VISUAL network analysis reveals the role of BEH3 as a stabilizer in the secondary vascular development in Arabidopsis

Abstract

During secondary growth in plants, vascular stem cells located in the cambium continuously undergo self-renewal and differentiation throughout the lifetime. Recent cell-sorting technique enables to uncover transcriptional regulatory framework for cambial cells. However, the mechanisms underlying the robust control of vascular stem cells have not been understood yet. By coexpression network analysis using multiple transcriptome datasets of an ectopic vascular cell transdifferentiation system using Arabidopsis cotyledons, VISUAL, we newly identified a cambium-specific gene module from an alternative approach. The cambium gene list included a transcription factor BES1/BZR1 homolog 3 (BEH3), whose homolog BES1 is known to control vascular stem cell maintenance negatively. Interestingly, the vascular size of the beh3 mutants showed a large variation, implying the role of BEH3 as a stabilizer. BEH3 almost lost the transcriptional repressor activity and functioned antagonistically with other BES/BZR members via competitive binding to the same motif BRRE. Indeed, mathematical modeling suggests that the competitive relationship among BES/BZRs leads to the robust regulation of vascular stem cells.

Spatio-temporal imaging of cell fate dynamics in single plant cells using luminescence microscope

“…5A, B, Supplemental Movie S9,S10). Results showed that the activation of the GH3.1 promoter occurred earlier than that of the NAC004 promoter, which is consistent with findings from the co-expression gene network analysis (Furuya et al, 2021).…”

“…2A, Supplemental Movie S3, S4, S5, S6). Quantitative analysis of luminescence intensity revealed that temporal changes of ELUC signals followed similar trends as UBQ14 and AtHB8 expression changes in the VISUAL time-course microarray experiments (Furuya et al, 2021, Supplemental Fig. S7A-D).…”

“…4A, Supplemental Movie S8). Furthermore, simultaneous imaging of GH3.1 and NAC004 promoters, which were identified in the procambial gene module and cambial gene module, respectively, was performed (Furuya et al, 2021). The promoter activities of both genes increased in a common order (i.e., from GH3.1 to NAC004) among the cells that ultimately differentiated into xylem and phloem.…”

“…Our previous co-expression network analysis of vascular development with VISUAL categorized vasculature-related genes into four distinct modules: procambium-, cambium-, xylem-, and phloem-modules (Furuya et al, 2021). To capture the process of acquiring cambial identity in a spatial-temporal manner, the GRETCHEN HAGEN 3.1 (GH3.1) genes from the procambialrelated module, and the NAC004 gene from cambium-related module, were selected.…”

“…VISUAL was recently used to obtain time-course transcriptome data at 6-hour intervals. This led to the identification of gene modules corresponding to each stage of vascular development by co-expression network analysis (Furuya et al, 2021). In addition, fluorescence imaging combined with tissue clearing methods in VISUAL-induced cotyledons revealed the importance of positional information in determining whether vascular stem cells differentiate into xylem or phloem cells (Nurani et al, 2020).…”