The genes in question encode proteins from the BRI1 EMS SUPPRESSOR 1/BRASSINAZOLE RESISTANT 1 family, usually abbreviated BES1/BZR1. These transcription factors sit at the very end of the brassinosteroid signaling pathway, the cascade that carries instructions from steroid hormones at the cell surface down to the DNA in the nucleus. When brassinosteroids are abundant, BES1 and BZR1 proteins accumulate in the nucleus and switch large sets of genes on or off, promoting stem elongation, leaf expansion, flowering, and other growth processes. When the hormone signal is absent or when stress conditions demand a change of priorities, the proteins are phosphorylated and retained in the cytoplasm, effectively putting growth on hold. Because of this dual role, BES1/BZR1 factors have become a major focus for researchers trying to breed crops that grow vigorously while still tolerating hostile environments.

Despite their importance in the model plant Arabidopsis thaliana and in major cereals, the BES1/BZR1 family had not been systematically cataloged in flowering Chinese cabbage. A team led by Haobo Yang, Jinpeng Lu, Jia Li, and Hongyong Shi of Guangzhou University set out to close that gap. Using the recently available genome annotation of the crop, they searched the entire genome for sequences encoding the characteristic BES1-type DNA-binding motif, the molecular signature that allows these proteins to recognize their target genes. The search returned ten genes, which the team named BraBES1, each carrying the conserved motif that defines the family. That number fits the general pattern seen across the Brassica genus, whose genomes expanded through an ancient whole-genome triplication event that left many gene families larger than their counterparts in Arabidopsis.

Identifying the genes was only the first step. To understand how the ten BraBES1 proteins relate to one another and to their relatives in other species, the researchers carried out phylogenetic analysis, constructing an evolutionary tree of BES1/BZR1 proteins. The analysis sorted the wider family into six groups, designated A through F. The ten BraBES1 proteins from flowering Chinese cabbage fell into five of those groups, namely A, C, D, E, and F, with no member assigned to group B. This distribution matters because group membership often predicts function: proteins that cluster together tend to share DNA-binding preferences, interaction partners, and expression patterns inherited from a common ancestor. The absence of a group B representative suggests that whatever ancestral gene gave rise to that lineage was lost or diverged beyond recognition in this species.

The team also examined where the genes sit on the chromosomes and how their neighborhoods compare with those of Arabidopsis. The ten BraBES1 genes were distributed across seven chromosomes, and synteny analysis revealed strong conservation of genomic context with the BES1/BZR1 homologs of Arabidopsis. Synteny, the preservation of gene order across chromosomes of different species, is a powerful clue to evolutionary history. It indicates that the BraBES1 family members are true orthologs, descended from the same ancestral genes as their Arabidopsis counterparts rather than arising through unrelated duplications. For breeders and molecular biologists, this conserved synteny is practical good news, because it means that decades of functional knowledge accumulated in Arabidopsis can serve as a reasonable starting hypothesis for interpreting how the Brassica genes behave.

Subcellular localization provided the next layer of insight. Transcription factors must enter the nucleus to do their work, so where a protein accumulates within the cell often hints at how it is regulated. Using transient expression in tobacco leaves, the researchers found that BraBES1 proteins from groups A, E, and F localized to both the nucleus and the cytoplasm, while proteins from groups C and D were found predominantly in the nucleus. The cytoplasmic fraction in the first group is consistent with the canonical brassinosteroid logic, in which the GSK3-like kinase BIN2 phosphorylates BES1 and BZR1 in the absence of hormone, holding them outside the nucleus until brassinosteroid signaling releases them. The predominantly nuclear behavior of the C and D groups hints at a different regulatory logic, one that may not depend so heavily on hormone-controlled shuttling.

That interpretation gained support from protein interaction assays. Using yeast two-hybrid tests, which detect physical binding between two proteins inside yeast cells, the team showed that all ten BraBES1 proteins interact with BraSK21, a SHAGGY-LIKE KINASE 21 in the crop. In Arabidopsis, the equivalent kinase family, which includes BIN2, acts as the central brake on brassinosteroid signaling, phosphorylating BES1 and BZR1 to inactivate them. The finding that every BraBES1 member binds BraSK21 points to a conserved BR-associated regulatory module: a kinase-and-transcription-factor circuit that has been maintained across hundreds of millions of years of evolution and across the divergence of the Brassica and Arabidopsis lineages. Conservation at this level underscores how fundamental the pathway is to plant life, and it gives researchers an immediate entry point for manipulating the pathway in the vegetable.

Where the family truly diverges is in its regulatory wiring. The researchers found sequence variation among the ten genes, and their promoter regions, the stretches of DNA upstream of each gene that control when and where it is switched on, carried divergent cis-elements, the short motifs that bind other regulatory proteins. Consistent with that promoter diversity, the genes showed distinct expression profiles across tissues and conditions. When the team exposed plants to a panel of hormones, including brassinolide, the active brassinosteroid, along with gibberellic acid, the auxin indole-3-acetic acid, abscisic acid, and salicylic acid, each BraBES1 gene responded in its own characteristic pattern. The same held true under abiotic stresses: cold and heat, drought, high light, and salt each elicited gene-specific changes in expression. This is the signature of a gene family that has undergone subfunctionalization, in which duplicated copies shed redundant roles and each specialized for particular signals, tissues, or conditions.

One pattern stood out from the stress and hormone experiments. Genes in group A showed especially strong responsiveness to hormones and to high temperature in the cultivar Sijiu-19, a traditional variety of flowering Chinese cabbage. Given that heat stress is an increasingly serious constraint on vegetable production in southern China, a transcription factor family member that couples brassinosteroid signaling with heat responsiveness is an obvious candidate for further study. If group A BraBES1 genes turn out to mediate the well-documented role of brassinosteroids in thermotolerance, they could become targets for marker-assisted selection or genome editing aimed at producing varieties that hold their yield through heat waves. The authors position the whole dataset as a resource for exactly this kind of functional analysis of BR-linked development and stress adaptation.

The study is a reminder of how much modern crop improvement depends on cataloging the parts list before tinkering with the machine. By combining genome-wide identification, evolutionary classification, chromosomal synteny, protein localization, interaction mapping, and expression profiling under a dozen different treatments, the Guangzhou University team has built a multi-layered picture of a single transcription factor family in a crop that had been largely invisible to this kind of analysis. The conserved features, the shared DNA-binding motif, the interaction with BraSK21, the syntenic anchors to Arabidopsis, give the field confidence that established brassinosteroid biology transfers to flowering Chinese cabbage. The divergent features, the split localization patterns, the varied promoters, and the gene-specific responses to hormones and stresses, show where the interesting specialization lies. The next step, functional validation of individual BraBES1 genes in the crop itself, will determine whether this catalog becomes a toolkit for breeding leafy vegetables that grow fast, flower on schedule, and shrug off the stresses of a warming climate.

Subject of Research: BES1/BZR1 transcription factor gene family identification and brassinosteroid signaling in flowering Chinese cabbage

Article Title: Genome-wide identification of BraBES1 genes reveals conserved BR-module features and differential hormone/stress responsiveness in Brassica rapa var. parachinensis

Article References: Yang, H., Lu, J., Li, J., & Shi, H. (2026). Genome-wide identification of BraBES1 genes reveals conserved BR-module features and differential hormone/stress responsiveness in Brassica rapa var. parachinensis. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10215-3

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10215-3

Keywords: Brassica rapa, flowering Chinese cabbage, BES1/BZR1, brassinosteroid, transcription factors, gene family, phylogenetics, synteny, abiotic stress, hormone signaling, plant biotechnology, Guangzhou University