What is it about?
This study reconstructs when and how C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) emerged as major cold-acclimation regulators in angiosperms. By combining phylogenies of AP2/ERF genes, genome collinearity, and multi-omics data (genomes, RNA-seq, and CBF/DREB1 genome-wide binding profiles) from algae to angiosperms, the authors infer that CBF/DREB1 genes originated from a tandem-duplication-derived DREB III gene. An additional ε-whole-genome duplication produced two ancestral CBF/DREB1 archetypes that later diverged into two paralogous clades. Clade I is cold-insensitive and appears mainly in basal angiosperms and a subset of eudicots, whereas Clade II is cold-sensitive and is broadly retained across studied plants. Conserved AP2/ERF signatures support shared functional capacity, and repeated duplication/expansion events led to convergent CBF/DREB1 diversification in monocots and eudicots. The lineage history also shows that tandem arrays and gene losses shaped complements, such as the lack of Clade I in Arabidopsis and monocots, while expansion peaks correlate with cooling periods.
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Why is it important?
Cold acclimation relies on fast gene-expression programs. By pinpointing how CBF/DREB1 regulators originated from specific duplication events and then partitioned into clades with different cold responsiveness, this work explains why cold-regulatory networks vary across plant lineages. The identified conserved sequence signatures and the inferred retention/loss patterns (for example, Clade I mainly in basal angiosperms and some eudicots) provide testable evolutionary hypotheses. It also links bursts of CBF/DREB1 duplication/expansion to paleotemperature change, offering a framework to study how repeated environmental cooling can shape transcription-factor families. Overall, the study delivers evolutionary maps that can guide selection of candidate regulators for improving crop cold tolerance. Such knowledge helps researchers design experiments that connect evolutionary history to present-day cold-response outputs in diverse, climate-relevant plants.
Perspectives
Future work can test whether clade-specific signatures translate into measurable differences in target-gene choice and splicing/regulatory kinetics during freezing stress. Comparative functional assays across representative monocots, eudicots, and basal angiosperms would clarify how tandem arrays, whole-genome duplication, and subsequent losses shaped current cold tolerance. Integrating CBF/DREB1 binding profiles with time-resolved transcriptomics under realistic temperature regimes could reveal when the regulators switch from activation to repression. Finally, the inferred paleotemperature-linked expansion events suggest using evolutionary information to prioritize candidate genes for breeding more resilient crops. If supported, these results could connect past climate change to strategies for future temperature extremes directly.
Wenwu Wu
Zhejiang A and F University
Read the Original
This page is a summary of: Innovations and stepwise evolution of CBFs/DREB1s and their regulatory networks in angiosperms, Journal of Integrative Plant Biology, October 2022, Wiley,
DOI: 10.1111/jipb.13357.
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Resources
Convergent evolution of AP2/ERF III and IX cold regulators via WGD and tandem duplication
This related study investigated transcription factor gene families at the whole-genome level and found convergent evolution of two AP2/ERF subfamilies (III and IX) driven by recurrent whole-genome duplication (WGD) and tandem duplication related to climatic changes.
WGD-shaped RNA-binding proteins for cold adaptation across angiosperms
This related study investigated RNA-binding protein (RBP) gene evolution at the whole-genome level and found that whole-genome duplication (WGD) and subsequent biased retention of stress-related RBPs, including cold-induced duplicates, which helped shape cold-adaptation gene regulatory networks.
Regulatory divergence of CBF/DREB1 orthologs: OsDREB1C vs AtCBF2/3/1
This related study, unlike the previous work focused on shared cold-response pathways, investigated CBF/DREB1 orthologs and found functional divergence between rice OsDREB1C and Arabidopsis AtCBF2/3/1, driven by lineage-specific evolutionary clades, transposon-related events, and distinct DNA-binding motif preferences, which leads to different regulatory roles in nitrogen/photosynthesis versus cold acclimation.
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