protein-protein interactions and enzymatic reactions in the model were implemented from the data obtained by previously conducted experiments. On the other hand, parameter values of gene expression and translation were determined by comparing the kinetics of gene expression in the model to those of ABA-induced RD29A (response to desiccation 29A) in actual plants. Based on the analyses of the optimized model, we hypothesized that the translation rate of PP2C (protein phosphatase type 2C) is downregulated by ABA to increase the ABRE (ABA-responsive element) promoter activity. The hypotheses were preliminarily supported by newly conducted experiments using transgenic Arabidopsis plants that carry a luciferase expression cassette driven by the RD29A promoter (RD29A::LUC). The model suggests that identifying a mechanism that alters PP2C translation rate would be one of the next research frontiers in the ABA signaling pathway.

systems biology↗

bioRxiv2020

The CDK inhibitor SIAMESE targets both CDKA;1 and CDKB1 complexes to establish endoreplication in trichomes

Endoreplication, also known as endoreduplication, is a modified cell cycle in which DNA is replicated without subsequent cell division. Endoreplication plays important roles in both normal plant development and in stress responses. The SIAMESE (SIM) gene of Arabidopsis (Arabidopsis thaliana) encodes a cyclin-dependent kinase inhibitor that plays an central role in establishing endoreplication, and is the founding member of the SIAMESE-RELATED (SMR) family of plant-specific cyclin-dependent kinase inhibitors genes. However, there has been conflicting evidence regarding which specific cyclin/CDK complexes are inhibited by SIM in vivo. In this work, we use genetic evidence to show that SIM likely inhibits both CDKA;1- and CDKB1-containing CDK complexes in vivo to promote endoreplication in developing Arabidopsis trichomes. We also show that SIM interacts with CYCA2;3, a binding partner of CDKB1;1, via SIM Motif A, which we previously identified as a CDK-binding motif. In contrast, SIM Motif C, which has been indicated as a cyclin binding motif in other contexts, appears to be relatively unimportant for interaction between SIM and CYCA2;3. Together with earlier results, our work suggests that SIM and other SMRs likely have a multivalent interaction with CYC/CDK complexes. One sentence summaryThe cyclin-dependent kinase inhibitor SIAMESE (SIM) targets both CDKA;1 and CDKB1 complexes to establish endoreplication, and that SIM interacts with the cyclin CYCA2;3 via SIM Motif A.

plant biology↗