Arabidopsis thaliana ICE2 gene: phylogeny, structural evolution and functional diversification from ICE1

In-Silico Identification, Characterization and Expression Analysis of Genes Involved in Resistant Starch Biosynthesis in Potato (Solanum tuberosum L.) Varieties

Potato (Solanum tuberosum L.), an important horticultural crop is a member of the family Solanaceae and is mainly grown for consumption at global level. Starch, the principal component of tubers, is one of the significant elements for food and non-food-based applications. The genes associated with biosynthesis of starch have been investigated extensively over the last few decades. However, a complete regulation pathway of constituent of amylose and amylopectin are still not deeply explored. The current in-silico study of genes related to amylose and amylopectin synthesis and their genomic organization in potato is still lacking. In the current study, the nucleotide and amino acid arrangement in genome and twenty-two genes linked to starch biosynthesis pathway in potato were analysed. The genomic structure analysis was also performed to find out the structural pattern and phylogenetic relationship of genes. The genome mining and structure analysis identified ten specific motifs and phylogenetic analysis of starch biosynthesis genes divided them into three different clades on the basis of their functioning and phylogeny. Quantitative real-time PCR (qRT-PCR) of amylose biosynthesis pathway genes in three contrast genotypes revealed the down-gene expression that leads to identify potential cultivar for functional genomic approaches. These potential lines may help to achieve higher content of resistant starch.

A systematic regulatory network related to bulbil formation in Lilium lancifolium based on metabolome and transcriptome analyses

BACKGROUND

Lilium lancifolium is a special wild triploid species native to China and can produce abundant bulbils on its stem under natural conditions, which is very valuable to study bulbil organogenesis in plants. Although similar to the lateral and tillering principles, the molecular mechanism underlying bulbil formation has remained incompletely understood.

RESULTS

The metabolome and transcriptome of L. lancifolium bulbils across four development stages were analyzed. The pairwise comparison of metabolomes across the four stages identified 17 differential hormones, predominantly auxin (IAA), cytokinin (CK), and jasmonic acid (JA). Short Time-series Expression Miner (STEM) trend analysis of differential genes revealed four significant trends across these stages. The KEGG enrichment analysis of the four clusters highlighted pathways, such as plant hormone signal transduction, which were speculated to play a crucial role in development stages. these pathways were speculated to play a crucial role in development stages. To explore the key differential expressed genes and transcription factors associated with bulbil occurrence, two periods were focused on: Ll_UN and Ll_DN, which represented the stages with and without bulbils, respectively. Through correlation analysis and qRT-PCR analysis, 11 candidate differentially expressed genes and 27 candidate transcription factors were selected. By spraying exogenous hormones to validate these candidates, LlbHLH128, LlTIFY10A, LlbHLH93, and LlMYB108, were identified as the key genes for L. lancifolium bulbils.

CONCLUSION

A regulatory network of L. lancifolium bulbil development was predicted. LlTIFY10A and LlbHLH93 might be involved in the JA and auxin signal transduction pathways, which jointly formed a regulatory network to affect the occurrence of L. lancifolium bulbil. This study not only provided more information about the differentially expressed genes and metabolites through transcriptome and metabolomics analyses, but also provided a clearer understanding of the effect of hormones on bulbil formation in lily.

Brassica rapa BrICE1 and BrICE2 Positively Regulate the Cold Tolerance via CBF and ROS Pathways, Balancing Growth and Defense in Transgenic Arabidopsis

Winter rapeseed (Brassica rapa) has a good chilling and freezing tolerance. inducer of CBF expression 1 (ICE1) plays a crucial role in cold signaling in plants; however, its role in Brassica rapa remains unclear. In this study, we identified 41 ICE1 homologous genes from six widely cultivated Brassica species. These genes exhibited high conservation, with evolutionary complexity between diploid and allotetraploid species. Cold stress induced ICE1 homolog expression, with differences between strongly and weakly cold-tolerant varieties. Two novel ICE1 paralogs, BrICE1 and BrICE2, were cloned from Brassica rapa Longyou 6. Subcellular localization assays showed that they localized to the nucleus, and low temperature did not affect their nuclear localization. The overexpression of BrICE1 and BrICE2 increased cold tolerance in transgenic Arabidopsis and enhanced reactive oxygen species' (ROS) scavenging ability. Furthermore, our data demonstrate that overexpression of BrICE1 and BrICE2 inhibited root growth in Arabidopsis, and low temperatures could induce the degradation of BrICE1 and BrICE2 via the 26S-proteasome pathway. In summary, ICE1 homologous genes exhibit complex evolutionary relationships in Brassica species and are involved in the C-repeat/DREB binding factor (CBF) pathway and ROS scavenging mechanism in response to cold stress; these regulating mechanisms might also be responsible for balancing the development and cold defense of Brassica rapa.

Transcriptomic Analysis Reveals CBF-Dependent and CBF-Independent Pathways under Low-Temperature Stress in Teak (Tectona grandis)

Teak is a rare tropical tree with high economic value, and it is one of the world's main afforestation trees. Low temperature is the main problem for introducing and planting this species in subtropical or temperate zones. Low-temperature acclimation can enhance the resistance of teak to low-temperature stress, but the mechanism for this is still unclear. We studied the gene expression of two-year-old teak seedlings under a rapid temperature drop from 20 °C to 4 °C using RNA-seq and WGCNA analyses. The leaves in the upper part of the plants developed chlorosis 3 h after the quick transition, and the grades of chlorosis were increased after 9 h, with the addition of water stains and necrotic spots. Meanwhile, the SOD and proline contents in teak leaves increased with the prolonged cold stress time. We also identified 36,901 differentially expressed genes, among which 1055 were novel. Notably, CBF2 and CBF4 were significantly induced by low temperatures, while CBF1 and CBF3 were not. Furthermore, WGCNA successfully identified a total of fourteen modules, which consist of three modules associated with cold stress response genes, two modules linked to CBF2 and CBF4, and one module correlated with the CBF-independent pathway gene HY5. The transformation experiments showed that TgCBF2 and TgCBF4 improved cold resistance in Arabidopsis plants.

Identification of Brassica rapa BrEBF1 homologs and their characterization in cold signaling

EIN3-binding F-box 1 (EBF1) is involved in cold tolerance in Arabidopsis; however, its exact roles in cold signaling in Brassica rapa remain uncertain. Herein, we demonstrated that EBF1 homologs are highly conserved in Brassica species, but their copy numbers are diverse, with some motifs being species specific. Cold treatment activated the expression of EBF1 homologs BrEBF1 and BrEBF2 in B. rapa; however, their expression schemas were diverse in different cold-resistant varieties of the plant. Subcellular localization analysis revealed that BrEBF1 is a nuclear-localized F-box protein, and cold treatment did not alter its localization but induced its degradation. BrEBF1 overexpression enhanced cold tolerance, reduced cold-induced ROS accumulation, and enhanced MPK3 and MPK6 kinase activity in Arabidopsis. Our study revealed that BrEBF1 positively regulates cold tolerance in B. rapa and that BrEBF1-regulated cold tolerance is associated with ROS scavenging and MPK3 and MPK6 kinase activity through the C-repeat binding factor pathway.

Genome-wide identification and functional analysis of ICE genes reveal that Gossypium thurberi "GthICE2" is responsible for cold and drought stress tolerance

Cold stress has been found to have a negative impact on cotton growth and annual production. To address this issue, the utilization of cold-tolerant gene resources from wild species of Gossypium is crucial for genetic improvements in cultivated cotton. ICE (inducer of CBF expression) are the key regulators of cold tolerance in plants, however, there is relatively little information on ICE genes in cotton. Herein, we performed comprehensive bioinformatics analyses of the ICE gene family in eight cotton species. Phylogenetic analysis showed that 52 ICE genes were clustered into four subgroups. Cis-regulatory elements analysis suggests that the expression of ICE genes might be regulated by light, plant hormones, and various environment stresses. Higher expression of GthICE2 was observed in leaves as compared to roots and stems, in response to cold, drought, and exogenous hormone ABA. Furthermore, overexpression of GthICE2 in A. thaliana led to higher germination and survival rates, longer root length, lower ion leakage, and induction under cold and drought stress. Histochemical staining showed that oxidative damage in transgenic lines was much lower compared to wild-type plants. Lower MDA contents and higher SOD and POD activities were observed in overexpressed plants. Y1H and LUC assays revealed that GthICE2 might activate the expression of GthCBF4, a cold-responsive gene, by connecting with the MYC cis-element present in the promoter of GthCBF4. GthICE2 confers cold and drought stress tolerance in cotton. Our findings add significantly to the existing knowledge regarding cold stress tolerance and helps to elucidate cold response mechanisms in cotton.

Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima

The basic helix-loop-helix (bHLH) transcription factors (TFs) gene family is an important gene family in plants, and participates in regulation of plant apical meristem growth, metabolic regulation and stress resistance. However, its characteristics and potential functions have not been studied in chestnut (Castanea mollissima), an important nut with high ecological and economic value. In the present study, 94 CmbHLHs were identified in chestnut genome, of which 88 were unevenly distributed on chromosomes, and other six were located on five unanchored scaffolds. Almost all CmbHLH proteins were predicted in the nucleus, and subcellular localization demonstrated the correctness of the above predictions. Based on the phylogenetic analysis, all of the CmbHLH genes were divided into 19 subgroups with distinct features. Abundant cis-acting regulatory elements related to endosperm expression, meristem expression, and responses to gibberellin (GA) and auxin were identified in the upstream sequences of CmbHLH genes. This indicates that these genes may have potential functions in the morphogenesis of chestnut. Comparative genome analysis showed that dispersed duplication was the main driving force for the expansion of the CmbHLH gene family inferred to have evolved through purifying selection. Transcriptome analysis and qRT-PCR experiments showed that the expression patterns of CmbHLHs were different in different chestnut tissues, and revealed some members may have potential functions in chestnut buds, nuts, fertile/abortive ovules development. The results from this study will be helpful to understand the characteristics and potential functions of the bHLH gene family in chestnut.

Genome-Wide Identification of bHLH Transcription Factor in Medicago sativa in Response to Cold Stress

Alfalfa represents one of the most important legume forages, and it is also applied as an organic fertilizer to improve soil quality. However, this perennial plant is native to warmer temperate regions, and its valuable cold-acclimation-related regulatory mechanisms are still less known. In higher plants, the bHLH transcription factors play pleiotropic regulatory roles in response to abiotic stresses. The recently released whole genome sequencing data of alfalfa allowed us to identify 469 MsbHLHs by multi-step homolog search. Herein, we primarily identified 65 MsbHLH genes that significantly upregulated under cold stress, and such bHLHs were classified into six clades according to their expression patterns. Interestingly, the phylogenetic analysis and conserved motif screening of the cold-induced MsbHLHs showed that the expression pattern is relatively varied in each bHLH subfamily, this result indicating that the 65 MsbHLHs may be involved in a complex cold-responsive regulatory network. Hence, we analyzed the TFBSs at promoter regions that unraveled a relatively conserved TFBS distribution with genes exhibiting similar expression patterns. Eventually, to verify the core components involved in long-term cold acclimation, we examined transcriptome data from a freezing-tolerant species (cv. Zhaodong) in the field and compared the expression of cold-sensitive/tolerant subspecies of alfalfa, giving 11 bHLH as candidates, which could be important for further cold-tolerance enhancement and molecular breeding through genetic engineering in alfalfa.

Pleiotropic ZmICE1 Is an Important Transcriptional Regulator of Maize Endosperm Starch Biosynthesis

Starch, the major component of cereal grains, affects crop yield and quality and is widely used in food and industrial applications. The biosynthesis of maize starch is a complex process involving a series of functional enzymes. However, the sophisticated regulatory mechanisms of starch biosynthetic genes have not been fully elaborated. The basic/helix-loop-helix (bHLH) transcription factors are widely distributed in eukaryotes and participate in many physiological processes. In this study, 202 bHLH encoding genes were identified in the maize genome by Blast method. ZmICE1 gene, which belongs to the ICE subfamily of the bHLH family, was obtained and expressed mainly in maize filling endosperm and co-expressed with 14 starch biosynthesis genes. Based on the comparative analyses across different plant species, we revealed that the gene structures and protein domains of the ICE subfamily were conserved between monocots and dicots, suggesting their functional conservation feature. Yeast activation and subcellular localization assays suggested that ZmICE1 had transcriptional activation activity and localized in the nucleus. Yeast one-hybrid assays confirmed that ZmICE1 could directly bind to the promoters of ZmSSIIa and ZmGBSSI. Transient gene expression analysis in maize endosperm revealed that ZmICE1 positively regulated the expression of ZmSSIIa, but inhibited the expression of ZmGBSSI. Our results indicated that ZmICE1 could function as a regulator of maize starch biosynthesis.

Cold stress regulates accumulation of flavonoids and terpenoids in plants by phytohormone, transcription process, functional enzyme, and epigenetics

Plants make different defense mechanisms in response to different environmental stresses. One common way is to produce secondary metabolites. Temperature is the main environmental factor that regulates plant secondary metabolites, especially flavonoids and terpenoids. Stress caused by temperature decreasing to 4-10 °C is conducive to the accumulation of flavonoids and terpenoids. However, the accumulation mechanism under cold stress still lacks a systematic explanation. In this review, we summarize three aspects of cold stress promoting the accumulation of flavonoids and terpenoids in plants, that is, by affecting (1) the content of endogenous plant hormones, especially jasmonic acid and abscisic acid; (2) the expression level and activity of important transcription factors, such as bHLH and MYB families. This aspect also includes post-translational modification of transcription factors caused by cold stress; (3) key enzyme genes expression and activity in the biosynthesis pathway, in addition, the rate-limiting enzyme and glycosyltransferases genes are responsive to cold stress. The systematic understanding of cold stress regulates flavonoids, and terpenoids will contribute to the future research of genetic engineering breeding, metabolism regulation, glycosyltransferases mining, and plant synthetic biology.

ICE-CBF-COR Signaling Cascade and Its Regulation in Plants Responding to Cold Stress

Cold stress limits plant geographical distribution and influences plant growth, development, and yields. Plants as sessile organisms have evolved complex biochemical and physiological mechanisms to adapt to cold stress. These mechanisms are regulated by a series of transcription factors and proteins for efficient cold stress acclimation. It has been established that the ICE-CBF-COR signaling pathway in plants regulates how plants acclimatize to cold stress. Cold stress is perceived by receptor proteins, triggering signal transduction, and Inducer of CBF Expression (ICE) genes are activated and regulated, consequently upregulating the transcription and expression of the C-repeat Binding Factor (CBF) genes. The CBF protein binds to the C-repeat/Dehydration Responsive Element (CRT/DRE), a homeopathic element of the Cold Regulated genes (COR gene) promoter, activating their transcription. Transcriptional regulations and post-translational modifications regulate and modify these entities at different response levels by altering their expression or activities in the signaling cascade. These activities then lead to efficient cold stress tolerance. This paper contains a concise summary of the ICE-CBF-COR pathway elucidating on the cross interconnections with other repressors, inhibitors, and activators to induce cold stress acclimation in plants.

Identification of bHLH genes through genome-wide association study and antisense expression of ZjbHLH076/ZjICE1 influence tolerance to low temperature and salinity in Zoysia japonica

Abiotic stress greatly affects plant growth and developmental processes, resulting in poor productivity. A variety of basic helix-loop-helix (bHLH) transcription factors (TFs) that play important roles in plant abiotic stress response pathways have been identified. However, bHLH proteins of Zoysia japonica, one of the warm-season turfgrasses, have not been widely studied. In this study, 141 bHLH genes (ZjbHLHs) were identified and classified into 22 subfamilies. The ZjbHLHs were mapped on 19 chromosomes except for Chr17 and one pair of the tandemly arrayed genes was identified on Chr06. Also, the co-linearity of ZjbHLHs was found to have been driven mostly by segmental duplication events. The subfamily IIIb genes of our present interest, possessed various stress responsive cis-elements in their promoters. ZjbHLH076/ZjICE1, a MYC-type bHLH TF in subfamily IIIb was analyzed by overexpression and its loss-of-function via overexpressing a short ZjbHLH076/ZjICE1 fragment in the antisense direction. The overexpression of ZjbHLH076/ZjICE1 enhanced the tolerance to cold and salinity stress in the transgenic Z. japonica plants. However, the anti-sense expression of ZjbHLH076/ZjICE1 showed sensitive to these abiotic stresses. These results suggest that ZjbHLH076/ZjICE1 would be a promising candidate for the molecular breeding program to improve the abiotic stress tolerance of Z. japonica.

Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume

Prunus mume is an illustrious ornamental woody plant with colorful flowers, delicate fragrances, and graceful tree forms. Low temperature limits its geographical distribution. The basic helix-loop-helix (bHLH) proteins exist in most eukaryotes as a transcription factor superfamily, which play a crucial role in metabolism, physiology, development, and response to various stresses of higher organisms. However, the characteristics of the bHLH gene family and low-temperature response remain unknown in P. mume. In the present study, we distinguished 95 PmbHLH genes in the P. mume whole-genome and analyzed their features. PmbHLHs were divided into 23 subfamilies and one orphan by phylogenetic analysis. Similar gene structures and conserved motifs appeared in the same subfamily. These genes were situated in eight chromosomes and scaffolds. Gene duplication events performed a close relationship to P. mume, P. persica, and P. avium. Tandem duplications probably promoted the expansion of PmbHLHs. According to predicted binding activities, the PmbHLHs were defined as the Non-DNA-binding proteins and DNA-binding proteins. Furthermore, PmbHLHs exhibited tissue-specific and low-temperature induced expression patterns. By analyzing transcriptome data, 10 PmbHLHs which are responsive to low-temperature stress were selected. The qRT-PCR results showed that the ten PmbHLH genes could respond to low-temperature stress at different degrees. There were differences in multiple variations among different varieties. This study provides a basis to research the evolution and low-temperature tolerance of PmbHLHs, and might enhance breeding programs of P. mume by improving low-temperature tolerance.

Saussurea involucrata (Snow Lotus) ICE1 and ICE2 Orthologues Involved in Regulating Cold Stress Tolerance in Transgenic Arabidopsis

As with other environmental stresses, cold stress limits plant growth, geographical distribution, and agricultural productivity. CBF/DREB (CRT-binding factors/DRE-binding proteins) regulate tolerance to cold/freezing stress across plant species. ICE (inducer of CBF expression) is regarded as the upstream inducer of CBF expression and plays a crucial role as a main regulator of cold acclimation. Snow lotus (Saussurea involucrata) is a well-known traditional Chinese herb. This herb is known to have greater tolerance to cold/freezing stress compared to other plants. According to transcriptome datasets, two putative ICE homologous genes, SiICE1 and SiICE2, were identified in snow lotus. The predicted SiICE1 cDNA contains an ORF of 1506 bp, encoding a protein of 501 amino acids, whereas SiICE2 cDNA has an ORF of 1482 bp, coding for a protein of 493 amino acids. Sequence alignment and structure analysis show SiICE1 and SiICE2 possess a S-rich motif at the N-terminal region, while the conserved ZIP-bHLH domain and ACT domain are at the C-terminus. Both SiICE1 and SiICE2 transcripts were cold-inducible. Subcellular localization and yeast one-hybrid assays revealed that SiICE1 and SiICE2 are transcriptional regulators. Overexpression of SiICE1 (35S::SiICE1) and SiICE2 (35S::SiICE2) in transgenic Arabidopsis increased the cold tolerance. In addition, the expression patterns of downstream stress-related genes, CBF1, CBF2, CBF3, COR15A, COR47, and KIN1, were up-regulated when compared to the wild type. These results thus provide evidence that SiICE1 and SiICE2 function in cold acclimation and this cold/freezing tolerance may be regulated through a CBF-controlling pathway.

Basic Helix-Loop-Helix (bHLH) Transcription Factors Regulate a Wide Range of Functions in Arabidopsis

The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor gene families in Arabidopsis thaliana, and contains a bHLH motif that is highly conserved throughout eukaryotic organisms. Members of this family have two conserved motifs, a basic DNA binding region and a helix-loop-helix (HLH) region. These proteins containing bHLH domain usually act as homo- or heterodimers to regulate the expression of their target genes, which are involved in many physiological processes and have a broad range of functions in biosynthesis, metabolism and transduction of plant hormones. Although there are a number of articles on different aspects to provide detailed information on this family in plants, an overall summary is not available. In this review, we summarize various aspects of related studies that provide an overview of insights into the pleiotropic regulatory roles of these transcription factors in plant growth and development, stress response, biochemical functions and the web of signaling networks. We then provide an overview of the functional profile of the bHLH family and the regulatory mechanisms of other proteins.

Chloroplasts in C3 grasses move in response to blue-light

KEY MESSAGE

Brachypodium distachyon is a good model for studying chloropla st movements in the crop plants, wheat, rye and barley. The movements are activated only by blue light, similar to Arabidopsis. Chloroplast translocations are ubiquitous in photosynthetic organisms. On the one hand, they serve to optimize energy capture under limiting light, on the other hand, they minimize potential photodamage to the photosynthetic apparatus in excess light. In higher plants chloroplast movements are mediated by phototropins (phots), blue light receptors that also control other light acclimation responses. So far, Arabidopsis thaliana has been the main model for studying the mechanism of blue light signaling to chloroplast translocations in terrestrial plants. Here, we propose Brachypodium distachyon as a model in research into chloroplast movements in C3 cereals. Brachypodium chloroplasts respond to light in a similar way to those in Arabidopsis. The amino acid sequence of Brachypodium PHOT1 is 79.3% identical, and that of PHOT2 is 73.6% identical to the sequence of the corresponding phototropin in Arabidopsis. Both phototropin1 and 2 are expressed in Brachypodium, as shown using quantitative real-time PCR. Intriguingly, the light-expression pattern of BradiPHOT1 and BradiPHOT2 is the opposite of that for Arabidopsis phototropins, suggesting potential unique light signaling in C3 grasses. To investigate if Brachypodium is a good model for studying grass chloroplast movements we analyzed these movements in the leaves of three C3 crop grasses, namely wheat, rye and barley. Similarly to Brachypodium, chloroplasts only respond to blue light in all these species.

Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.)

The basic helix-loop-helix (bHLH) transcription factors (TFs) have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya (Carica papaya L.) has been reported previously. Here, a total of 73 CpbHLHs were identified in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis. Almost all of the CpbHLHs in the same subfamily shared similar gene structures and protein motifs according to analysis of exon/intron organizations and motif compositions. The number of exons in CpbHLHs varied from one to 10 with an average of five. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis-element analysis revealed that most of the CpbHLHs contained cis-elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that CpbHLHs mainly functions in protein dimerization activity and DNA-binding, and most CpbHLHs were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some important candidate CpbHLHs that might be responsible for abiotic stress responses in papaya. These findings would lay a foundation for further investigate of the molecular functions of CpbHLHs.

Phylogenomic Evidence for the Monophyly of Bryophytes and the Reductive Evolution of Stomata

The origin of land plants was accompanied by new adaptations to life on land, including the evolution of stomata-pores on the surface of plants that regulate gas exchange. The genes that underpin the development and function of stomata have been extensively studied in model angiosperms, such as Arabidopsis. However, little is known about stomata in bryophytes, and their evolutionary origins and ancestral function remain poorly understood. Here, we resolve the position of bryophytes in the land plant tree and investigate the evolutionary origins of genes that specify stomatal development and function. Our analyses recover bryophyte monophyly and demonstrate that the guard cell toolkit is more ancient than has been appreciated previously. We show that a range of core guard cell genes, including SPCH/MUTE, SMF, and FAMA, map back to the common ancestor of embryophytes or even earlier. These analyses suggest that the first embryophytes possessed stomata that were more sophisticated than previously envisioned and that the stomata of bryophytes have undergone reductive evolution, including their complete loss from liverworts.

Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

Background

Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the regulation of Fe homeostasis and a series of other biological and developmental processes in plants. However, this family of members in citrus and their functions in citrus Fe deficiency are still largely unknown.

Results

In this study, we identified a total of 128 CgbHLHs from pummelo (Citrus grandis) genome that were classified into 18 subfamilies by phylogenetic comparison with Arabidopsis thaliana bHLH proteins. All of these CgbHLHs were randomly distributed on nine known (125 genes) and one unknown (3 genes) chromosomes, and 12 and 47 of them were identified to be tandem and segmental duplicated genes, respectively. Sequence analysis showed detailed characteristics of their intron-exon structures, bHLH domain and conserved motifs. Gene ontology (GO) analysis suggested that most of CgbHLHs were annotated to the nucleus, DNA-binding transcription factor activity, response to abiotic stimulus, reproduction, post-embryonic development, flower development and photosynthesis. In addition, 27 CgbHLH proteins were predicted to have direct or indirect protein-protein interactions. Based on GO annotation, RNA sequencing data in public database and qRT-PCR results, several of CgbHLHs were identified as the key candidates that respond to iron deficiency.

Conclusions

In total, 128 CgbHLH proteins were identified from pummelo, and their detailed sequence and structure characteristics and putative functions were analyzed. This study provides comprehensive information for further functional elucidation of CgbHLH genes in citrus.

A novel basic helix-loop-helix transcription factor, ZjICE2 from Zoysia japonica confers abiotic stress tolerance to transgenic plants via activating the DREB/CBF regulon and enhancing ROS scavenging

ZjICE2 works as a positive regulator in abiotic stress responses and ZjICE2 is a valuable genetic resource to improve abiotic stress tolerance in the molecular breeding program of Zoysia japonica. The basic helix-loop-helix (bHLH) family transcription factors (TFs) play an important role in response to biotic or abiotic stresses in plants. However, the functions of bHLH TFs in Zoysia japonica, one of the warm-season turfgrasses, remain poorly understood. Here, we identified ZjICE2 from Z. japonica, a novel MYC-type bHLH transcription factor that was closely related to ICE homologs in the phylogenetic tree, and its expression was regulated by various abiotic stresses. Transient expression of ZjICE2-GFP in onion epidermal cells revealed that ZjICE2 was a nuclear-localized protein. Also, ZjICE2 bound the MYC cis-element in the promoter of dehydration responsive element binding 1 of Z. japonica (ZjDREB1) using yeast one-hybrid assay. A phenotypic analysis showed that overexpression of the ZjICE2 in Arabidopsis enhanced tolerance to cold, drought, and salt stresses. The transgenic Arabidopsis and Z. japonica accumulated more transcripts of cold-responsive DREB/CBFs and their downstream genes than the wild type (WT) after cold treatment. Furthermore, the transgenic plants exhibited an enhanced Reactive oxygen species (ROS) scavenging ability, which resulted in an efficient maintenance of oxidant-antioxidant homeostasis. In addition, overexpression of the ZjICE2 in Z. japonica displayed intensive cold tolerance with increases in chlorophyll contents and photosynthetic efficiency. Our study suggests that ZjICE2 works as a positive regulator in abiotic stress responses and the ICE-DREB/CBFs response pathway involved in cold stress tolerance is also conserved in Z. japonica. These results provide a valuable genetic resource for the molecular breeding program especially for warm-season grasses as well as other leaf crop plants.

Investigation of the Nature of CgCDPK and CgbHLH001 Interaction and the Function of bHLH Transcription Factor in Stress Tolerance in Chenopodium glaucum

Calcium-dependent protein kinase (CDPK) and its substrates play important roles in plant response to stress. So far, the documentation on the characterization of the CDPK and downstream interaction components (especially transcription factors, TFs) is limited. In the present study, an interaction between CgCDPK (protein kinase) (accession no. MW26306) and CgbHLH001 (TF) (accession no. MT797813) from a halophyte Chenopodium glaucum was further dissected. Firstly, we revealed that the probable nature between the CgCDPK and CgbHLH001 interaction was the phosphorylation, and the N-terminus of CgbHLH001, especially the 96th serine (the potential phosphorylation site) within it, was essential for the interaction, whereas the mutation of ⁹⁶Ser to alanine did not change its nuclear localization, which was determined by the N-terminus and bHLH domain together. Furthermore, we verified the function of CgbHLH001 gene in response to stress by ectopic overexpression in tobacco; the transgenic lines presented enhanced stress tolerance probably by improving physiological performance and stress-related gene expression. In conclusion, we characterized the biological significance of the interaction between CDPK and bHLH in C. glaucum and verified the positive function of CgbHLH001 in stress tolerance, which may supply more evidence in better understanding of the CDPK signaling pathway in response to adversity.

Comparative transcriptome, physiological and biochemical analyses reveal response mechanism mediated by CBF4 and ICE2 in enhancing cold stress tolerance in Gossypium thurberi

Low temperature is one of the key environmental stresses that impair plant growth and significantly restricts the productivity and spatial distribution of crop plants. Gossypium thurberi, a wild diploid cotton species, has adapted to a wide range of temperatures and exhibits a better tolerance to chilling stress. Here, we compared phenotypes and physiochemical changes in G. thurberi under cold stress and found this species indeed showed better cold tolerance. Therefore, to understand the molecular mechanisms of the cold tolerance in G. thurberi, we compared transcription changes in leaves of G. thurberi under cold stress by high-throughput transcriptome sequencing. In total, 35 617 unigenes were identified in the whole-genome transcription profile, and 4226 differentially expressed genes (DEGs) were discovered in the leaves upon cold treatment. Gene Ontology (GO) classification analyses showed that the majority of DEGs belonged to categories of signal transduction, transcription factors (TFs) and carbohydrate transport and metabolism. The expression of several cold-responsive genes such as ICE1, CBF4, RAP2-7 and abscisic acid (ABA) biosynthesis genes involved in different signalling pathways were induced after G. thurberi seedlings were exposed to cold stress. Furthermore, cold sensitivity was increased in CBF4 and ICE2 virus-induced gene silencing (VIGS) plants, and high level of malondialdehyde (MDA) showed that the CBF4 and ICE2 silenced plants were under oxidative stress compared to their wild types, which relatively had higher levels of antioxidant enzyme activity, as evident by high levels of proline and superoxide dismutase (SOD) content. In conclusion, our findings reveal a new regulatory network of cold stress response in G. thurberi and broaden our understanding of the cold tolerance mechanism in cotton, which might accelerate functional genomics studies and genetic improvement for cold stress tolerance in cultivated cotton.

Zoysia japonica MYC type transcription factor ZjICE1 regulates cold tolerance in transgenic Arabidopsis

ICE1 (Inducer of CBF Expression 1) is a regulator of cold-induced transcriptome, which plays an important role in plant cold response pathway. To enhance the cold tolerance of Zoysia japonica, one of the warm-season turfgrasses, it is helpful to understand the cold response mechanism in Zoysia japonica. We identified stress-responsive ZjICE1 from Zoysia japonica and characterized its function in cold stress. Our results showed that ZjICE1 shared the typical feature of ICE homolog proteins belonging to a nucleic protein. Transactivation activity assay revealed that ZjICE1 bound to the MYC cis-element in the ZjDREB1's promotor. The ZjICE1 overexpressed transgenic Arabidopsis showed enhanced tolerance to cold stress with an increases in SOD, POD, and free proline content and reduction in MDA content. They also induced the transcripts abundance of cold-responsive genes (CBF1, CBF2, CBF3, COR47A, KIN1, and RD29A) after cold treatment. These results suggest that ZjICE1 is a positive regulator in Zoysia japonica plant during cold stress and can be a useful gene for the molecular breeding program to develop the cold tolerant zoysiagrass. Furthermore, the ZjICE1 also conferred resistance to salt and drought stresses, providing the better understanding of the basic helix-loop-helix (bHLH) gene family in abiotic stress responses.

Genome-Wide Analysis of Basic Helix-Loop-Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.)

Basic helix–loop–helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24 h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.

The Tomato Genome Encodes SPCH, MUTE, and FAMA Candidates That Can Replace the Endogenous Functions of Their Arabidopsis Orthologs

Stomatal abundance determines the maximum potential for gas exchange between the plant and the atmosphere. In Arabidopsis, it is set during organ development through complex genetic networks linking epidermal differentiation programs with environmental response circuits. Three related bHLH transcription factors, SPCH, MUTE, and FAMA, act as positive drivers of stomata differentiation. Mutant alleles of some of these genes sustain different stomatal numbers in the mature organs and have potential to modify plant performance under different environmental conditions. However, knowledge about stomatal genes in dicotyledoneous crops is scarce. In this work, we identified the Solanum lycopersicum putative orthologs of these three master regulators and assessed their functional orthology by their ability to complement Arabidopsis loss-of-function mutants, the epidermal phenotypes elicited by their conditional overexpression, and the expression patterns of their promoter regions in Arabidopsis. Our results indicate that the tomato proteins are functionally equivalent to their Arabidopsis counterparts and that the tomato putative promoter regions display temporal and spatial expression domains similar to those reported for the Arabidopsis genes. In vivo tracking of tomato stomatal lineages in developing cotyledons revealed cell division and differentiation histories similar to those of Arabidopsis. Interestingly, the S. lycopersicum genome harbors a FAMA-like gene, expressed in leaves but functionally distinct from the true FAMA orthologue. Thus, the basic program for stomatal development in S. lycopersicum uses key conserved genetic determinants. This opens the possibility of modifying stomatal abundance in tomato through previously tested Arabidopsis alleles conferring altered stomata abundance phenotypes that correlate with physiological traits related to water status, leaf cooling, or photosynthesis.

The cold-induced transcription factor bHLH112 promotes artemisinin biosynthesis indirectly via ERF1 in Artemisia annua

Basic helix-loop-helix (bHLH) proteins are the second largest family of transcription factors (TFs) involved in developmental and physiological processes in plants. In this study, 205 putative bHLH TF genes were identified in the genome of Artemisia annua and expression of 122 of these was determined from transcriptomes used to construct the genetic map of A. annua. Analysis of gene expression association allowed division of the 122 bHLH TFs into five groups. Group V, containing 15 members, was tightly associated with artemisinin biosynthesis genes. Phylogenetic analysis indicated that two bHLH TFs, AabHLH106 and AabHLH112, were clustered with Arabidopsis ICE proteins. AabHLH112 was induced by low temperature, while AabHLH106 was not. We therefore chose AabHLH112 for further examination. AabHLH112 was highly expressed in glandular secretory trichomes, flower buds, and leaves. Dual-luciferase assays demonstrated that AabHLH112 enhanced the promoter activity of artemisinin biosynthesis genes and AaERF1, an AP2/ERF TF that directly and positively regulates artemisinin biosynthesis genes. Yeast one-hybrid assays indicated that AabHLH112 could bind to the AaERF1 promoter, but not to the promoters of artemisinin biosynthesis genes. Overexpression of AabHLH112 significantly up-regulated the expression levels of AaERF1 and artemisinin biosynthesis genes and consequently promoted artemisinin production.

The non-DNA binding bHLH transcription factor Paclobutrazol Resistances are involved in the regulation of ABA and salt responses in Arabidopsis

Abscisic acid (ABA) is the key hormone that regulating plant responses to abiotic stresses. Several basic helix-loop-helix (bHLH) transcription factors have been reported to regulate ABA signaling in Arabidopsis. Paclobutrazol Resistances (PREs) are non-DNA binding bHLH transcription factors involved in the regulation of plant response to several different plant hormones including gibberellin, brassinosteroid and auxin. Here, we show that PREs are involved in the regulation of ABA and salt responses in Arabidopsis. Quantitative RT-PCR results showed that the expression levels of PRE6 as well as several other PRE genes were reduced in response to ABA treatment, but increased to salt treatment. Seed germination assays indicated that ABA sensitivity is reduced in the pre6 mutants, but increased in transgenic plants overexpressing PRE6. On the other hand, the 35S:PRE6 transgenic plants showed enhanced tolerance to salt, whereas little, if any changes were observed in the pre6 mutants. Similar responses to ABA and salt treatments were observed in the pre2 mutants and the transgenic plants overexpressing PRE2, and a slight increased resistance to ABA in seed germination was observed in the pre2 pre6 double mutants. Taken together, our results suggest that at least some of the PRE genes are ABA responsive genes, and PREs may function redundantly to regulate ABA and salt responses in Arabidopsis.

Two ICE isoforms showing differential transcriptional regulation by cold and hormones participate in Brassica juncea cold stress signaling

C-repeat binding factor (CBF) dependent cold stress signaling cascade is well studied in the model plant arabidopsis but is relatively lesser studied in the crop plants. In the present study, two novel isoforms of an upstream regulator of CBF, Inducer of CBF expression (ICE), BjICE46 (1314 bp, accession number HQ446510) and BjICE53 (1494 bp, accession number HQ857208) were isolated from Brassica juncea seedlings. Genomic clones of both the isoforms (accession numbers HQ433510 and JX571043) showed three introns, out of which one intron was spanning the bHLH (basic helix-loop-helix) domain. Interestingly, the constitutive expression of BjICE53 was 21 fold higher than BjICE46. Real time quantitative expression (RT-qPCR) showed BjICE53 to be cold induced but non-responsive to phytohormones. Interestingly, BjICE46 was salinity stress induced and showed upregulation with methyl jasmonate (MeJa) and abscisic acid (ABA). This was supported by the presence of ABA, MeJa and defense related cis- acting regulatory elements in the promoter region of BjICE46. The downstream transcription factor BjCBF (645 bp) was also isolated. The promoter region of BjCBF showed three E-boxes, the binding site for ICE. BjCBF was expressed and purified from E. coli and binding of purified BjCBF with the DRE/CRT elements (present in the promoter of cold responsive genes) was EMSA confirmed. Overall, this study shows that ICE-CBF pathway is conserved in Brassica juncea along with the differential regulation of the ICE isoforms indicating cross-talk between cold and defense signaling.

Low-temperature tolerance in land plants: Are transcript and membrane responses conserved?

Plants' tolerance of low temperatures is an economically and ecologically important limitation on geographic distributions and growing seasons. Tolerance for low temperatures varies significantly across different plant species, and different mechanisms likely act in different species. In order to survive low-temperature stress, plant membranes must maintain their fluidity in increasingly cold and oxidative cellular environments. The responses of different species to low-temperature stress include changes to the types and desaturation levels of membrane lipids, though the precise lipids affected tend to vary by species. Regulation of membrane dynamics and other low-temperature tolerance factors are controlled by both transcriptional and post-transcriptional mechanisms. Here, we review low-temperature induced changes in both membrane lipid composition and gene transcription across multiple related plant species with differing degrees of low-temperature tolerance. We attempt to define a core set of changes for transcripts and lipids across species and treatment variations. Some responses appear to be consistent across all species for which data are available, while many others appear likely to be species or family-specific. Potential rationales are presented, including variance in testing, reporting and the importance of considering the level of stress perceived by the plant.

Role of carbon ion beams irradiation in mitigating cold stress in Arabidopsis thaliana

Carbon ion beams irradiation as an important type of ionizing radiation is one of the major approaches used to create mutants in plants. This study investigated the role of carbon ion beams irradiation in mitigating cold stress in Arabidopsis thaliana seedlings. The results showed that 50-Gy carbon ion beam irradiation appeared stimulatory effects on root length and fresh weight in Arabidopsis seedlings under cold stress. In comparison with control, the content of hydrogen peroxide, the production rate of superoxide anion radical, hydroxyl radical generation activity, and malondialdehyde content were obviously decreased in 50-Gy carbon ion beam irradiated seedlings in response to cold stress. Moreover, irradiated 50-Gy carbon ion beam in Arabidopsis seedlings were significantly triggered the efficiency of antioxidant under cold stress. Furthermore, we investigated the expression of cold-related genes in irradiated and non-irradiated samples. Carbon ion beams irradiation up-regulated the expression levels of C-REPEAT BINDING FACTORS (CBFs), INDUCER OF CBF EXPRESSION 1 (ICE1), ICE2, CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 3 (CAMTA3) and cold-regulated COR genes, in response to cold stress. This study suggests that low-dose carbon ion beams irradiation can modulate the physiological responses and up-regulate cold signaling genes in mitigating cold stress in the growth of Arabidopsis seedlings.

INDUCER OF CBF EXPRESSION 1 is a male fertility regulator impacting anther dehydration in Arabidopsis

INDUCER OF CBF EXPRESSION 1 (ICE1) encodes a MYC-like basic helix-loop-helix (bHLH) transcription factor playing a critical role in plant responses to chilling and freezing stresses and leaf stomata development. However, no information connecting ICE1 and reproductive development has been reported. In this study, we show that ICE1 controls plant male fertility via impacting anther dehydration. The loss-of-function mutation in ICE1 gene in Arabidopsis caused anther indehiscence and decreased pollen viability as well as germination rate. Further analysis revealed that the anthers in the mutant of ICE1 (ice1-2) had the structure of stomium, though the epidermis did not shrink to dehisce. The anther indehiscence and influenced pollen viability as well as germination in ice1-2 were due to abnormal anther dehydration, for most of anthers dehisced with drought treatment and pollen grains from those dehydrated anthers had similar viability and germination rates compared with wild type. Accordingly, the sterility of ice1-2 could be rescued by ambient dehydration treatments. Likewise, the stomatal differentiation of ice1-2 anther epidermis was disrupted in a different manner compared with that in leaves. ICE1 specifically bound to MYC-recognition elements in the promoter of FAMA, a key regulator of guard cell differentiation, to activate FAMA expression. Transcriptome profiling in the anther tissues further exhibited ICE1-modulated genes associated with water transport and ion exchange in the anther. Together, this work reveals the key role of ICE1 in male fertility control and establishes a regulatory network mediated by ICE1 for stomata development and water movement in the anther.

Identification of JAZ-interacting MYC transcription factors involved in latex drainage in Hevea brasiliensis

Hevea brasiliensis Müll. Arg. is one of the most frequently wounded plants worldwide. Expelling latex upon mechanical injury is a wound response of rubber trees. However, JA-mediated wound responses in rubber trees are not well documented. In this work, three JAZ-interacting MYC transcription factors of H. brasiliensis (termed HbMYC2/3/4) were identified by yeast two-hybrid screening. HbMYC2/3/4 each showed specific interaction profiles with HbJAZs. HbMYC2/3/4 each localized in the nucleus and exhibited strong transcriptional activity. To identify the target genes potentially regulated by HbMYC2/3/4, cis-elements interacting with HbMYC2/3/4 were first screened by yeast one-hybrid assays; the results indicated that HbMYC2/3/4 each could bind G-box elements. Additional analysis confirmed that HbMYC2/3/4 bound the HbPIP2;1 promoter, which contains five G-box cis-elements, and regulated the expression of reporter genes in yeast cells and in planta. HbMYC2/3/4 were induced by exogenous JA treatment but suppressed by ethylene (ET) treatment; in contrast, HbPIP2;1 was positively regulated by ET but negatively regulated by JA treatment. Given that HbPIP2;1 is involved in latex drainage, it could be proposed that HbMYC2/3/4 are involved in the regulation of HbPIP2;1 expression as well as latex drainage, both of which are coordinated by the JA and ET signalling pathways.

Gene Regulation and Signal Transduction in the ICE-CBF-COR Signaling Pathway during Cold Stress in Plants

Low temperature is an abiotic stress that adversely affects the growth and production of plants. Resistance and adaptation of plants to cold stress is dependent upon the activation of molecular networks and pathways involved in signal transduction and the regulation of cold-stress related genes. Because it has numerous and complex genes, regulation factors, and pathways, research on the ICE-CBF-COR signaling pathway is the most studied and detailed, which is thought to be rather important for cold resistance of plants. In this review, we focus on the function of each member, interrelation among members, and the influence of manipulators and repressors in the ICE-CBF-COR pathway. In addition, regulation and signal transduction concerning plant hormones, circadian clock, and light are discussed. The studies presented provide a detailed picture of the ICE-CBF-COR pathway.

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon

BACKGROUND

As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae.

RESULTS

A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions.

CONCLUSION

One hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of BdbHLH genes.

A novel Zea mays ssp. mexicana L. MYC-type ICE-like transcription factor gene ZmmICE1, enhances freezing tolerance in transgenic Arabidopsis thaliana

The annual Zea mays ssp. mexicana L., a member of the teosinte group, is a close wild relative of maize and thus can be effectively used in maize improvement. In this study, an ICE-like gene, ZmmICE1, was isolated from a cDNA library of RNA-Seq from cold-treated seedling tissues of Zea mays ssp. mexicana L. The deduced protein of ZmmICE1 contains a highly conserved basic helix-loop-helix (bHLH) domain and C-terminal region of ICE-like proteins. The ZmmICE1 protein localizes to the nucleus and shows sumoylation when expressed in an Escherichia coli reconstitution system. In addition, yeast one hybrid assays indicated that ZmmICE1 has transactivation activities. Moreover, ectopic expression of ZmmICE1 in the Arabidopsis ice1-2 mutant increased freezing tolerance. The ZmmICE1 overexpressed plants showed lower electrolyte leakage (EL), reduced contents of malondialdehyde (MDA). The expression of downstream cold related genes of Arabidopsis C-repeat-binding factors (AtCBF1, AtCBF2 and AtCBF3), cold-responsive genes (AtCOR15A and AtCOR47), kinesin-1 member gene (AtKIN1) and responsive to desiccation gene (AtRD29A) was significantly induced when compared with wild type under low temperature treatment. Taken together, these results indicated that ZmmICE1 is the homolog of Arabidopsis inducer of CBF expression genes (AtICE1/2) and plays an important role in the regulation of freezing stress response.

An ABA down-regulated bHLH transcription repressor gene, bHLH129 regulates root elongation and ABA response when overexpressed in Arabidopsis

Plant hormone abscisic acid (ABA) plays a crucial role in modulating plant responses to environmental stresses. Basic helix-loop-helix (bHLH) transcription factors are one of the largest transcription factor families that regulate multiple aspects of plant growth and development, as well as of plant metabolism in Arabidopsis. Several bHLH transcription factors have been shown to be involved in the regulation of ABA signaling. We report here the characterization of bHLH129, a bHLH transcription factor in Arabidopsis. We found that the expression level of bHLH129 was reduced in response to exogenously applied ABA, and elevated in the ABA biosynthesis mutant aba1-5. Florescence observation of transgenic plants expressing bHLH129-GFP showed that bHLH129 was localized in the nucleus, and transient expression of bHLH129 in protoplasts inhibited reporter gene expression. When expressed in Arabidopsis under the control of the 35S promoter, bHLH129 promoted root elongation, and the transgenic plants were less sensitivity to ABA in root elongation assays. Quantitative RT-PCR results showed that ABA response of several genes involved in ABA signaling, including ABI1, SnRK2.2, SnRK2.3 and SnRK2.6 were altered in the transgenic plants overexpressing bHLH129. Taken together, our study suggests that bHLH129 is a transcription repressor that negatively regulates ABA response in Arabidopsis.

The unified ICE-CBF pathway provides a transcriptional feedback control of freezing tolerance during cold acclimation in Arabidopsis

During cold acclimation, C-repeat binding factors (CBFs) activate downstream targets, such as cold-regulated genes, leading to the acquisition of freezing tolerance in plants. Inducer of CBF expression 1 (ICE1) plays a key role by activating CBF3 expression in shaping the cold-induced transcriptome. While the ICE1-CBF3 regulon constitutes a major cold acclimation pathway, gene regulatory networks governing the CBF signaling are poorly understood. Here, we demonstrated that ICE1 and its paralog ICE2 induce CBF1, CBF2, and CBF3 by binding to the gene promoters. ICE2, like ICE1, was ubiquitinated by the high expression of osmotically responsive gene 1 (HOS1) E3 ubiquitin ligase. Whereas ICE2-defective ice2-2 mutant did not exhibit any discernible freezing-sensitive phenotypes, ice1-2 ice2-2/+ plant, which is defective in ICE1 and has a heterozygotic ice2 mutation, exhibited significantly reduced freezing tolerance. Accordingly, all three CBF genes were markedly down-regulated in the ice1-2 ice2-2/+ plant, indicating that ICE1 and ICE2 are functionally redundant with different implementations in inducing CBF genes. Together with the negative regulation of CBF3 by CBF2, we propose that the unified ICE-CBF pathway provides a transcriptional feedback of freezing tolerance to sustain plant development and survival during cold acclimation.

Exploring the pleiotropy of hos1

Understanding of the roles that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 (HOS1) plays in the plant's ability to sense and respond to environmental signals has grown dramatically. Mechanisms through which HOS1 affects plant development have been uncovered, and the broader consequences of hos1 on the plant's ability to perceive and respond to its environment have been investigated. As such, it has been possible to place HOS1 as a key integrator of temperature information in response to both acute signals and cues that indicate time of year into developmental processes that are essential for plant survival. This review summarizes knowledge of HOS1's form and function, and contextualizes this information so that it is relevant for better understanding the processes of cold signalling, flowering time, and nuclear pore complex function more broadly.