Mutational Evidence for the Critical Role of CBF Transcription Factors in Cold Acclimation in Arabidopsis

Overview

Journal Plant Physiol

Specialty Physiology

Date 2016 Jun 3

PMID 27252305

Citations 219

Authors

Chunzhao Zhao

Zhengjing Zhang

Shaojun Xie

Tong Si

Yuanya Li

Jian-Kang Zhu

Affiliations

Soon will be listed here.

Abstract

The three tandemly arranged CBF genes, CBF1, CBF2, and CBF3, are involved in cold acclimation. Due to the lack of stable loss-of-function Arabidopsis (Arabidopsis thaliana) mutants deficient in all three CBF genes, it is still unclear whether the CBF genes are essential for freezing tolerance and whether they may have other functions besides cold acclimation. In this study, we used the CRISPR/Cas9 system to generate cbf single, double, and triple mutants. Compared to the wild type, the cbf triple mutants are extremely sensitive to freezing after cold acclimation, demonstrating that the three CBF genes are essential for cold acclimation. Our results show that the three CBF genes also contribute to basal freezing tolerance. Unexpectedly, we found that the cbf triple mutants are defective in seedling development and salt stress tolerance. Transcript profiling revealed that the CBF genes regulate 414 cold-responsive (COR) genes, of which 346 are CBF-activated genes and 68 are CBF-repressed genes. The analysis suggested that CBF proteins are extensively involved in the regulation of carbohydrate and lipid metabolism, cell wall modification, and gene transcription. Interestingly, like the triple mutants, cbf2 cbf3 double mutants are more sensitive to freezing after cold acclimation compared to the wild type, but cbf1 cbf3 double mutants are more resistant, suggesting that CBF2 is more important than CBF1 and CBF3 in cold acclimation-dependent freezing tolerance. Our results not only demonstrate that the three CBF genes together are required for cold acclimation and freezing tolerance, but also reveal that they are important for salt tolerance and seedling development.

Citing Articles

Adaptation of High-Altitude Plants to Plateau Abiotic Stresses: A Case Study of the Qinghai-Tibet Plateau.

Sun P, Hao R, Fan F, Wang Y, Zhu F Int J Mol Sci. 2025; 26(5).

PMID: 40076909 PMC: 11900590. DOI: 10.3390/ijms26052292.

Regulation of alternative splicing by CBF-mediated protein condensation in plant response to cold stress.

Fu D, Song Y, Wu S, Peng Y, Ming Y, Li Z Nat Plants. 2025; .

PMID: 40044940 DOI: 10.1038/s41477-025-01933-x.

Dynamic changes in the transcriptome of tropical region-originated king grasses in response to cold stress.

Lai X, Yan J, Chen Z, Zhang Y, Luo F, Cai G Front Plant Sci. 2025; 16:1511466.

PMID: 40041019 PMC: 11876387. DOI: 10.3389/fpls.2025.1511466.

Genome-Wide Identification and Expression Divergence of Family in and Functional Analysis of Under Cold Stress.

Li S, Zhang Q, Zhang Z, Zhang P, Li C, Sun L Life (Basel). 2025; 15(2).

PMID: 40003636 PMC: 11856347. DOI: 10.3390/life15020227.

Molecular and Physiological Responses of Plants that Enhance Cold Tolerance.

Zhou L, Ullah F, Zou J, Zeng X Int J Mol Sci. 2025; 26(3).

PMID: 39940925 PMC: 11818088. DOI: 10.3390/ijms26031157.

References

Gong Z, Lee H, Xiong L, Jagendorf A, Stevenson B, Zhu J . RNA helicase-like protein as an early regulator of transcription factors for plant chilling and freezing tolerance. Proc Natl Acad Sci U S A. 2002; 99(17):11507-12. PMC: 123286. DOI: 10.1073/pnas.172399299. View

Du Z, Zhou X, Ling Y, Zhang Z, Su Z . agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010; 38(Web Server issue):W64-70. PMC: 2896167. DOI: 10.1093/nar/gkq310. View

Zarka D, Vogel J, Cook D, Thomashow M . Cold induction of Arabidopsis CBF genes involves multiple ICE (inducer of CBF expression) promoter elements and a cold-regulatory circuit that is desensitized by low temperature. Plant Physiol. 2003; 133(2):910-8. PMC: 219064. DOI: 10.1104/pp.103.027169. View

Gilmour S, Zarka D, Stockinger E, Salazar M, Houghton J, Thomashow M . Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 1999; 16(4):433-42. DOI: 10.1046/j.1365-313x.1998.00310.x. View

Harmer S, Hogenesch J, Straume M, Chang H, Han B, Zhu T . Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science. 2000; 290(5499):2110-3. DOI: 10.1126/science.290.5499.2110. View

Knight M, Knight H . Low-temperature perception leading to gene expression and cold tolerance in higher plants. New Phytol. 2012; 195(4):737-751. DOI: 10.1111/j.1469-8137.2012.04239.x. View

Chinnusamy V, Ohta M, Kanrar S, Lee B, Hong X, Agarwal M . ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev. 2003; 17(8):1043-54. PMC: 196034. DOI: 10.1101/gad.1077503. View

Oh S, Song S, Kim Y, Jang H, Kim S, Kim M . Arabidopsis CBF3/DREB1A and ABF3 in transgenic rice increased tolerance to abiotic stress without stunting growth. Plant Physiol. 2005; 138(1):341-51. PMC: 1104188. DOI: 10.1104/pp.104.059147. View

Gaj T, Gersbach C, Barbas 3rd C . ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013; 31(7):397-405. PMC: 3694601. DOI: 10.1016/j.tibtech.2013.04.004. View

10.

Zhao C, Lang Z, Zhu J . Cold responsive gene transcription becomes more complex. Trends Plant Sci. 2015; 20(8):466-8. PMC: 4536100. DOI: 10.1016/j.tplants.2015.06.001. View

11.

Sasaki K, Christov N, Tsuda S, Imai R . Identification of a novel LEA protein involved in freezing tolerance in wheat. Plant Cell Physiol. 2013; 55(1):136-47. DOI: 10.1093/pcp/pct164. View

12.

Cook D, Fowler S, Fiehn O, Thomashow M . A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc Natl Acad Sci U S A. 2004; 101(42):15243-8. PMC: 524070. DOI: 10.1073/pnas.0406069101. View

13.

Achard P, Gong F, Cheminant S, Alioua M, Hedden P, Genschik P . The cold-inducible CBF1 factor-dependent signaling pathway modulates the accumulation of the growth-repressing DELLA proteins via its effect on gibberellin metabolism. Plant Cell. 2008; 20(8):2117-29. PMC: 2553604. DOI: 10.1105/tpc.108.058941. View

14.

Thalhammer A, Hincha D . A mechanistic model of COR15 protein function in plant freezing tolerance: integration of structural and functional characteristics. Plant Signal Behav. 2014; 9(12):e977722. PMC: 4623512. DOI: 10.4161/15592324.2014.977722. View

15.

Gehan M, Park S, Gilmour S, An C, Lee C, Thomashow M . Natural variation in the C-repeat binding factor cold response pathway correlates with local adaptation of Arabidopsis ecotypes. Plant J. 2015; 84(4):682-93. DOI: 10.1111/tpj.13027. View

16.

Sakuma Y, Liu Q, Dubouzet J, Abe H, Shinozaki K, Yamaguchi-Shinozaki K . DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. Biochem Biophys Res Commun. 2002; 290(3):998-1009. DOI: 10.1006/bbrc.2001.6299. View

17.

Lee B, Henderson D, Zhu J . The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. Plant Cell. 2005; 17(11):3155-75. PMC: 1276035. DOI: 10.1105/tpc.105.035568. View

18.

Popova A, Rausch S, Hundertmark M, Gibon Y, Hincha D . The intrinsically disordered protein LEA7 from Arabidopsis thaliana protects the isolated enzyme lactate dehydrogenase and enzymes in a soluble leaf proteome during freezing and drying. Biochim Biophys Acta. 2015; 1854(10 Pt A):1517-25. DOI: 10.1016/j.bbapap.2015.05.002. View

19.

Wang Y, Hua J . A moderate decrease in temperature induces COR15a expression through the CBF signaling cascade and enhances freezing tolerance. Plant J. 2009; 60(2):340-9. DOI: 10.1111/j.1365-313X.2009.03959.x. View

20.

Thomashow M . PLANT COLD ACCLIMATION: Freezing Tolerance Genes and Regulatory Mechanisms. Annu Rev Plant Physiol Plant Mol Biol. 2004; 50:571-599. DOI: 10.1146/annurev.arplant.50.1.571. View