Dataset Information

Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum.

ABSTRACT: BACKGROUND:Plants are easily affected by temperature variations, and high temperature (heat stress) and low temperature (cold stress) will lead to poor plant development and reduce crop yields. Therefore, it is very important to identify resistance genes for improving the ability of plants to resist heat stress or cold stress by using modern biotechnology. Members of the C-repeat binding factor/Dehydration responsive element-binding 1 (CBF/DREB1) protein family are related to the stress resistance of many plant species. These proteins affect the growth and development of plants and play vital roles during environmental stress (cold, heat, drought, salt, etc.). In this study, we identified CBF/DREB1 genes from 43 plant species (including algae, moss, ferns, gymnosperms, angiosperms) by using bioinformatic methods to clarify the characteristics of the CBF/DREB1 protein family members and their functions in potato under heat and cold stresses. RESULTS:In this study, we identified 292 CBF/DREB1 proteins from 43 plant species. However, no CBF/DREB1 protein was found in algae, moss, ferns, or gymnosperms; members of this protein family exist only in angiosperms. Phylogenetic analysis of all the CBF/DREB1 proteins revealed five independent groups. Among them, the genes of group I do not exist in eudicots and are found only in monocots, indicating that these genes have a special effect on monocots. The analysis of motifs, gene duplication events, and the expression data from the PGSC website revealed the gene structures, evolutionary relationships, and expression patterns of the CBF/DREB1 proteins. In addition, analysis of the transcript levels of the 8 CBF/DREB1 genes in potato (Solanum tuberosum) under low-temperature and high-temperature stresses showed that these genes were related to temperature stresses. In particular, the expression levels of StCBF3 and StCBF4 in the leaves, stems, and roots significantly increased under high-temperature conditions, which suggested that StCBF3 and StCBF4 may be closely related to heat tolerance in potato. CONCLUSION:Overall, members of the CBF/DREB1 protein family exist only in angiosperms and plays an important role in the growth and development of plants. In addition, the CBF/DREB1 protein family is related to the heat and cold resistance of potato. Our research revealed the evolution of the CBF/DREB1 family, and is useful for studying the precise functions of the CBF/DREB1 proteins when the plants are developing and are under temperature stress.

SUBMITTER: Li W

PROVIDER: S-EPMC7607821 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum.

Li Wan W Chen Yue Y Ye Minghui M Lu Haibin H Wang Dongdong D Chen Qin Q

BMC evolutionary biology 20201103 1

<h4>Background</h4>Plants are easily affected by temperature variations, and high temperature (heat stress) and low temperature (cold stress) will lead to poor plant development and reduce crop yields. Therefore, it is very important to identify resistance genes for improving the ability of plants to resist heat stress or cold stress by using modern biotechnology. Members of the C-repeat binding factor/Dehydration responsive element-binding 1 (CBF/DREB1) protein family are related to the stress ...[more]

PMID: 33143637

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Project description:Dehydration Responsive Element Binding (DREB) regulates the expression of numerous stress-responsive genes, and hence plays a pivotal role in abiotic stress responses and tolerance in plants. The study aimed to develop a complete overview of the cis-acting regulatory elements (CAREs) present in S. tuberosum DREB gene promoters. A total of one hundred and four (104) cis-regulatory elements (CREs) were identified from 2.5kbp upstream of the start codon (ATG). The in-silico promoter analysis revealed variable sets of cis-elements and functional diversity with the predominance of light-responsive (30%), development-related (20%), abiotic stress-responsive (14%), and hormone-responsive (12%) elements in StDREBs. Among them, two light-responsive elements (Box-4 and G-box) were predicted in 64 and 61 StDREB genes, respectively. Two development-related motifs (AAGAA-motif and as-1) were abundant in StDREB gene promoters. Most of the DREB genes contained one or more Myeloblastosis (MYB) and Myelocytometosis (MYC) elements associated with abiotic stress responses. Hormone-responsive element i.e. ABRE was found in 59 out of 66 StDREB genes, which implied their role in dehydration and salinity stress. Moreover, six proteins were chosen corresponding to A1-A6 StDREB subgroups for secondary structure analysis and three-dimensional protein modeling followed by model validation through PROCHECK server by Ramachandran Plot. The predicted models demonstrated >90% of the residues in the favorable region, which further ensured their reliability. The present study also anticipated pocket binding sites and disordered regions (DRs) to gain insights into the structural flexibility and functional annotation of StDREB proteins. The protein association network determined the interaction of six selected StDREB proteins with potato proteins encoded by other gene families such as MYB and NAC, suggesting their similar functional roles in biological and molecular pathways. Overall, our results provide fundamental information for future functional analysis to understand the precise molecular mechanisms of the DREB gene family in S. tuberosum.

Project description:Cassava (Manihot esculenta) is a major staple food, animal feed and energy crop in the tropics and subtropics. It is one of the most drought-tolerant crops, however, the mechanisms of cassava drought tolerance remain unclear. Abscisic acid (ABA)-responsive element (ABRE)-binding factors (ABFs) are transcription factors that regulate expression of target genes involved in plant tolerance to drought, high salinity, and osmotic stress by binding ABRE cis-elements in the promoter regions of these genes. However, there is little information about ABF genes in cassava. A comprehensive analysis of Manihot esculenta ABFs (MeABFs) described the phylogeny, genome location, cis-acting elements, expression profiles, and regulatory relationship between these factors and Manihot esculenta betaine aldehyde dehydrogenase genes (MeBADHs). Here we conducted genome-wide searches and subsequent molecular cloning to identify seven MeABFs that are distributed unevenly across six chromosomes in cassava. These MeABFs can be clustered into three groups according to their phylogenetic relationships to their Arabidopsis (Arabidopsis thaliana) counterparts. Analysis of the 5'-upstream region of MeABFs revealed putative cis-acting elements related to hormone signaling, stress, light, and circadian clock. MeABF expression profiles displayed clear differences among leaf, stem, root, and tuberous root tissues under non-stress and drought, osmotic, or salt stress conditions. Drought stress in cassava leaves and roots, osmotic stress in tuberous roots, and salt stress in stems induced expression of the highest number of MeABFs showing significantly elevated expression. The glycine betaine (GB) content of cassava leaves also was elevated after drought, osmotic, or salt stress treatments. BADH1 is involved in GB synthesis. We show that MeBADH1 promoter sequences contained ABREs and that MeBADH1 expression correlated with MeABF expression profiles in cassava leaves after the three stress treatments. Taken together, these results suggest that in response to various dehydration stresses, MeABFs in cassava may activate transcriptional expression of MeBADH1 by binding the MeBADH1 promoter that in turn promotes GB biosynthesis and accumulation via an increase in MeBADH1 gene expression levels and MeBADH1 enzymatic activity. These responses protect cells against dehydration stresses by preserving an osmotic balance that enhances cassava tolerance to dehydration stresses.

Dataset Information

Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum.

Publications

Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum.

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