1
|
Tong C, Jia Y, Hu H, Zeng Z, Chapman B, Li C. Pangenome and pantranscriptome as the new reference for gene-family characterization: A case study of basic helix-loop-helix (bHLH) genes in barley. PLANT COMMUNICATIONS 2025; 6:101190. [PMID: 39521956 DOI: 10.1016/j.xplc.2024.101190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/21/2024] [Accepted: 11/08/2024] [Indexed: 11/16/2024]
Abstract
Genome-wide identification and comparative gene-family analyses have commonly been performed to investigate species-specific evolution linked to various traits and molecular pathways. However, most previous studies have been limited to gene screening in a single reference genome, failing to account for the gene presence/absence variations (gPAVs) in a species. Here, we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups (OGGs). Using the basic helix-loop-helix (bHLH) transcription factor family in barley as an example, we identified 161-176 bHLHs in 20 barley genomes, which can be classified into 201 OGGs. These 201 OGGs were further classified into 140 core, 12 softcore, 29 shell, and 20 line-specific/cloud bHLHs, revealing the complete profile of bHLH genes in barley. Using a genome-scanning approach, we overcame the genome annotation bias and identified an average of 1.5 un-annotated core bHLHs per barley genome. We found that whole-genome/segmental duplicates are predominant mechanisms contributing to the expansion of most core/softcore bHLHs, whereas dispensable bHLHs are more likely to result from small-scale duplication events. Interestingly, we noticed that the dispensable bHLHs tend to be enriched in the specific subfamilies SF13, SF27, and SF28, implying the potentially biased expansion of specific bHLHs in barley. We found that 50% of the bHLHs contain at least 1 intact transposon element (TE) within the 2-kb upstream-to-downstream region. bHLHs with copy-number variations (CNVs) have 1.48 TEs on average, significantly more than core bHLHs without CNVs (1.36), supporting a potential role of TEs in bHLH expansion. Analyses of selection pressure showed that dispensable bHLHs have experienced clear relaxation of selection compared with core bHLHs, consistent with their conservation patterns. We also integrated the pangenome data with recently available barley pantranscriptome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH subfamilies. We conclude that pangenome-based gene-family analyses can better describe the previously untapped, genuine evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley. We expect that this study will inspire similar analyses in many other gene families and species.
Collapse
Affiliation(s)
- Cen Tong
- Western Crop Genetic Alliance, Murdoch University, Murdoch, WA 6150, Australia; State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Yong Jia
- Western Crop Genetic Alliance, Murdoch University, Murdoch, WA 6150, Australia; State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
| | - Haifei Hu
- Western Crop Genetic Alliance, Murdoch University, Murdoch, WA 6150, Australia; State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Brett Chapman
- Western Crop Genetic Alliance, Murdoch University, Murdoch, WA 6150, Australia; State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Chengdao Li
- Western Crop Genetic Alliance, Murdoch University, Murdoch, WA 6150, Australia; State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia; Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA 6155, Australia; College of Agriculture, Shandong Agricultural University, TaiAn, China.
| |
Collapse
|
2
|
Zhi QQ, Chen Y, Hu H, Huang WQ, Bao GG, Wan XR. Physiological and transcriptome analyses reveal tissue-specific responses of Leucaena plants to drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108926. [PMID: 38996715 DOI: 10.1016/j.plaphy.2024.108926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024]
Abstract
Leucaena leucocephala (Leucaena) is a leguminous tree widely cultivated in tropical and subtropical regions due to its strong environmental suitability for abiotic stresses, especially drought. However, the molecular mechanisms and key pathways involved in Leucaena's drought response require further elucidation. Here, we comparatively analyzed the physiological and early transcriptional responses of Leucaena leaves and roots under drought stress simulated by polyethylene glycol (PEG) treatments. Drought stress induced physiological changes in Leucaena seedlings, including decreases in relative water content (RWC) and increases in relative electrolyte leakage (REL), malondialdehyde (MDA), proline contents as well as antioxidant enzyme activities. In response to drought stress, 6461 and 8295 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. In both tissues, the signaling transduction pathway of plant hormones was notably the most enriched. Specifically, abscisic acid (ABA) biosynthesis and signaling related genes (NCED, PP2C, SnRK2 and ABF) were strongly upregulated particularly in leaves. The circadian rhythm, DNA replication, alpha-linolenic acid metabolism, and secondary metabolites biosynthesis related pathways were repressed in leaves, while the glycolysis/gluconeogenesis and alpha-linolenic acid metabolism and amino acid biosynthesis processes were promoted in roots. Furthermore, heterologous overexpression of Leucaena drought-inducible genes (PYL5, PP2CA, bHLH130, HSP70 and AUX22D) individually in yeast increased the tolerance to drought and heat stresses. Overall, these results deepen our understanding of the tissue-specific mechanisms of Leucaena in response to drought and provide target genes for future drought-tolerance breeding engineering in crops.
Collapse
Affiliation(s)
- Qing-Qing Zhi
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ying Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Han Hu
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wen-Qi Huang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ge-Gen Bao
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
| | - Xiao-Rong Wan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
| |
Collapse
|
3
|
Zhang JF, Chu HH, Liao D, Ma GJ, Tong YK, Liu YY, Li J, Ren F. Comprehensive Evolution and Expression anaLysis of PHOSPHATE 1 Gene Family in Allotetraploid Brassica napus and Its Diploid Ancestors. Biochem Genet 2023; 61:2330-2347. [PMID: 37036640 DOI: 10.1007/s10528-023-10375-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/29/2023] [Indexed: 04/11/2023]
Abstract
The members of PHOSPHATE 1 (PHO1) family play important roles in plant phosphate (Pi) transport and adaptation to Pi deficiency. The functions of PHO1 family proteins have been reported in several plant species, with the exception of Brassica species. Here, we identified 23, 23, and 44 putative PHO1 family genes in Brassica rapa, Brassica oleracea, and Brassica napus by whole genome analysis, respectively. The phylogenetic analysis divided PHO1 family proteins into eight groups, which represented the orthologous relationships among PHO1 members. The gene structure and the conserved motif analysis indicated that the most PHO1 family genes had similar gene structures and the PHO1 proteins shared mutual conserved motifs. The chromosome distribution analysis showed that the majority of BnPHO1 family genes distributed analogously at chromosomes with BrPHO1 and BoPHO1 family genes. The data showed that PHO1 family genes were highly conserved during evolution from diploid to tetraploid. Furthermore, the expression analysis showed that PHO1 family genes had different expression patterns in plant tissues, suggesting the diversity of gene functions in Brassica species. Meanwhile, the expression analysis also revealed that some PHO1 family genes were significantly responsive to Pi deficiency, suggesting that PHO1 family genes play critical roles in Pi uptake and homeostasis under low Pi stress. Altogether, the characteristics of PHO1 family genes provide a reliable groundwork for further dissecting their functions in Brassica species.
Collapse
Affiliation(s)
- Jian-Feng Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Hui-Hui Chu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Dan Liao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Guang-Jing Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yi-Kai Tong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ying-Ying Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| |
Collapse
|
4
|
Wang R, Li Y, Gao M, Han M, Liu H. Genome-wide identification and characterization of the bHLH gene family and analysis of their potential relevance to chlorophyll metabolism in Raphanus sativus L. BMC Genomics 2022; 23:548. [PMID: 35915410 DOI: 10.1186/s12864-022-08782-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Green-fleshed radish (Raphanus sativus L.) is an economically important root vegetable of the Brassicaceae family, and chlorophyll accumulates in its root tissues. It was reported that the basic helix-loop-helix (bHLH) transcription factors play vital roles in the process of chlorophyll metabolism. Nevertheless, a comprehensive study on the bHLH gene family has not been performed in Raphanus sativus L. RESULTS In this study, a total of 213 Raphanus sativus L. bHLH (RsbHLH) genes were screened in the radish genome, which were grouped into 22 subfamilies. 204 RsbHLH genes were unevenly distributed on nine chromosomes, and nine RsbHLH genes were located on the scaffolds. Gene structure analysis showed that 25 RsbHLH genes were intron-less. Collineation analysis revealed the syntenic orthologous bHLH gene pairs between radish and Arabidopsis thaliana/Brassica rapa/Brassica oleracea. 162 RsbHLH genes were duplicated and retained from the whole genome duplication event, indicating that the whole genome duplication contributed to the expansion of the RsbHLH gene family. RNA-seq results revealed that RsbHLH genes had a variety of expression patterns at five development stages of green-fleshed radish and white-fleshed radish. In addition, the weighted gene co-expression network analysis confirmed four RsbHLH genes closely related to chlorophyll content. CONCLUSIONS A total of 213 RsbHLH genes were identified, and we systematically analyzed their gene structure, evolutionary and collineation relationships, conserved motifs, gene duplication, cis-regulatory elements and expression patterns. Finally, four bHLH genes closely involved in chlorophyll content were identified, which may be associated with the photosynthesis of the green-fleshed radish. The current study would provide valuable information for further functional exploration of RsbHLH genes, and facilitate clarifying the molecular mechanism underlying photosynthesis process in green-fleshed radish.
Collapse
Affiliation(s)
- Ruihua Wang
- Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China
| | - Yuanyuan Li
- Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China.
| | - Minggang Gao
- Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China
| | - Min Han
- Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China
| | - Huilian Liu
- Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China
| |
Collapse
|
5
|
Chen N, Zhang H, Zang E, Liu ZX, Lan YF, Hao WL, He S, Fan X, Sun GL, Wang YL. Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains. BMC Genomics 2022; 23:466. [PMID: 35751010 PMCID: PMC9233376 DOI: 10.1186/s12864-022-08703-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/13/2022] [Indexed: 11/29/2022] Open
Abstract
Opisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus showed higher level of expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus revealed that 1203 genes were related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Differential expressions of PSG occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Several PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights into adaptation of the two species to different environments that characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species in Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.
Collapse
Affiliation(s)
- Ning Chen
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Hao Zhang
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - En Zang
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Zhi-Xia Liu
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Ya-Fei Lan
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Wei-Li Hao
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Shan He
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gen-Lou Sun
- Department of Biology, Saint Mary's University, Halifax, B3H3C3, Canada.
| | - Yi-Ling Wang
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China.
| |
Collapse
|
6
|
Chen H, Wang Y, Liu J, Zhao T, Yang C, Ding Q, Zhang Y, Mu J, Wang D. Identification of WRKY transcription factors responding to abiotic stresses in Brassica napus L. PLANTA 2021; 255:3. [PMID: 34837557 DOI: 10.1007/s00425-021-03733-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
A total of 278 BnWRKYs were identified and analyzed. Ectopic expression of BnWRKY149 and BnWRKY217 suggests that they function in the ABA signaling pathway. WRKY transcription factors play an important role in plant development, however, their function in Brassica napus L. abiotic stress response is still unclear. In this study, a total of 278 BnWRKY transcription factors were identified from the B. napus genome data, and they were subsequently distributed in three main groups. The protein motifs and classification of BnWRKY transcription factors were analyzed, and the locations of their corresponding encoding genes were mapped on the chromosomes of B. napus. Transcriptome analysis of rapeseed seedlings exposed to drought, salt, heat, cold and abscisic acid treatment revealed that 99 BnWRKYs responded to at least one of these stresses. The expression profiles of 12 BnWRKYs were examined with qPCR and the result coincided with RNA-seq analysis. Two genes of interest, BnWRKY149 and BnWRKY217 (homologs of AtWRKY40), were overexpressed in Arabidopsis, and the corresponding proteins were located to the nucleus. Transgene plants of BnWRKY149 and BnWRKY217 were less sensitive to ABA than Arabidopsis Col-0 plants, suggesting they might play important roles in the responses of rapeseed to abiotic stress.
Collapse
Affiliation(s)
- Hao Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Yongfeng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Jiong Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Tian Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Cuiling Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Qunying Ding
- School of Biological and Environmental Engineering, Xi'an University, Xi'an, 710065, Shaanxi, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shanxi Province, Yangling, 712100, Shaanxi, China
| | - Jianxin Mu
- Hybrid Rapeseed Research Center of Shanxi Province, Yangling, 712100, Shaanxi, China
| | - DaoJie Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China.
| |
Collapse
|
7
|
Nguyen NH, Sng BJR, Yeo HC, Jang IC. Comparative phenotypic and transcriptomic analyses unravel conserved and distinct mechanisms underlying shade avoidance syndrome in Brassicaceae vegetables. BMC Genomics 2021; 22:760. [PMID: 34696740 PMCID: PMC8546956 DOI: 10.1186/s12864-021-08076-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background Plants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). Shade negatively influences plant growth, leading to a reduction in agricultural productivity. Understanding of SAS is crucial for sustainable agricultural practices, especially for high-density indoor farming. Brassicaceae vegetables are widely consumed around the world and are commonly cultivated in indoor farms. However, our understanding of SAS in Brassicaceae vegetables and their genome-wide transcriptional regulatory networks are still largely unexplored. Results Shade induced common signs of SAS, including hypocotyl elongation and reduced carotenoids/anthocyanins biosynthesis, in two different Brassicaceae species: Brassica rapa (Choy Sum and Pak Choy) and Brassica oleracea (Kai Lan). Phenotype-assisted transcriptome analysis identified a set of genes induced by shade in these species, many of which were related to auxin biosynthesis and signaling [e.g. YUCCA8 (YUC8), YUC9, and INDOLE-3-ACETIC ACID INDUCIBLE (IAAs)] and other phytohormones signaling pathways including brassinosteroids and ethylene. The genes functioning in plant defense (e.g. MYB29 and JASMONATE-ZIM-DOMAIN PROTEIN 9) as well as in biosynthesis of anthocyanins and glucosinolates were repressed upon shade. Besides, each species also exhibited distinct SAS phenotypes. Shade strongly reduced primary roots and elongated petioles of B. oleracea, Kai Lan. However, these SAS phenotypes were not clearly recognized in B. rapa, Choy Sum and Pak Choy. Some auxin signaling genes (e.g. AUXIN RESPONSE FACTOR 19, IAA10, and IAA20) were specifically induced in B. oleracea, while homologs in B. rapa were not up-regulated under shade. Contrastingly, shade-exposed B. rapa vegetables triggered the ethylene signaling pathway earlier than B. oleracea, Kai Lan. Interestingly, shade induced the transcript levels of LONG HYPOCOTYL IN FAR-RED 1 (HFR1) homolog in only Pak Choy as B. rapa. As HFR1 is a key negative regulator of SAS in Arabidopsis, our finding suggests that Pak Choy HFR1 homolog may also function in conferring higher shade tolerance in this variety. Conclusions Our study shows that two Brassicaceae species not only share a conserved SAS mechanism but also exhibit distinct responses to shade, which will provide comprehensive information to develop new shade-tolerant cultivars that are suitable for high-density indoor farms. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08076-1.
Collapse
Affiliation(s)
- Nguyen Hoai Nguyen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Benny Jian Rong Sng
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Hock Chuan Yeo
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
| |
Collapse
|
8
|
Qian Y, Zhang T, Yu Y, Gou L, Yang J, Xu J, Pi E. Regulatory Mechanisms of bHLH Transcription Factors in Plant Adaptive Responses to Various Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:677611. [PMID: 34220896 PMCID: PMC8250158 DOI: 10.3389/fpls.2021.677611] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/19/2021] [Indexed: 05/05/2023]
Abstract
Basic helix-loop-helix proteins (bHLHs) comprise one of the largest families of transcription factors in plants. They have been shown to be involved in responses to various abiotic stresses, such as drought, salinity, chilling, heavy metal toxicity, iron deficiency, and osmotic damages. By specifically binding to cis-elements in the promoter region of stress related genes, bHLHs can regulate their transcriptional expression, thereby regulating the plant's adaptive responses. This review focuses on the structural characteristics of bHLHs, the regulatory mechanism of how bHLHs are involved transcriptional activation, and the mechanism of how bHLHs regulate the transcription of target genes under various stresses. Finally, as increasing research demonstrates that flavonoids are usually induced under fluctuating environments, the latest research progress and future research prospects are described on the mechanisms of how flavonoid biosynthesis is regulated by bHLHs in the regulation of the plant's responses to abiotic stresses.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| |
Collapse
|
9
|
Genome-Wide In Silico Identification and Comparative Analysis of Dof Gene Family in Brassica napus. PLANTS 2021; 10:plants10040709. [PMID: 33916912 PMCID: PMC8067633 DOI: 10.3390/plants10040709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023]
Abstract
DNA binding with one finger (DOF) proteins are plant-specific transcription factors that play roles in diverse plant functions. However, little is known about the DOF protein repertoire of the allopolyploid crop, Brassica napus. This in silico study identified 117 Brassica napus Dof genes (BnaDofs) and classified them into nine groups (A, B1, B2, C1, C2.1, C2.2, C3, D1, and D2), based on phylogenetic analysis. Most members belonging to a particular group displayed conserved gene structural organisation and protein motif distribution. Evolutionary analysis exemplified that the divergence of the Brassica genus from Arabidopsis, the whole-genome triplication event, and the hybridisation of Brassica oleracea and Brassica rapa to form B. napus, followed by gene loss and rearrangements, led to the expansion and divergence of the Dof transcription factor (TF) gene family in B. napus. So far, this is the largest number of Dof genes reported in a single eudicot species. Functional annotation of BnaDof proteins, cis-element analysis of their promoters, and transcriptomic analysis suggested potential roles in organ development, the transition from the vegetative to the reproductive stage, light responsiveness, phytohormone responsiveness, as well as potential regulatory roles in abiotic stress. Overall, our results provide a comprehensive understanding of the molecular structure, evolution, and possible functional roles of Dof genes in plant development and abiotic stress response.
Collapse
|
10
|
Functional Characterization of a Sugar Beet BvbHLH93 Transcription Factor in Salt Stress Tolerance. Int J Mol Sci 2021; 22:ijms22073669. [PMID: 33915978 PMCID: PMC8037259 DOI: 10.3390/ijms22073669] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 12/25/2022] Open
Abstract
The basic/helix–loop–helix (bHLH) transcription factor (TF) plays an important role for plant growth, development, and stress responses. Previously, proteomics of NaCl treated sugar beet leaves revealed that a bHLH TF, BvbHLH93, was significantly increased under salt stress. The BvbHLH93 protein localized in the nucleus and exhibited activation activity. The expression of BvbHLH93 was significantly up-regulated in roots and leaves by salt stress, and the highest expression level in roots and leaves was 24 and 48 h after salt stress, respectively. Furthermore, constitutive expression of BvbHLH93 conferred enhanced salt tolerance in Arabidopsis, as indicated by longer roots and higher content of chlorophyll than wild type. Additionally, the ectopic expression lines accumulated less Na+ and MDA, but more K+ than the WT. Overexpression of the BvBHLH93 enhanced the activities of antioxidant enzymes by positively regulating the expression of antioxidant genes SOD and POD. Compared to WT, the overexpression plants also had low expression levels of RbohD and RbohF, which are involved in reactive oxygen species (ROS) production. These results suggest that BvbHLH93 plays a key role in enhancing salt stress tolerance by enhancing antioxidant enzymes and decreasing ROS generation.
Collapse
|