Gene regulation during cold acclimation in plants


  • Viswanathan Chinnusamy,

    1. Institute for Integrative Genome Biology and Department of Botany & Plant Sciences, University of California-Riverside, Riverside, CA 92521, USA
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  • Jianhua Zhu,

    1. Institute for Integrative Genome Biology and Department of Botany & Plant Sciences, University of California-Riverside, Riverside, CA 92521, USA
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  • Jian-Kang Zhu

    Corresponding author
    1. Institute for Integrative Genome Biology and Department of Botany & Plant Sciences, University of California-Riverside, Riverside, CA 92521, USA
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    • 1

      Present address: Water Technology Centre, Indian Agricultural Research Institute, New Delhi, India

  • Edited by C. Guy



Cold acclimation involves precise signaling and regulation of the transcriptome. The plasma membrane may be the primary cold-stress sensor, and FRY1/HOS2 inositol polyphosphate 1-phosphatase regulates cytosolic inositol-1,4,5-triphosphate levels, which in turn control cytosolic Ca2+ signatures and cold acclimation. Cold-induced reactive oxygen species may activate a mitogen-activated protein kinase cascade (AtMEKK1-AtMKK2-AtMPK4/6) that regulates tolerance to freezing and other abiotic stresses. Cold acclimation induces the expression of the C-repeat binding transcription factors (CBF), which in turn activate many downstream genes that confer chilling and freezing tolerance to plants. The constitutively expressed myelocytomatosis-type basic helix-loop-helix transcription factor inducer of CBF expression 1 (ICE1) regulates the transcription of CBFs and other cold-induced regulons and freezing tolerance. ICE1 is probably negatively regulated by ubiquitination, which may be mediated by the HOS1 RING finger protein. The ICE1-CBF pathway positively regulates the expression of cysteine-2 and histidine-2 zinc finger transcriptional repressors, which are under the negative control of LOS2, a bi-functional enolase. In a CBF-independent pathway, the transcription factors HOS9 (a homeodomain type) and HOS10 (a R2R3 myeloblastosis type) play pivotal roles in the regulation of cold-responsive genes and freezing tolerance. The signaling process from sensors to transcription factors and to cellular responses needs further understanding. Also, cold-stress signaling in reproductive tissues is still largely unknown.

Abbreviations – 

abscisic acid


ABA-responsive element


transcriptional adaptor


Arabidopsis Nicotiana protein kinase 1 (NPK1)-related protein kinase 1


Arabidopsis thaliana


Arabidopsis zinc-finger 2


basic helix-loop-helix


basic-leucine zipper


cysteine-2 and histidine-2


C-repeat binding factors


calcineurin B-like calcium-binding protein


cold regulated


C-repeat elements


dehydration-responsive elements


dehydration-responsive element-binding protein






general control of amino acid synthesis


high expression of osmotically responsive genes


inducer of CBF expression 1




low expression of osmotically responsive genes


MAPKKK, mitogen-activated protein kinase kinase kinase


MAPKK, mitogen-activated protein kinase kinase


MAPK, mitogen-activated protein kinase




MYB recognition sequences




MYC recognition sequences


responsive to dehydration


reactive oxygen species


soybean cold-inducible zinc finger protein


soybean G-Box-binding factor 1


salt-tolerance zinc finger.


Cold stress is one of the major environmental stresses that limit crop productivity, quality, and post-harvest life. Most temperate plants acquire chilling and freezing tolerance upon prior exposure to sublethal cold stress, a process called cold acclimation, although many agronomically important crops are incapable of cold acclimation. Cold acclimation involves precise regulation of expression of transcription factors and effector genes collectively called cold-regulated (COR) genes (Thomashow 1999, Viswanathan and Zhu 2002, Xiong et al. 2002a). Significant progress has been made in identifying transcriptional, post-transcriptional, and post-translational regulators of cold-induced expression of COR genes. Promoters of many of the COR genes contain cis-elements such as dehydration-responsive elements/C-repeat elements (DRE/CRT, A/GCCGAC), abscisic acid (ABA)-responsive element (ABRE, PyACGTGGC), and myeloblastosis (MYB) (C/TAACNA/G) and/or myelocytomatosis (MYC) recognition sequences (CANNTG) (Yamaguchi-Shinozaki and Shinozaki 2005, Zhu 2002). Freezing tolerance-based genetic screens have led to the isolation of several interesting Arabidopsis mutants with increased (Xin and Browse 1998) or decreased freezing tolerance (Boyce et al. 2003). Ishitani et al. (1997) developed a bioluminescent genetic screen involving stress-inducible RD29A promoter-driven luciferase-reporter (PRD29A::LUC). Use of stress-responsive bioluminescent PRD29A::LUC and PCBF3::LUC genetic screens (Chinnusamy et al. 2002, Ishitani et al. 1997) in Arabidopsis led to the identification of upstream signaling components that have provided novel insight into cold-stress signaling and gene regulation, which will be discussed here.

Cold sensing and secondary signals

Plant cells may sense cold stress-induced change in membrane fluidity and protein conformation. Cold stress-induced rigidification of the plasma membrane at microdomains may lead to actin cytoskeletal re-arrangement, which may be followed by activation of Ca2+ channels and increased cytosolic Ca2+ level, triggering the expression of COR genes during cold acclimation (Orvar et al. 2000, Sangwan et al. 2001). ABA serves as a secondary signal to transduce, at least in part, cold signals, as evidenced by the los5 (low expression of osmotically responsive genes) mutant isolated through bioluminescent PRD29A::LUC genetic screening. The los5 mutant is impaired in molybdenum co-factor (MoCo) sulphurase, which synthesizes MoCo for abscisic aldehyde oxidase, and is thus defective in ABA synthesis. The los5 mutant showed significant reduction in cold- and salt/drought-induced expression of COR genes (RD29A, COR15, COR47, RD22, and pyrroline-5-carboxylate synthetase) and is unable to acquire freezing tolerance. Thus, ABA plays a significant role in cold acclimation of plants (Xiong et al. 2001a). ABA may transduce cold-stress signals through second messengers such as H2O2 and Ca2+.

Second messengers and phosphorelay

Cold-stress signals perceived by the yet to be identified sensors induce a transient increase in cytosolic Ca2+ level (Plieth et al. 1999, Tahtiharju et al. 1997). Results of studies involving gadolinium (Gd3+, a mechanosensitive Ca2+ channel blocker) and cyclic ADP-ribose (cADPR) implicated the involvement of mechanosensitive and cADPR-gated Ca2+ channels, respectively, in COR gene transcription and cold acclimation in Brassica napus (Sangwan et al. 2001). An inhibitor of inositol-1,4,5-triphosphate (IP3) receptor has been shown to block IP3-induced RD29A/KIN1 promoter-driven GUS expression in tomato (Wu et al. 1997). A search for mutants defective in COR gene expression by PRD29A::LUC screening resulted in identification of a FIERY1 (FRY1) locus involved in IP3-mediated cold and ABA signaling. FRY1 encodes an inositol polyphosphate 1-phosphatase, which dephosphorylates inositol phosphates such as IP3 and thus negatively regulates IP3 levels in cells. fry1 mutant plants accumulated significantly higher and sustained levels of IP3 instead of the transient increase observed in wild-type plants in response to ABA. This higher and sustained level of IP3 led to enhanced induction of COR genes (RD29A, KIN1, COR15A, COR47A, and ADH) under ABA, cold and osmotic stress in fry1 mutant plants compared with that in wild-type plants (Xiong et al. 2001b). A single amino acid substitution in the FRY1 protein of Arabidopsis caused by the hos2 (high expression of osmotically responsive genes) mutation resulted in enhanced induction of COR genes and the PRD29A::LUC reporter under cold stress but not ABA treatment. Transcript levels of C-repeat binding factors (CBF2 and CBF3) and their target COR genes were significantly higher in hos2 mutants than in wild-type plants under cold stress (Xiong et al. 2004). These results suggest that Ca2+ release from internal cellular stores mediated by IP3 is upstream of the expression of CBFs and COR genes in the cold-signaling pathway(s). Furthermore, the calcium exchanger 1 (cax1) mutant of Arabidopsis defective in a vacuolar Ca2+/H+ antiporter exhibited enhanced expression of CBF/DREBs and their target COR genes and enhanced freezing tolerance (Catala et al. 2003). Thus, regulation of [Ca2+]cyt levels by mechanosensitive and ligand-gated channels is upstream of the expression of CBFs and COR genes in cold-stress signaling.

Results of genetic and transgenic studies have suggested some calcium-dependent protein kinases as positive regulators (Saijo et al. 2000), with some calmodulins (Townley and Knight 2002), a protein phosphatase 2C (AtPP2CA, Tahtiharju and Palva 2001) and a salt overly sensitive 3-like or calcineurin B-like calcium-binding protein (CBL1, Cheong et al. 2003) as negative regulators of expression of COR genes.

Cold acclimation has been shown to induce reactive oxygen species (ROS) such as H2O2 (Prasad et al. 1994). ROS may alter Ca2+ signatures and activate mitogen-activated protein kinases (MAPKs) and redox-responsive transcription factors. Molecular analysis of the FROSTBITE1 (FRO1) locus suggested that the expression of COR genes is regulated by ROS levels. The fro1 mutant displayed a constitutively higher accumulation of ROS. The FRO1 gene encodes a Fe-S subunit of complex I (NADH dehydrogenase) of the electron-transfer chain in the mitochondrion, a potential site of ROS generation under abiotic stresses. In fro1, constitutively higher accumulation of ROS probably triggers Ca2+ signaling in the absence of cold stress, which may desensitize the cells to cold-induced Ca2+ signaling. This could be the cause of reduced cold induction of COR genes and reduced cold acclimation in fro1 mutant plants (Lee et al. 2002a).

Cold and other abiotic stresses regulate the expression and activity of various kinases of MAPK pathways, which suggests that MAPK cascades act as a converging point in abiotic stress signaling (Chinnusamy et al. 2004). Under cold stress, ROS activates the AtMEKK1/ANP1 (MAPKKK)-AtMKK2 (MAPKK)-AtMPK4/6 (MAPK) MAPK cascade that is necessary for cold acclimation in plants (Kovtun et al. 2000, Teige et al. 2004).

Regulation of cold-responsive transcriptome by CBFs

A significant step toward understanding the regulation of COR genes involved identification of cold-stress-inducible CBFs or DRE-binding factors in Arabidopsis. Cold stress induces AtCBF1 (DREB1B), AtCBF2 (DREB1C), and AtCBF3 (DREB1A) genes. The CBF proteins activate the transcription of DRE/CRT cis-element containing COR genes (Liu et al. 1998, Stockinger et al. 1997). Constitutive or stress-inducible overexpression of AtCBF1 or AtCBF3 in transgenic plants resulted in constitutive or enhanced expression of COR genes and increased abiotic-stress tolerance, including freezing tolerance, in Arabidopsis (Jaglo-Ottosen et al. 1998, Kasuga et al. 1999, Liu et al. 1998). Overexpression of AtCBF1/3 enhanced chilling, freezing, drought and/or salt-stress tolerance in Brassica (Jaglo et al. 2001), tomato (Hsieh et al. 2002), tobacco (Kasuga et al. 2004), wheat (Pellegrineschi et al. 2004), and rice (Oh et al. 2005). Similarly, overexpression of rice (Dubouzet et al. 2003) and maize (Qin et al. 2004) DREB1 in transgenic Arabidopsis was sufficient to induce constitutive expression of CBF-target COR genes and conferred tolerance to freezing/drought stresses. Hence, CBF-dependent gene expression is an important, evolutionarily conserved component of cold acclimation in diverse plant species (Nakashima and Yamaguchi-Shinozaki 2006, this issue). Transcriptome analysis of CBF-overexpression transgenic Arabidopsis revealed that only about 12% of the cold-responsive genes are certain members of the CBF regulon (Fowler and Thomashow 2002). This observation suggests that other transcriptional activators/repressors also play a significant role in cold acclimation.

ICE1, a master regulator of cold acclimation

Because CBF genes are cold induced, an upstream transcription factor present in the cell at normal growth temperatures may be activated by cold stress, which in turn induces the expression of CBFs. Using the PCBF3::LUC bioluminescent genetic screen, we identified an upstream transcriptio n factor called inducer of CBF expression 1 (ICE1). The dominant ice1 mutation blocks expression of CBF3 and decreases the expression of many CBF-target genes. ICE1 encodes a MYC-type basic helix-loop-helix (bHLH) transcription factor that binds to MYC cis-element in the CBF3 promoter and may be able to activate the expression of CBF3 upon cold stress. The ice1 mutant showed impaired chilling tolerance and cold acclimation, while constitutive overexpression of ICE1 enhanced the expression of CBFs and COR genes and freezing tolerance of transgenic Arabidopsis. ICE1 is constitutively expressed and localized in the nucleus, but activation of CBF expression requires cold treatment. This observation suggests that cold-induced modification of ICE1 is necessary for activation of its target genes (Chinnusamy et al. 2003). Transcriptome analysis revealed that a large percentage of cold-induced genes are either not induced or their induction in the ice1 mutant is less than 50% of that in wild-type plants. Thirty-two of these genes encode transcription factors, nine with highly preferable ICE1-binding cis-elements and five with CBF3-binding cis-elements in their promoters (Table 1, supplementary data from Chinnusamy et al. 2003). These results show that ICE1 is a master switch that controls many cold-responsive CBF-dependent and independent regulons (Fig. 1). Probably, ICE1-like bHLH transcription factors may be involved in the regulation of CBF1 and/or CBF2 ((Van Buskirk and Thomashour 2006, this issue) Zarka et al. 2003). The CBF2 expression appears to be under the positive control of a mitogen-activated protein kinase (MAPK)-signaling pathway, AtMEKK1-AtMKK2-AtMPK4/6, because AtMKK2-overexpressing Arabidopsis plants showed constitutive expression of CBF2 (Teige et al. 2004).

Table 1.  Inducer of C-repeat binding factor (CBF) expression 1 (ICE1) and CBF3-binding sites in the promoter of some of the transcription-factor genes for which the cold-stress-induction level in ice1 mutant is less than 50% of that in wild-type Arabidopsis.
Transcription factor geneAGICBF3-binding cis-elementPositionICE1-binding cis-elementPosition
CBF3At4g25480  CTGGACACATGGCAGA−193 to −188
−918 to −913
−764 to −759
−755 to −750
MYBAt1g01520  ATGTCCACATGGCTTG−209 to −204
RGA-like proteinAt5g17490  GCCGCCACATGTCGAC−562 to −557
−698 to −693
−91 to −86
Zinc finger-like proteinAt3g52800  CTTTACACATGATCAA−382 to −377
STZAt1g27730TTATAGCCGACCTCTTCT−285 to −278  
C2H2 zinc fingerAt5g04340AAGTAGCCGACTTAATTT
−412 to −405
−250 to −243
AP2-likeAt2g23340TGTCCACCGACCTAATTT−834 to −827  
Tiny-like (AP2)At4g32800GGGTTGCCGACTTGACCA−437 to −430  
Figure 1.

Regulation of transcription factors under cold stress. Cold-stress-induced calcium signature is necessary for cold acclimation. Cold stress activates the ICE1 protein which induces transcription of CBFs and other transcription factors. CBFs also self regulate their transcription to optimize their expression levels. C2H2 zinc finger transcriptional repressors are positively regulated by CBFs and negatively regulated by the LOS2. These zinc finger transcriptional repressors downregulate the expression of CBFs and their target COR genes. (HOS2, high expression of osmotically responsive genes 2; FRY1, FIERY1, inositol polyphosphate 1-phosphatase; HOS1, high expression of osmotically responsive genes 1, a RING finger E3 ubiquitin ligase; ICE1, inducer of CBF expression 1, a myelocytomatosis (MYC)-type basic helix-loop-helix (bHLH) transcription factor; CBF, C-repeat-binding factor, AP2-type transcription factor; LOS2, low expression of osmotically responsive genes 2, a bi-functional enolase with transcriptional repression activity; AZF2, STZ, and ZAT12, cysteine-2 and histidine-2 type zinc finger transcriptional repressors; EP2, a cis-element originally identified in 5-enolpyruvylshikimate-3-phosphate synthase gene promoter; CRT, C-repeat elements; DRE, dehydration-responsive elements; MYCRS, MYC-type bHLH transcription factor recognition sequences; block arrow, activation; line arrow, induction of expression; line ending with bar, repression).

ABA also induces the expression of CBF1, CBF2, and CBF3 genes but to a significantly lower level than that with cold induction (Knight et al. 2004). Similarly, we have also observed that cold, ABA, and salt stress induce the expression of the PCBF3::LUC reporter, although to a significantly lower extent than with cold induction. The ice1 mutant showed significantly less ABA-induced expression of the PCBF3::LUC reporter as compared with the wild-type (Fig. 2; unpublished data). In addition to cold stress, salt and ABA stress slightly enhance the expression of ICE1 (Chinnusamy et al. 2003). Thus, ICE1 may also regulate ABA-mediated expression of CBF genes. Because cold-induced expression of CBFs is transient, ABA may activate ICE1-CBF-dependent and -independent pathways, which may be necessary to maintain the expression of COR genes during prolonged chilling.

Figure 2.

Induction of PCBF3::LUC expression by cold, abscisic acid (ABA), and salt stresses. (A and B) Wild-type (WT) (on the left) and ice1 (on the right) seedlings grown on an agar plate for 1 week. (C) WT (on the left) and ice1 (on the right) seedlings grown on an agar plate for 1 week were transferred on to filter paper saturated with 300 mM NaCl. (D) Luminescence of (A) after low-temperature treatment at 0° C for 12 h. (E) Luminescence of (B) after treatment with 100 µM ABA for 3 h. (F) Luminescence of (C) after treatment with 300 mM NaCl for 3 h. (G) Quantification of the luminescence intensity in D (cold), E (ABA), and F (NaCl).

Self-regulation of CBF expression

CBF proteins may be involved in optimization of CBF expression. The los1 mutant of Arabidopsis, defective in the translational elongation factor 2, showed superinduction of CBF genes but little induction of COR genes in the cold. Because los1 is defective in protein synthesis under cold temperatures, the lack of CBF proteins for feedback repression of CBF genes might lead to superinduction of CBFs (Guo et al. 2002). Characterization of the cbf2 null mutant of Arabidopsis provided further evidence for CBF2-mediated downregulation of CBF1 and CBF3. As compared with the wild-type, cbf2 mutant plants showed increased expression of CBF1 and CBF3 and higher freezing, salt and dehydration stress tolerance. This evidence indicates that the CBF2 protein is involved in feedback regulation of CBF1 and CBF3 expression during cold acclimation (Novillo et al. 2004). CBF2 expression levels may be regulated by CBF3, because impaired CBF3 expression in the ice1 mutant is accompanied by enhanced expression of CBF2 (Chinnusamy et al. 2003). Analysis of null mutants of cbf1 and cbf3 will be required to further define the role of individual CBFs in self-regulation and cold acclimation.

Repressors of cold-induced transcriptome

Cold acclimation involves adjustment of metabolism and growth and thus involves not only induction and upregulation but also downregulation of many genes in plants (Kreps et al. 2002). Moreover, feedback repression is required to maintain the optimal protein levels of cold-induced transcriptomes. Cysteine-2 and histidine-2-type (C2H2) zinc finger proteins and a double-stranded RNA-binding protein have been identified as negative regulators of CBF expression.

In Arabidopsis, cold, ABA, drought, and salt stress induce the expression of C2H2 zinc fingers, namely, Arabidopsis zinc-finger 2 (AZF2) and salt-tolerance zinc finger ZAT10 (STZ) (Lee et al. 2002b, Sakamoto et al. 2004). Promoters of both AZF2 and STZ contain the DRE, MYB recognition, and MYC recognition cis-elements. Hence, the expression of these genes may be under the control of transcription factors that bind to these cis-elements during cold stress. Transgenic plants overexpressing CBF3 showed enhanced expression of STZ (Maruyama et al. 2004). Conversely, defective CBF3 expression caused by the ice1 mutation significantly reduced the cold induction of STZ and AZF2 as compared with the wild-type (Table 1) (Chinnusamy et al. 2003). Hence, ICE1-induced CBF3 expression may positively regulate the expression of AZF2 and STZ through the DRE cis-element (Fig. 1).

The cold-stress induction of STZ is rapid and transient in wild-type plants, while its induction is stronger and more sustained in the los2 mutant of Arabidopsis. Also, LOS2 bi-functional enolase binds to the MYC recognition sequence in the promoter of STZ. Thus, the expression of STZ is under the negative regulation of LOS2 (Lee et al. 2002b) (Fig. 1). The Arabidopsis ada2b-1 mutant defective in a histone acetyltransferase complex also showed higher expression of STZ and ZAT12 and more constitutive freezing tolerance than wild-type plants (Vlachonasios et al. 2003). Thus, the ICE1-CBF pathway positively regulates the expression of these zinc finger transcriptional repressors, while LOS2 and ADA2b negatively regulate them. STZ is also probably positively regulated by a MAPK-signaling pathway, AtMEKK1-AtMKK2-AtMPK4/6, as is evident from transcriptome profiling of AtMKK2-overexpression Arabidopsis plants (Teige et al. 2004).

These zinc finger repressors repress the expression of COR genes directly and/or through the repression of CBFs. Transient expression studies have shown that STZ is a repressor of RD29A. A los2 mutation that enhanced STZ expression resulted in reduced cold induction of a CRT cis-element containing COR genes. STZ appears to repress RD29A expression by binding to the STZ recognition site at −554 to −522 (ACTAGTGTAN13TCTAGTAAG) in the promoter of RD29A (Lee et al. 2002b) (Fig. 1). Gel mobility-shift assays showed that AZF2 and STZ bind specifically to an A(G/C)T cis-element within the EP2 sequence (a cis-element where a negative regulator binds). Co-expression of AZF2 and STZ with DREB1A in an Arabidopsis protoplast resulted in inhibition of DREB1A-induced expression of a chimeric EP2-fused RD29A promoter-driven reporter gene (Sakamoto et al. 2004). Similarly, ada2 and gcn5 mutants with a higher induction of STZ and ZAT12 showed reduced expression of COR47 and COR6.6 genes (Vlachonasios et al. 2003). Transgenic plants constitutively overexpressing CBFs showed higher induction of STZ, which may repress genes involved in photosynthesis and carbohydrate metabolism and thus reduce the growth of these transgenic plants (Maruyama et al. 2004). CBF-induced zinc fingers also appear to be involved in feedback repression of CBFs, because ZAT12-overexpression transgenic Arabidopsis showed decreased expression levels of CBFs (Vogel et al. 2005).

Genetic analyses of fiery2 (fry2) mutant of Arabidopsis revealed that the FRY2 RNA polymerase II C-terminal domain phosphatase, which controls transcription and mRNA processing by de-phosphorylation of RNA polymerase II, is a regulator of COR genes (Koiwa et al. 2002, Xiong et al. 2002b). fry2 mutants exhibited hypersensitivity to freezing damage as compared with wild-type plants. fry2 mutation enhanced the expression of CBFs and COR genes under cold and ABA stress. This observation suggests that FRY2 is a negative regulator of CBFs and their target COR genes (Xiong et al. 2002b). The increased freezing sensitivity in fry2 mutant plants implies that FRY2 may positively regulate the expression of certain genes critical for freezing tolerance.

CBF-independent pathways of cold responses

Both ABA-independent and -dependent pathways regulate cold-responsive genes, and ABA acts synergistically with the cold signal (Xiong et al. 1999). ABA-dependent gene expression is regulated by transcription factors that belong to the bZIP (ABRE-binding factors or AREBs), MYC, and MYB families. A cold- and ABA-inducible bZIP gene, ABRE-binding factor 1 (ABF1), has been cloned from Arabidopsis (Choi et al. 2000), but its target genes are not known. However, a C2H2-type zinc finger protein that activates a bZIP transcription factor has been found to regulate COR gene expression through ABRE elements. Over-expression in Arabidopsis of a cold-inducible zinc finger protein from soybean, SCOF1, resulted in constitutive expression of COR genes and freezing tolerance. SCOF1 enhanced the DNA-binding activity of a cold-inducible bZIP transcription factor, soybean G-Box-binding factor 1 (SGBF1), which induces the expression of COR genes in an ABA-dependent pathway during cold acclimation (Kim et al. 2001).

In rice, a member of MYB family transcription factors, OsMYB4, has been shown to be inducible by cold (10–15° C) but not by ABA. Transient expression analysis showed that OsMYB4 could transactivate the expression of COR genes (RD29A, COR15a, and PAL2). Furthermore, transgenic Arabidopsis plants overexpressing OsMYB4 exhibited enhanced induction of COR genes, increased proline content and enhanced freezing tolerance (Vannini et al. 2004). Genetic evidence for the involvement of MYB transcription factors in cold acclimation came from the analysis of a freezing hypersensitive hos10 mutant of Arabidopsis. The hos10-1 mutant showed enhanced expression of PRD29A::LUC and COR genes under cold, ABA, and salt stress. The HOS10 gene encodes a putative R2R3-type MYB transcription factor. Interestingly, HOS10 is required for ABA accumulation, because hos10-1 mutant plants showed reduced induction of NCED3 (9-cis-epoxycarotenoid dioxygenase) and thus low ABA accumulation under osmotic stress (Zhu et al. 2005).

A PRD29A::LUC reporter genetic screen also led to the identification of a freezing-sensitive hos9 mutant in Arabidopsis. HOS9 encodes a putative homeodomain transcription factor that is constitutively expressed and localized to the nucleus. As compared with the wild-type, the hos9 mutant is hypersensitive to freezing with or without cold acclimation, although cold induction of CBFs was not altered. Furthermore, transcriptome analysis of hos9-1 mutant plants under cold stress suggested that the HOS9 regulon is different from that of the CBFs. Thus, HOS9 plays an important role in regulating cold acclimation through a CBF-independent pathway (Zhu et al. 2004).

Post-transcriptional regulation

Post-transcriptional regulation of gene expression is mediated through pre-mRNA splicing, nucleocytoplasmic transport, RNA stability, translation, post-translational modification, and proteolysis. The use of a PRD29A::LUC genetic screen led to the identification of one of the proteins involved in RNA export, a DEAD-box RNA helicase (LOS4), as a positive regulator of CBF expression during cold acclimation. Cold induction of CBF3 is blocked, while that of CBF1 and CBF2 is delayed in the los4 mutant, and thus, the mutant is impaired in the cold induction of COR genes. The los4-1 mutant was sensitive to chilling stress, and ectopic expression of CBF3 rescued the mutant from chilling sensitivity. LOS4 may unwind the cold-stabilized secondary structure in the 5′-untranslated region of RNA or may directly control the transcript stability of CBFs or regulators of CBF genes (Gong et al. 2002). The cryophyte mutant isolated by a PRD29A::LUC genetic screen is allelic to los4-1. It showed enhanced cold induction of CBF2 and more chilling and freezing tolerance than the wild-type Arabidopsis. The CRYOPHYTE/LOS4 protein is enriched in the nuclear rim. In situ poly(A) hybridization analysis revealed that mRNA export from the nucleus is blocked in the cryophyte/los4-2 mutant only at warm temperatures, while the los4-1 mutation weakens mRNA export at both cold and warm temperatures. These results suggest that the LOS4 RNA helicase is crucial in mRNA export and important in the regulation of CBF and COR gene expression (Gong et al. 2005).

In the sensitive to freezing 6 (sfr6) mutant of Arabidopsis, cold-stress induction of CBF1, CBF2, CBF3, and DREB2 was not impaired, but induction of their target COR genes was significantly less as compared with that of the wild-type. These results suggest that the sfr6 mutation probably controls the trans-activation capacity of CBFs and/or post-transcriptional regulation of COR genes (Boyce et al. 2003). The regulatory small RNAs such as microRNAs (miRNAs) and short interfering RNAs (siRNAs) play a vital role in the post-transcriptional gene regulation. Cold and other abiotic stress-regulated regulatory RNAs have been identified in Arabidopsis (Sunkar and Zhu 2004), which will help in understanding post-transcriptional gene regulation during abiotic stresses.

Although ICE1 is constitutively expressed, it activates CBF gene expression only upon cold treatment (Chinnusamy et al. 2003), which suggests that ICE1 requires either interaction with additional factors induced by cold or post-translational regulation under cold stress for its activity. Use of a PRD29A::LUC genetic screen identified HOS1 (Ishitani et al. 1998) as an upstream negative regulator of CBFs. HOS1 encodes a RING finger ubiquitin E3 ligase, which may target certain signaling proteins for proteolysis. Since the hos1 mutant showed superinduction of CBF genes under cold stress, HOS1 is a negative regulator of CBF expression (Lee et al. 2001). HOS1 may target upstream positive regulator(s) of CBFs such as ICE1 for proteolysis and thus negatively regulate the expression of ICE1 target genes.

Conclusions and perspectives

Although a cold sensor has yet to be identified, current evidence suggests that cold stress may be perceived by plant cells through changes in the plasma membrane fluidity state. Cold-induced calcium signaling is decoded and transduced by calcium sensory proteins. Cold and other abiotic stresses induce ROS, which can activate a MAPK cascade, AtMEKK1-MKK2-MPK4/6. However, the molecular link between the kinases and transcription factors is still unknown. Molecular analyses have shown that CBFs play a vital role in regulation of genes encoding late-embryogensis-abundant (LEA) type COR proteins and osmoprotectant biosynthesis across plant species. ICE1, a MYC-type bHLH transcription factor, and perhaps ICE1-like proteins are upstream master regulators of CBFs and many cold-responsive subregulons. The HOS1 RING finger protein appears to negatively regulate the ICE1-CBF pathway possibly by targeting ICE1 for proteolysis. CBFs probably repress some genes through C2H2 zinc fingers. CBF-independent pathways of gene regulation are mediated by proteins such as HOS9, a homeodomain transcription factor, and HOS10, a MYB-type transcription factor.

The reproductive phase, particularly, pollen maturation/germination is very sensitive to cold and other abiotic stresses. Many genes necessary for cold acclimation in vegetative tissues were either not or weakly induced in pollen under cold stress (Lee and Lee 2003). This observation suggests that the mechanism of cold tolerance is different in vegetative and reproductive tissues, the understanding of which warrants serious attention. A thorough understanding of cold-stress signaling will help in transcriptome engineering of crop plants for enhanced tolerance to cold and other abiotic stresses. Stress-responsive promoter::LUC genetic screening will continue to be of help in dissecting stress-signaling components that activate cold-responsive transcriptome.

Acknowledgements –  Work in our lab has been supported by NSF grants IBN-0212346 and MCB-0241450 and by a USDA NRI grant 2003-00751 (J.-K. Zhu).