Gene co-expression network analysis identifies BEH3 as a stabilizer of secondary vascular development in Arabidopsis

Abstract

In plants, vascular stem cells located in the cambium continuously undergo self-renewal and differentiation during secondary growth. Recent advancements in cell sorting techniques have enabled access to the transcriptional regulatory framework of cambial cells. However, mechanisms underlying the robust control of vascular stem cells remain unclear. Here, we identified a new cambium-related regulatory module through co-expression network analysis using multiple transcriptome datasets obtained from an ectopic vascular cell transdifferentiation system using Arabidopsis cotyledons, VISUAL. The cambium gene list included a gene encoding the transcription factor BES1/BZR1 Homolog 3 (BEH3), whose homolog BES1 negatively affects vascular stem cell maintenance. Interestingly, null beh3 mutant alleles showed a large variation in their vascular size, indicating that BEH3 functions as a stabilizer of vascular stem cells. Genetic analysis revealed that BEH3 and BES1 perform opposite functions in the regulation of vascular stem cells and the differentiation of vascular cells in the context of the VISUAL system. At the biochemical level, BEH3 showed weak transcriptional repressor activity and functioned antagonistically to other BES/BZR members by competing for binding to the brassinosteroid (BR) response element. Furthermore, mathematical modeling suggested that the competitive relationship between BES/BZR homologs leads to the robust regulation of vascular stem cells.

Behavior and possible function of Arabidopsis BES1/BZR1 homolog 2 in brassinosteroid signaling

“…Our expression analysis unveiled the detailed patterns of BEH2 expression at the tissue level ( Figure 1a ): BEH2 was expressed in the confined regions in each organ; its expression was more intense in roots than shoots, suggesting that roots are likely the primary site of BEH2 expression; BEH2 expression pattern was quite different from those of BES1 and BEH4 that are ubiquitously expressed 18 , 33 , 36 and from BEH3 that is expressed in leaves and petioles, especially their vascular tissues. 37 , 38 Together, these results indicate that each BES1/BZR1 family member might play distinct physiological roles by differently modulating their expression, despite their common roles based on their structural similarity.…”

Characterization of Transcriptome Dynamics during Early Fruit Development in Olive (Olea europaea L.)

“…MYB factors are involved in regulating the transcription of cyclin genes via MYB recognition elements in cyclin promoters [ 116 ]. The RNA-Seq analysis showed that the upregulation of MYB3R-4 (3R-MYB, AT5G11510.1), which activates mitotic gene expression and CK response [ 117 ], and MYB3R-5 (3R-MYB, AT5G02320.1), which is a member of the DREAM complex [ 118 ], are probably associated with the cell division phase, while the upregulation of MYB3R-1 (3R-MYR, AT4G32730.2) is likely associated with the cell expansion phase during early olive fruit development ( Table S20 ). Additionally, members of the R2R3-MYB family have been identified in olive fruit, as in the case for Zm1, which is involved in the regulation of flavonoid biosynthesis [ 119 ].…”

Competitive action between Brassinosteroid and tracheary element differentiation inhibitory factor in controlling xylem cell differentiation

“…As another case, the competitive action among BES/BZR family members contributes to fine-tuned regulation of the vascular meristem. BES1 HOMOLOG 3 (BEH3), which possesses much weaker transcriptional repressor activity, competes with other BES1 family proteins via competitive binding to the BRRE cis element (Furuya et al 2021). Here we found the competitive relationship of TDIF and BR upstream of GSK3-like kinases and BES/BZR transcription factors.…”

“…Then, the signal is transduced from intracellular kinase domain of TDR to GSK3-like kinases including BRASSINOSTEROID INSENSITIVE 2 (BIN2) (Kondo et al 2014). Ultimately, transcription factors BRI1-EMS-SUPPRESSOR 1 (BES1) and BRASSINAZOLE RESISTANT 1 (BZR1) are inactivated via direct phosphorylation by GSK3-like kinases to inhibit the differentiation into xylem cells (XYs) (Furuya et al 2021;He et al 2002;Saito et al 2018;Yin et al 2002). On the other hand, brassinosteroid (BR) promotes XY differentiation in Zinnia tracheary element culture (Yamamoto et al 2001(Yamamoto et al , 2007.…”