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Zhai X, Wang X, Yang X, Huang Q, Wu D, Wang Y, Kang H, Sha L, Fan X, Zhou Y, Zhang H. Genome-wide identification of bHLH transcription factors and expression analysis under drought stress in Pseudoroegneria libanotica at germination. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:467-481. [PMID: 38633269 PMCID: PMC11018577 DOI: 10.1007/s12298-024-01433-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/24/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
The basic helix-loop-helix (bHLH) transcription factor family is the second largest in plants. bHLH transcription factor is not only universally involved in plant growth and metabolism, including photomorphogenesis, light signal transduction, and secondary metabolism, but also plays an important role in plant response to stress. However, the function of bHLH TFs in Pseudoroegneria species has not been studied yet. Pseudoroegneria (Nevski) Á. Löve is a perennial genus of the Triticeae. Pseudoroegneria species are mostly distributed in arid/semi-arid areas and they show good drought tolerance. In this study, we identified 152 PlbHLH TFs in Pseudoroegneria libanotica, which could be classified into 15 groups. Collinearity analysis indicates that 122 PlbHLH genes share homology with wbHLH genes in wheat, and it has lower homology with AtbHLH genes in Arabidopsis. Based on transcriptome profiling under an experiment with three PEG concentrations (0%, 10%, and 20%), 10 up-regulated genes and 11 down-regulated PlbHLH genes were screened. Among them, PlbHLH6, PlbHLH55 and PlbHLH64 as candidate genes may be the key genes related to drought tolerance response at germination, and they have been demonstrated to respond to drought, salt, oxidative, heat, and heavy metal stress in yeast. This study lays the foundation for an in-depth study of the biological roles of PlbHLHs in Pse. libanotica, and discovered new drought-tolerance candidate genes to enhance the genetic background of Triticeae crops. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01433-w.
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Affiliation(s)
- Xingguan Zhai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xia Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xunzhe Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Qingxiang Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
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Liu Y, Lin L, Liu Y, Mo Q, Zhang D, Li W, Xiong X, Yu X, Li Y. Genome-Wide Analysis of the bHLH Gene Family in Loropetalum chinense var. rubrum: Identification, Classification, Evolution, and Diversity of Expression Patterns under Cultivation. PLANTS (BASEL, SWITZERLAND) 2023; 12:3392. [PMID: 37836132 PMCID: PMC10574408 DOI: 10.3390/plants12193392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 10/15/2023]
Abstract
The basic helix-loop-helix (bHLH) transcription factor family is the second-largest transcription factor family in plants. Members of this family are involved in the processes of growth and development, secondary metabolic biosynthesis, signal transduction, and plant resistance. Loropetalum chinense var. rubrum is a critical woody plant with higher ornamental and economic values, which has been used as ornamental architecture and traditional Chinese herbal medicine plants. However, the bHLH transcription factors in Loropetalum chinense var. rubrum (L. chinense var. rubrum) have not yet been systematically demonstrated, and their role in the biosynthesis of anthocyanin is still unclear. Here, we identified 165 potential LcbHLHs genes by using two methods, and they were unequally distributed on chromosomes 1 to 12 of the genome of L. chinense var. rubrum. Based on an evolutionary comparison with proteins from Arabidopsis and Oryza sativa, these bHLH proteins were categorized into 21 subfamilies. Most LcbHLHs in a particular subfamily had similar gene structures and conserved motifs. The Gene Ontology annotation and Cis-elements predicted that LcbHLHs had many molecular functions and were involved in processes of plant growth, including the biosynthesis of flavonoids and anthocyanins. Transcriptomic analysis revealed different expression patterns among different tissues and cultivars of L. chinense var. rubrum. Many LcbHLHs were expressed in the leaves, and only a few genes were highly expressed in the flowers. Six LcbHLHs candidate genes were identified by bioinformatics analysis and expression analysis. Further Real-time quantitative PCR analysis and protein interaction network analysis showed that LcbHLH156, which is one of the candidate proteins belonging to the IIIf subfamily, could interact with proteins related to anthocyanin synthesis. Therefore, LcbHLH156 was transiently expressed in L. chinense var. rubrum to verify its function in regulating anthocyanin synthesis. Compared with the control group, red pigment accumulation appeared at the wound after injection, and the total anthocyanin content increased at the wound of leaves. These results lay a foundation for the research of the regulation mechanism of leaf colors in L. chinense var. rubrum and also provide a basis for the function of the LcbHLH family.
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Affiliation(s)
- Yang Liu
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
| | - Ling Lin
- School of Economics, Hunan Agricultural University, Changsha 410128, China;
| | - Yang Liu
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
| | - Qiong Mo
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
| | - Damao Zhang
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
| | - Weidong Li
- Hunan Key Laboratory of Germplasm Innovation and Comprehensive Utilization of Garden Flowers, Hunan Horticulture Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China;
| | - Xingyao Xiong
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Kunpeng Institute of Modern Agriculture, Foshan 528225, China
| | - Xiaoying Yu
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
| | - Yanlin Li
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Kunpeng Institute of Modern Agriculture, Foshan 528225, China
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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Liu Q, Wen J, Wang S, Chen J, Sun Y, Liu Q, Li X, Dong S. Genome-wide identification, expression analysis, and potential roles under low-temperature stress of bHLH gene family in Prunus sibirica. FRONTIERS IN PLANT SCIENCE 2023; 14:1267107. [PMID: 37799546 PMCID: PMC10548393 DOI: 10.3389/fpls.2023.1267107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
The basic helix-loop-helix (bHLH) family is one of the most well-known transcription factor families in plants, and it regulates growth, development, and abiotic stress responses. However, systematic analyses of the bHLH gene family in Prunus sibirica have not been reported to date. In this study, 104 PsbHLHs were identified and classified into 23 subfamilies that were unevenly distributed on eight chromosomes. Nineteen pairs of segmental replication genes and ten pairs of tandem replication genes were identified, and all duplicated gene pairs were under purifying selection. PsbHLHs of the same subfamily usually share similar motif compositions and exon-intron structures. PsbHLHs contain multiple stress-responsive elements. PsbHLHs exhibit functional diversity by interacting and coordinating with other members. Twenty PsbHLHs showed varying degrees of expression. Eleven genes up-regulated and nine genes down-regulated in -4°C. The majority of PsbHLHs were highly expressed in the roots and pistils. Transient transfection experiments demonstrated that transgenic plants with overexpressed PsbHLH42 have better cold tolerance. In conclusion, the results of this study have significant implications for future research on the involvement of bHLH genes in the development and stress responses of Prunus sibirica.
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Affiliation(s)
- Quangang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Jiaxing Wen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Shipeng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Jianhua Chen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Yongqiang Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Qingbai Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Xi Li
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Shengjun Dong
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
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Liu W, Tian X, Feng Y, Hu J, Wang B, Chen S, Liu D, Liu Y. Genome-wide analysis of bHLH gene family in Coptis chinensis provides insights into the regulatory role in benzylisoquinoline alkaloid biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107846. [PMID: 37390693 DOI: 10.1016/j.plaphy.2023.107846] [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: 02/26/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 07/02/2023]
Abstract
Coptis chinensis Franch is a perennial species with high medical value. The rhizome of C. chinensis is a traditional Chinese medicine widely used for more than 2000 years in China. Its principal active ingredients are benzylisoquinoline alkaloids (BIAs). The basic helix-loop-helix (bHLH) transcription factors play an important regulatory role in the biosynthesis of plant secondary metabolites. However, the bHLH genes in C. chinensis have not been described, and little is known about their roles in alkaloid biosynthesis. In this study, a total of 143 CcbHLH genes (CcbHLHs) were identified and unevenly distributed on nine chromosomes. Phylogenetic analysis divided the 143 CcbHLH proteins into 26 subfamilies by comparison with Arabidopsis thaliana bHLH proteins. The majority CcbHLHs in each subgroup had similar gene structures and conserved motifs. Furthermore, the physicochemical properties, conserved motif, intron/exon composition, and cis-acting elements of CcbHLHs were analyzed. Transcriptome analysis revealed that 30 CcbHLHs were significantly expressed in the rhizomes of C. chinensis. Co-expression analysis revealed that 11 CcbHLHs were highly positively correlated with contents of various alkaloids of C. chinensis. Moreover, yeast one-hybrid experiments verified that CcbHLH001 and CcbHLH0002 could interact with the promoters of berberine biosynthesis pathway genes CcBBE and CcCAS, suggesting their regulatory roles in BIA biosynthesis. This study provides comprehensive insights into the bHLH gene family in C. chinensis and will support in-depth functional characterization of CcbHLHs involved in the regulation of protoberberine-type alkaloid biosynthesis.
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Affiliation(s)
- Wei Liu
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xufang Tian
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Ying Feng
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Juan Hu
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Bo Wang
- Hubei Institute for Drug Control, Wuhan, China
| | - Shilin Chen
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China; Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Di Liu
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China.
| | - Yifei Liu
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China.
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Quan X, Meng C, Zhang N, Liang X, Li J, Li H, He W. Genome-Wide Analysis of Barley bHLH Transcription Factors and the Functional Characterization of HvbHLH56 in Low Nitrogen Tolerance in Arabidopsis. Int J Mol Sci 2023; 24:ijms24119740. [PMID: 37298691 DOI: 10.3390/ijms24119740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Improvement of low nitrogen (LN) tolerance or nitrogen use efficiency (NUE) in crops is imperative for environment-friendly agriculture development. The basic helix-loop-helix (bHLH) transcription factors are involved in multiple abiotic stresses and are suitable as candidate genes for improving LN tolerance. Few studies were performed on the characterization of the HvbHLH gene family and their function in response to LN stress in barley. In this study, 103 HvbHLH genes were identified through genome-wide analysis. HvbHLH proteins were classified into 20 subfamilies based on phylogenetic analysis in barley, which was supported by conserved motifs and gene structure analysis. The stress-related cis-element analysis in the promoters showed that HvbHLHs are probably involved in multiple stress responses. By phylogenetic analysis of HvbHLHs and bHLHs in other plants, some HvbHLHs were predicted to play roles in response to nutrition deficiency stress. Furthermore, at least 16 HvbHLHs were differentially expressed in two barley genotypes differing in LN tolerance under LN stress. Finally, overexpression of HvbHLH56 enhanced LN stress tolerance in transgenic Arabidopsis, suggesting it is an important regulator in LN stress response. The differentially expressed HvbHLHs identified herein may be valuable for the breeding of barley cultivars with LN tolerance.
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Affiliation(s)
- Xiaoyan Quan
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Chen Meng
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Ning Zhang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Xiaoli Liang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Jialin Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Hongmei Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
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Genome-Wide Identification and Analysis of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Cymbidium ensifolium. Int J Mol Sci 2023; 24:ijms24043825. [PMID: 36835234 PMCID: PMC9963586 DOI: 10.3390/ijms24043825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
The basic helix-loop-helix (bHLH) transcription factors are widely distributed across eukaryotic kingdoms and participate in various physiological processes. To date, the bHLH family has been identified and functionally analyzed in many plants. However, systematic identification of bHLH transcription factors has yet to be reported in orchids. Here, 94 bHLH transcription factors were identified from the Cymbidium ensifolium genome and divided into 18 subfamilies. Most CebHLHs contain numerous cis-acting elements associated with abiotic stress responses and phytohormone responses. A total of 19 pairs of duplicated genes were found in the CebHLHs, of which 13 pairs were segmentally duplicated genes and six pairs were tandemly duplicated genes. Expression pattern analysis based on transcriptome data revealed that 84 CebHLHs were differentially expressed in four different color sepals, especially CebHLH13 and CebHLH75 of the S7 subfamily. The expression profiles of CebHLH13 and CebHLH75 in sepals, which are considered potential genes regulating anthocyanin biosynthesis, were confirmed through the qRT-PCR technique. Furthermore, subcellular localization results showed that CebHLH13 and CebHLH75 were located in the nucleus. This research lays a foundation for further exploration of the mechanism of CebHLHs in flower color formation.
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Zhang Y, Ji X, Xian J, Wang Y, Peng Y. Morphological characterization and transcriptome analysis of leaf angle mutant bhlh112 in maize [ Zea mays L.]. FRONTIERS IN PLANT SCIENCE 2022; 13:995815. [PMID: 36275532 PMCID: PMC9585351 DOI: 10.3389/fpls.2022.995815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Leaf angle is an important agronomic trait in maize [Zea mays L.]. The compact plant phenotype, with a smaller leaf angle, is suited for high-density planting and thus for increasing crop yields. Here, we studied the ethyl methane sulfonate (EMS)-induced mutant bhlh112. Leaf angle and plant height were significantly decreased in bhlh112 compared to the wild-type plants. After treatment of seedlings with exogenous IAA and ABA respectively, under the optimal concentration of exogenous hormones, the variation of leaf angle of the mutant was more obvious than that of the wild-type, which indicated that the mutant was more sensitive to exogenous hormones. Transcriptome analysis showed that the ZmbHLH112 gene was related to the biosynthesis of auxin and brassinosteroids, and involved in the activation of genes related to the auxin and brassinosteroid signal pathways as well as cell elongation. Among the GO enrichment terms, we found many differentially expressed genes (DEGs) enriched in the cell membrane and ribosomal biosynthesis, hormone biosynthesis and signaling pathways, and flavonoid biosynthesis, which could influence cell growth and the level of endogenous hormones affecting leaf angle. Therefore, ZmbHLH112 might regulate leaf angle development through the auxin signaling and the brassinosteroid biosynthesis pathways. 12 genes related to the development of leaf were screened by WGCNA; In GO enrichment and KEGG pathways, the genes were mainly enriched in rRNA binding, ribosome biogenesis, Structural constituent of ribosome; Arabidopsis ribosome RNA methyltransferase CMAL is involved in plant development, likely by modulating auxin derived signaling pathways; The free 60s ribosomes and polysomes in the functional defective mutant rice minute-like1 (rml1) were significantly reduced, resulting in plant phenotypic diminution, narrow leaves, and growth retardation; Hence, ribosomal subunits may play an important role in leaf development. These results provide a foundation for further elucidation of the molecular mechanism of the regulation of leaf angle in maize.
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Affiliation(s)
- Yunfang Zhang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Xiangzhuo Ji
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Jinhong Xian
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yinxia Wang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Yunling Peng
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
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Liu W, Yi Y, Zhuang J, Ge C, Cao Y, Zhang L, Liu M. Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree ( Vernicia fordii). PeerJ 2022; 10:e13981. [PMID: 36193421 PMCID: PMC9526410 DOI: 10.7717/peerj.13981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/10/2022] [Indexed: 01/19/2023] Open
Abstract
The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and is extensively involved in plant growth, development, biotic and abiotic stress responses. Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. However, the characteristics of the bHLH gene family in the tung tree genome are still unclear. Hence, VfbHLHs were first searched at a genome-wide level, and their expression levels in various tissues or under low temperature were investigated systematically. In this study, we identified 104 VfbHLHs in the tung tree genome, and these genes were classified into 18 subfamilies according to bHLH domains. Ninety-eight VfbHLHs were mapped to but not evenly distributed on 11 pseudochromosomes. The domain sequences among VfbHLHs were highly conserved, and their conserved residues were also identified. To explore their expression, we performed gene expression profiling using RNA-Seq and RT-qPCR. We identified five, 18 and 28 VfbHLH genes in female flowers, male flowers and seeds, respectively. Furthermore, we found that eight genes (VfbHLH29, VfbHLH31, VfbHLH47, VfbHLH51, VfbHLH57, VfbHLH59, VfbHLH70, VfbHLH72) were significant differential expressed in roots, leaves and petioles under low temperature stress. This study lays the foundation for future studies on bHLH gene cloning, transgenes, and biological mechanisms.
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Affiliation(s)
- Wenjuan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Yaqi Yi
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Jingyi Zhuang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Chang Ge
- School of Urban Design, Wuhan University, Wuhan, Hubei, China
| | - Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Meilan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
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Lu X, Zhang H, Hu J, Nie G, Khan I, Feng G, Zhang X, Wang X, Huang L. Genome-wide identification and characterization of bHLH family genes from orchardgrass and the functional characterization of DgbHLH46 and DgbHLH128 in drought and salt tolerance. Funct Integr Genomics 2022; 22:1331-1344. [PMID: 35941266 DOI: 10.1007/s10142-022-00890-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/28/2022]
Abstract
Basic helix-loop-helix (bHLH) is the second largest family of transcription factors that widely exist in plants and animals, and plays a key role in a variety of biological processes. As an important forage crop worldwide, little information is available about the bHLH family in orchardgrass (Dactylis glomerata L.), although a huge number of bHLH family have been identified and characterized in plants. In this study, we performed genome-wide analysis of bHLH transcription factor family of orchardgrass and identified 132 DgbHLH genes. The phylogenetic tree was constructed by using bHLH proteins of orchardgrass, with Arabidopsis thaliana and Oryza sativa bHLH proteins, to elucidate their homology and classify them into 22 subfamilies. The results of conserved motifs and gene structure support the classification of DgbHLH family. In addition, chromosomal location and gene duplication events of DgbHLH genes were further studied. Transcriptome data exhibited that DgbHLH genes were differentially expressed in different tissues of orchardgrass. We analyzed the gene expression level of 12 DgbHLH genes in orchardgrass under three types of abiotic stresses (heat, salt, and drought). Finally, heterologous expression assays in yeast indicated that DgbHLH46 and DgbHLH128 may enhance the resistance to drought and salt stress. Furthermore, DgbHLH128 may also be involved in abiotic stress by binding to the MYC element. Our study provides a comprehensive assessment of DgbHLH family of orchardgrass, revealing new insights for enhancing gene utilization and improving forage performance.
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Affiliation(s)
- Xiaowen Lu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Huan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jialing Hu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Imran Khan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.
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10
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Guo X, Fu Y, Lee YJ, Chern M, Li M, Cheng M, Dong H, Yuan Z, Gui L, Yin J, Qing H, Zhang C, Pu Z, Liu Y, Li W, Li W, Qi P, Chen G, Jiang Q, Ma J, Chen X, Wei Y, Zheng Y, Wu Y, Liu B, Wang J. The PGS1 basic helix-loop-helix protein regulates Fl3 to impact seed growth and grain yield in cereals. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1311-1326. [PMID: 35315196 PMCID: PMC9241376 DOI: 10.1111/pbi.13809] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 03/11/2022] [Indexed: 05/02/2023]
Abstract
Plant transcription factors (TFs), such as basic helix-loop-helix (bHLH) and AT-rich zinc-binding proteins (PLATZ), play critical roles in regulating the expression of developmental genes in cereals. We identified the bHLH protein TaPGS1 (T. aestivum Positive Regulator of Grain Size 1) specifically expressed in the seeds at 5-20 days post-anthesis in wheat. TaPGS1 was ectopically overexpressed (OE) in wheat and rice, leading to increased grain weight (up to 13.81% in wheat and 18.55% in rice lines) and grain size. Carbohydrate and total protein levels also increased. Scanning electron microscopy results indicated that the starch granules in the endosperm of TaPGS1 OE wheat and rice lines were smaller and tightly embedded in a proteinaceous matrix. Furthermore, TaPGS1 was bound directly to the E-box motif at the promoter of the PLATZ TF genes TaFl3 and OsFl3 and positively regulated their expression in wheat and rice. In rice, the OsFl3 CRISPR/Cas9 knockout lines showed reduced average thousand-grain weight, grain width, and grain length in rice. Our results reveal that TaPGS1 functions as a valuable trait-associated gene for improving cereal grain yield.
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Affiliation(s)
- Xiaojiang Guo
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- Department of Plant BiologyUniversity of CaliforniaDavisCAUSA
| | - Yuxin Fu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | | | - Mawsheng Chern
- Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
| | - Maolian Li
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Mengping Cheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Huixue Dong
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Zhongwei Yuan
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Lixuan Gui
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Hai Qing
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Chengbi Zhang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Zhien Pu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yujiao Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Weitao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Wei Li
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Pengfei Qi
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Guoyue Chen
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Qiantao Jiang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Jian Ma
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yuming Wei
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Youliang Zheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Bo Liu
- Department of Plant BiologyUniversity of CaliforniaDavisCAUSA
| | - Jirui Wang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityChengduChina
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11
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Pech R, Volná A, Hunt L, Bartas M, Červeň J, Pečinka P, Špunda V, Nezval J. Regulation of Phenolic Compound Production by Light Varying in Spectral Quality and Total Irradiance. Int J Mol Sci 2022; 23:ijms23126533. [PMID: 35742975 PMCID: PMC9223736 DOI: 10.3390/ijms23126533] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
Photosynthetically active radiation (PAR) is an important environmental cue inducing the production of many secondary metabolites involved in plant oxidative stress avoidance and tolerance. To examine the complex role of PAR irradiance and specific spectral components on the accumulation of phenolic compounds (PheCs), we acclimated spring barley (Hordeum vulgare) to different spectral qualities (white, blue, green, red) at three irradiances (100, 200, 400 µmol m−2 s−1). We confirmed that blue light irradiance is essential for the accumulation of PheCs in secondary barley leaves (in UV-lacking conditions), which underpins the importance of photoreceptor signals (especially cryptochrome). Increasing blue light irradiance most effectively induced the accumulation of B-dihydroxylated flavonoids, probably due to the significantly enhanced expression of the F3′H gene. These changes in PheC metabolism led to a steeper increase in antioxidant activity than epidermal UV-A shielding in leaf extracts containing PheCs. In addition, we examined the possible role of miRNAs in the complex regulation of gene expression related to PheC biosynthesis.
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Affiliation(s)
- Radomír Pech
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (R.P.); (A.V.)
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (R.P.); (A.V.)
| | - Lena Hunt
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 128 00 Praha, Czech Republic;
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (M.B.); (J.Č.); (P.P.)
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (M.B.); (J.Č.); (P.P.)
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (M.B.); (J.Č.); (P.P.)
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (R.P.); (A.V.)
- Global Change Research Institute, Czech Academy of Sciences, 603 00 Brno, Czech Republic
- Correspondence: (V.Š.); (J.N.)
| | - Jakub Nezval
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (R.P.); (A.V.)
- Correspondence: (V.Š.); (J.N.)
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12
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Biogenic Silver Nanoparticles as a Stress Alleviator in Plants: A Mechanistic Overview. Molecules 2022; 27:molecules27113378. [PMID: 35684312 PMCID: PMC9182038 DOI: 10.3390/molecules27113378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
Currently, the growth and yield of crops are restrained due to an increase in the occurrence of ecological stresses globally. Biogenic generation of nanomaterials is an important step in the development of environmentally friendly procedures in the nanotechnology field. Silver-based nanomaterials are significant because of their physical, chemical, and biological features along with their plentiful applications. In addition to useful microbes, the green synthesized Ag nanomaterials are considered to be an ecologically friendly and environmentally biocompatible method for the enhancement of crop yield by easing stresses. In the recent decade, due to regular droughts, infrequent precipitation, salinity, and increased temperature, the climate alternation has changed certain ecological systems. As a result of these environmental changes, crop yield has decreased worldwide. The role of biogenic Ag nanomaterials in enhancing methylglyoxal detoxification, antioxidant defense mechanisms, and generating tolerance to stresses-induced ROS injury has been methodically explained in plants over the past ten years. However, certain studies regarding stress tolerance and metal-based nanomaterials have been directed, but the particulars of silver nanomaterials arbitrated stresses tolerance have not been well-reviewed. Henceforth, there is a need to have a good understanding of plant responses during stressful conditions and to practice the combined literature to enhance tolerance for crops by utilization of Ag nanoparticles. This review article illustrates the mechanistic approach that biogenic Ag nanomaterials in plants adopt to alleviate stresses. Moreover, we have appraised the most significant activities by exogenous use of Ag nanomaterials for improving plant tolerance to salt, low and high temperature, and drought stresses.
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13
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Yang J, Chen Y, Gao M, Wu L, Xiong S, Wang S, Gao J, Zhao Y, Wang Y. Comprehensive identification of bHLH transcription factors in Litsea cubeba reveals candidate gene involved in the monoterpene biosynthesis pathway. FRONTIERS IN PLANT SCIENCE 2022; 13:1081335. [PMID: 36618662 PMCID: PMC9811127 DOI: 10.3389/fpls.2022.1081335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 05/13/2023]
Abstract
Litsea cubeba (Lour.) Person, an economically important aromatic plant producing essential oils, has lemon-like fragrance and 96.44-98.44% monoterpene contents. bHLH transcription factor plays an important role in plant secondary metabolism and terpene biosynthesis. In this study, we used bioinformatics to identify bHLH transcription factors in L. cubeba, 173 bHLH genes were identified from L. cubeba and divided these into 26 subfamilies based on phylogenetic analysis. The majority of bHLHs in each subfamily shared comparable structures and motifs. While LcbHLHs were unevenly distributed across 12 chromosomes, 10 tandem repeats were discovered. Expression profiles of bHLH genes in different tissues demonstrated that LcbHLH78 is a potential candidate gene for regulating monoterpene biosynthesis. LcbHLH78 and the terpene synthase LcTPS42 showed comparable expression patterns in various tissues and fruit development stages of L. cubeba. Subcellular localization analysis revealed that LcbHLH78 protein localizes to the nucleus, consistent with a transcription factor function. Importantly, transient overexpression of LcbHLH78 increased geraniol and linalol contents. Our research demonstrates that LcbHLH78 enhances terpenoid biosynthesis. This finding will be beneficial for improving the quality of L. cubeba and provides helpful insights for further research into the control mechanism of LcbHLH genes over terpenoid biosynthesis.
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Affiliation(s)
- Jiahui Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Liwen Wu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Shifa Xiong
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Siqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Jing Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
- *Correspondence: Yunxiao Zhao, ; Yangdong Wang,
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
- *Correspondence: Yunxiao Zhao, ; Yangdong Wang,
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14
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An F, Xiao X, Chen T, Xue J, Luo X, Ou W, Li K, Cai J, Chen S. Systematic Analysis of bHLH Transcription Factors in Cassava Uncovers Their Roles in Postharvest Physiological Deterioration and Cyanogenic Glycosides Biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:901128. [PMID: 35789698 PMCID: PMC9249602 DOI: 10.3389/fpls.2022.901128] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/09/2022] [Indexed: 05/15/2023]
Abstract
The basic helix-loop-helix (bHLH) proteins are a large superfamily of transcription factors, and play a central role in a wide range of metabolic, physiological, and developmental processes in higher organisms. However, systematic investigation of bHLH gene family in cassava (Manihot esculenta Crantz) has not been reported. In the present study, we performed a genome-wide survey and identified 148 MebHLHs genes were unevenly harbored in 18 chromosomes. Through phylogenetic analyses along with Arabidopsis counterparts, these MebHLHs genes were divided into 19 groups, and each gene contains a similar structure and conserved motifs. Moreover, many cis-acting regulatory elements related to various defense and stress responses showed in MebHLH genes. Interestingly, transcriptome data analyses unveiled 117 MebHLH genes during postharvest physiological deterioration (PPD) process of cassava tuberous roots, while 65 MebHLH genes showed significantly change. Meanwhile, the relative quantitative analysis of 15 MebHLH genes demonstrated that they were sensitive to PPD, suggesting they may involve in PPD process regulation. Cyanogenic glucosides (CGs) biosynthesis during PPD process was increased, silencing of MebHLH72 and MebHLH114 showed that linamarin content was significantly decreased in the leaves. To summarize, the genome-wide identification and expression profiling of MebHLH candidates pave a new avenue for uderstanding their function in PPD and CGs biosynthesis, which will accelerate the improvement of PPD tolerance and decrease CGs content in cassava tuberous roots.
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Affiliation(s)
- Feifei An
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
- School of Life Sciences, Hainan University, Haikou, China
| | - Xinhui Xiao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
| | - Ting Chen
- Postgraduate Department, Hainan Normal University, Haikou, China
| | - Jingjing Xue
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
| | - Xiuqin Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
| | - Wenjun Ou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
| | - Kaimian Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
| | - Jie Cai
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
- Jie Cai,
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
- *Correspondence: Songbi Chen,
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15
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Yang Y, Zhang Y, He J, Wu Q, Li Y, Li W, Zhou G, Kamol R, Yang X. Transcription factor GlbHLH regulates hyphal growth, stress resistance, and polysaccharide biosynthesis in Ganoderma lucidum. J Basic Microbiol 2021; 62:82-91. [PMID: 34927265 DOI: 10.1002/jobm.202100334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/18/2021] [Accepted: 10/31/2021] [Indexed: 11/12/2022]
Abstract
Basic helix-loop-helix (bHLH) transcription factors (TFs) participate in many physiological and cellular processes in eukaryotes. However, their functions remain unclear in the macro basidiomycete Ganoderma lucidum (G. lucidum). In this study, a gene encoding bHLH TF, GlbHLH, was identified in G. lucidum. The knockdown of GlbHLH by RNA interference reduced hyphal growth, hyphal branching, and resistant to osmotic, oxidative, and cell wall stress. The content of cell wall components β-1,3 glucan and chitin and the expression of their synthesis genes were decreased in the GlbHLH knockdown strains. The knockdown of GlbHLH led to an increase of intracellular reactive oxygen species by decreasing the enzyme activity and gene expression of antioxidant enzymes. Furthermore, the production of intracellular polysaccharides and extracellular polysaccharides was greatly decreased in the GlbHLH mutants. These results suggested that GlbHLH is involved in hyphal growth, stress response, and polysaccharide biosynthesis in G. lucidum.
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Affiliation(s)
- Yingyin Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yifan Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiahao He
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yanzeng Li
- Henan Shijixiang Edible Mushroom Co., Ltd., Xuchang, China
| | - Weipeng Li
- Henan Shijixiang Edible Mushroom Co., Ltd., Xuchang, China
| | - Gaoli Zhou
- Henan Shijixiang Edible Mushroom Co., Ltd., Xuchang, China
| | - Rajabov Kamol
- Russia Green Manor Co., Ltd., Leningrad Oblas, Russia
| | - Xiaobing Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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16
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Singh A, Mathan J, Yadav A, K. Goyal A, Chaudhury A. Molecular and Transcriptional Regulation of Seed Development in Cereals: Present Status and Future Prospects. CEREAL GRAINS - VOLUME 1 2021. [DOI: 10.5772/intechopen.99318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Cereals are a rich source of vitamins, minerals, carbohydrates, fats, oils and protein, making them the world’s most important source of nutrition. The influence of rising global population, as well as the emergence and spread of disease, has the major impact on cereal production. To meet the demand, there is a pressing need to increase cereal production. Optimal seed development is a key agronomical trait that contributes to crop yield. The seed development and maturation is a complex process that includes not only embryo and endosperm development, but also accompanied by huge physiological, biochemical, metabolic, molecular and transcriptional changes. This chapter discusses the growth of cereal seed and highlights the novel biological insights, with a focus on transgenic and new molecular breeding, as well as biotechnological intervention strategies that have improved crop yield in two major cereal crops, primarily wheat and rice, over the last 21 years (2000–2021).
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17
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Bai G, Yang DH, Chao P, Yao H, Fei M, Zhang Y, Chen X, Xiao B, Li F, Wang ZY, Yang J, Xie H. Genome-wide identification and expression analysis of NtbHLH gene family in tobacco ( Nicotiana tabacum) and the role of NtbHLH86 in drought adaptation. PLANT DIVERSITY 2021; 43:510-522. [PMID: 35024520 PMCID: PMC8720692 DOI: 10.1016/j.pld.2020.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/12/2020] [Accepted: 10/18/2020] [Indexed: 06/12/2023]
Abstract
The bHLH transcription factors play pivotal roles in plant growth and development, production of secondary metabolites and responses to various environmental stresses. Although the bHLH genes have been well studied in model plant species, a comprehensive investigation of the bHLH genes is required for tobacco with newly obtained high-quality genome. In the present study, a total of 309 NtbHLH genes were identified and can be divided into 23 subfamilies. The conserved amino acids which are essential for their function were predicted for the NtbHLH proteins. Moreover, the NtbHLH genes were conserved during evolution through analyzing the gene structures and conserved motifs. A total of 265 NtbHLH genes were localized in the 24 tobacco chromosomes while the remained 44 NtbHLH genes were mapped to the scaffolds due to the complexity of tobacco genome. Moreover, transcripts of NtbHLH genes were obviously tissue-specific expressed from the gene-chip data from 23 tobacco tissues, and expressions of 20 random selected NtbHLH genes were further confirmed by quantitative real-time PCR, indicating their potential functions in the plant growth and development. Importantly, overexpressed NtbHLH86 gene confers improve drought tolerance in tobacco indicating that it might be involved in the regulation of drought stress. Therefore, our findings here provide a valuable information on the characterization of NtbHLH genes and further investigation of their functions in tobacco.
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Affiliation(s)
- Ge Bai
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Da-Hai Yang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Peijian Chao
- National Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, Henan, China
| | - Heng Yao
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - MingLiang Fei
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Yihan Zhang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Xuejun Chen
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Bingguang Xiao
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Feng Li
- National Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, Henan, China
| | - Zhen-Yu Wang
- Institute ofBioengineering, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510316, China
| | - Jun Yang
- National Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, Henan, China
| | - He Xie
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
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18
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Zuo ZF, Sun HJ, Lee HY, Kang HG. 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. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111088. [PMID: 34763873 DOI: 10.1016/j.plantsci.2021.111088] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/07/2021] [Accepted: 10/10/2021] [Indexed: 06/13/2023]
Abstract
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.
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Affiliation(s)
- Zhi-Fang Zuo
- Department of Biotechnology, Jeju National University, Jeju, Republic of Korea; Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
| | - Hyo-Yeon Lee
- Department of Biotechnology, Jeju National University, Jeju, Republic of Korea; Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea.
| | - Hong-Gyu Kang
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea.
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19
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Transcriptomic Analyses Shed Light on Critical Genes Associated with Bibenzyl Biosynthesis in Dendrobium officinale. PLANTS 2021; 10:plants10040633. [PMID: 33810588 PMCID: PMC8065740 DOI: 10.3390/plants10040633] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 11/25/2022]
Abstract
The Dendrobium plants (members of the Orchidaceae family) are used as traditional Chinese medicinal herbs. Bibenzyl, one of the active compounds in Dendrobium officinale, occurs in low amounts among different tissues. However, market demands require a higher content of thes compounds to meet the threshold for drug production. There is, therefore, an immediate need to dissect the physiological and molecular mechanisms underlying how bibenzyl compounds are biosynthesized in D. officinale tissues. In this study, the accumulation of erianin and gigantol in tissues were studied as representative compounds of bibenzyl. Exogenous application of Methyl-Jasmonate (MeJA) promotes the biosynthesis of bibenzyl compounds; therefore, transcriptomic analyses were conducted between D. officinale-treated root tissues and a control. Our results show that the root tissues contained the highest content of bibenzyl (erianin and gigantol). We identified 1342 differentially expressed genes (DEGs) with 912 up-regulated and 430 down-regulated genes in our transcriptome dataset. Most of the identified DEGs are functionally involved in the JA signaling pathway and the biosynthesis of secondary metabolites. We also identified two candidate cytochrome P450 genes and nine other enzymatic genes functionally involved in bibenzyl biosynthesis. Our study provides insights on the identification of critical genes associated with bibenzyl biosynthesis and accumulation in Dendrobium plants, paving the way for future research on dissecting the physiological and molecular mechanisms of bibenzyl synthesis in plants as well as guide genetic engineering for the improvement of Dendrobium varieties through increasing bibenzyl content for drug production and industrialization.
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20
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Ortolan F, Fonini LS, Pastori T, Mariath JEA, Saibo NJM, Margis-Pinheiro M, Lazzarotto F. Tightly controlled expression of OsbHLH35 is critical for anther development in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 302:110716. [PMID: 33288022 DOI: 10.1016/j.plantsci.2020.110716] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 05/08/2023]
Abstract
Anther development is a complex process regulated by a myriad of transcription factors belonging to distinct protein families. In this study, we focus on the functional characterization of OsbHLH35, a basic Helix-Loop-Helix (bHLH) TF that regulates anther development in rice. Plants overexpressing OsbHLH35 presented small and curved anthers, leading to a reduction of 72 % on seed production. Rice transgenic plants expressing GUS reporter gene under the control of OsbHLH35 promoter (pOsbHLH35::GUS) showed that this TF specifically accumulates in anthers at the meiosis stage and in other spikelet tissues. Yeast one-hybrid screening identified three members of the Growth-Regulating Factor (GRF) family, OsGRF3, OsGRF4, and OsGRF11, as transcriptional regulators of OsbHLH35. Transactivation assay showed that OsGRF11 negatively regulates OsbHLH35 expression in Arabidopsis protoplasts. This regulation was also observed in planta through the analysis of transgenic plants overexpressing OsGRF11 (OsGRF11OE), confirming that OsGRF11 is a negative regulator of OsbHLH35 in rice. Our data suggest that OsbHLH35 plays an essential role in anther development in rice and the fine control of its expression is crucial to ensure proper seed production.
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Affiliation(s)
- Francieli Ortolan
- Programa de Pós-graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900, RS, Brazil.
| | - Leila S Fonini
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900, RS, Brazil.
| | - Tamara Pastori
- Programa de Pós-graduação em Botânica, Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900, RS, Brazil.
| | - Jorge E A Mariath
- Programa de Pós-graduação em Botânica, Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900, RS, Brazil.
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal.
| | - Márcia Margis-Pinheiro
- Programa de Pós-graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900, RS, Brazil; Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900, RS, Brazil.
| | - Fernanda Lazzarotto
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900, RS, Brazil.
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21
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Song M, Wang H, Wang Z, Huang H, Chen S, Ma H. Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Fig ( Ficus carica L.). FRONTIERS IN PLANT SCIENCE 2021; 12:730692. [PMID: 34691109 PMCID: PMC8531510 DOI: 10.3389/fpls.2021.730692] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/03/2021] [Indexed: 05/14/2023]
Abstract
The basic helix-loop-helix (bHLH) transcription factor family is the second largest transcription factor family in plants, and participates in various plant growth and development processes. A total of 118 bHLH genes were identified from fig (Ficus carica L.) by whole-genome database search. Phylogenetic analysis with Arabidopsis homologs divided them into 25 subfamilies. Most of the bHLHs in each subfamily shared a similar gene structure and conserved motifs. Seventy-two bHLHs were found expressed at fragments per kilobase per million mapped (FPKM) > 10 in the fig fruit; among them, 15 bHLHs from eight subfamilies had FPKM > 100 in at least one sample. bHLH subfamilies had different expression patterns in the female flower tissue and peel during fig fruit development. Comparing green and purple peel mutants, 13 bHLH genes had a significantly different (≥ 2-fold) expression. Light deprivation resulted in 68 significantly upregulated and 22 downregulated bHLH genes in the peel of the fruit. Sixteen bHLH genes in subfamily III were selected by three sets of transcriptomic data as candidate genes related to anthocyanin synthesis. Interaction network prediction and yeast two-hybrid screening verified the interaction between FcbHLH42 and anthocyanin synthesis-related genes. The transient expression of FcbHLH42 in tobacco led to an apparent anthocyanin accumulation. Our results confirm the first fig bHLH gene involved in fruit color development, laying the foundation for an in-depth functional study on other FcbHLH genes in fig fruit quality formation, and contributing to our understanding of the evolution of bHLH genes in other horticulturally important Ficus species.
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Affiliation(s)
- Miaoyu Song
- College of Horticulture, China Agricultural University, Beijing, China
| | - Haomiao Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhe Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Hantang Huang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Shangwu Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Huiqin Ma
- College of Horticulture, China Agricultural University, Beijing, China
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- *Correspondence: Huiqin Ma
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22
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Bassolino L, Buti M, Fulvio F, Pennesi A, Mandolino G, Milc J, Francia E, Paris R. In Silico Identification of MYB and bHLH Families Reveals Candidate Transcription Factors for Secondary Metabolic Pathways in Cannabis sativa L. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1540. [PMID: 33187168 PMCID: PMC7697600 DOI: 10.3390/plants9111540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/12/2022]
Abstract
Plant secondary metabolic pathways are finely regulated by the activity of transcription factors, among which members of the bHLH and MYB subfamilies play a main role. Cannabis sativa L. is a unique officinal plant species with over 600 synthesized phytochemicals having diverse scale-up industrial and pharmaceutical usage. Despite comprehensive knowledge of cannabinoids' metabolic pathways, very little is known about their regulation, while the literature on flavonoids' metabolic pathways is still scarce. In this study, we provide the first genome-wide analysis of bHLH and MYB families in C. sativa reference cultivar CBDRx and identification of candidate coding sequences for these transcription factors. Cannabis sativa bHLHs and MYBs were then classified into functional subfamilies through comparative phylogenetic analysis with A. thaliana transcription factors. Analyses of gene structure and motif distribution confirmed that CsbHLHs and CsMYBs belonging to the same evolutionary clade share common features at both gene and amino acidic level. Candidate regulatory genes for key metabolic pathways leading to flavonoid and cannabinoid synthesis in Cannabis were also retrieved. Furthermore, a candidate gene approach was used to identify structural enzyme-coding genes for flavonoid and cannabinoid synthesis. Taken as a whole, this work represents a valuable resource of candidate genes for further investigation of the C. sativa cannabinoid and flavonoid metabolic pathways for genomic studies and breeding programs.
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Affiliation(s)
- Laura Bassolino
- CREA-Research Centre for Cereal and Industrial Crops, 40128 Bologna, Italy; (F.F.); (A.P.); (G.M.)
| | - Matteo Buti
- Department of Agriculture, Food, Environment and Forestry, University of Florence, 50144 Firenze, Italy;
| | - Flavia Fulvio
- CREA-Research Centre for Cereal and Industrial Crops, 40128 Bologna, Italy; (F.F.); (A.P.); (G.M.)
| | - Alessandro Pennesi
- CREA-Research Centre for Cereal and Industrial Crops, 40128 Bologna, Italy; (F.F.); (A.P.); (G.M.)
| | - Giuseppe Mandolino
- CREA-Research Centre for Cereal and Industrial Crops, 40128 Bologna, Italy; (F.F.); (A.P.); (G.M.)
| | - Justyna Milc
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy; (J.M.); (E.F.)
| | - Enrico Francia
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy; (J.M.); (E.F.)
| | - Roberta Paris
- CREA-Research Centre for Cereal and Industrial Crops, 40128 Bologna, Italy; (F.F.); (A.P.); (G.M.)
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23
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Lang Y, Liu Z. Basic Helix-Loop-Helix (bHLH) transcription factor family in Yellow horn (Xanthoceras sorbifolia Bunge): Genome-wide characterization, chromosome location, phylogeny, structures and expression patterns. Int J Biol Macromol 2020; 160:711-723. [DOI: 10.1016/j.ijbiomac.2020.05.253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/27/2022]
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24
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Zhu T, Liu Y, Ma L, Wang X, Zhang D, Han Y, Ding Q, Ma L. Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat. BMC PLANT BIOLOGY 2020; 20:420. [PMID: 32912142 PMCID: PMC7488452 DOI: 10.1186/s12870-020-02576-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/26/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. RESULTS In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). CONCLUSIONS The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.
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Affiliation(s)
- Ting Zhu
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yue Liu
- College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Liting Ma
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Xiaoying Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Dazhong Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yucui Han
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Yangling, 712100, China.
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25
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Kumar RR, Arora K, Goswami S, Sakhare A, Singh B, Chinnusamy V, Praveen S. MAPK Enzymes: a ROS Activated Signaling Sensors Involved in Modulating Heat Stress Response, Tolerance and Grain Stability of Wheat under Heat Stress. 3 Biotech 2020; 10:380. [PMID: 32802722 DOI: 10.1007/s13205-020-02377-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/31/2020] [Indexed: 01/21/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) signaling cascade is highly conserved across the species triggering the self-adjustment of the cells by transmitting the external signals to the nucleus. The cascade consists of MAPK kinase kinases (MAPKKKs), MAPK kinases (MAPKKs) and MAPKs. These kinases are functionally interrelated through activation by sequential phosphorylation. MAPK cascade is involved in modulating the tolerance and regulating the growth and developmental processes in plants through transcriptional programming. The cascade has been well characterized in Arabidopsis, Tobacco and rice, but limited information is available in wheat due to complexity of genome. MAPK-based sensors have been reported to be highly specific for the external or intracellular stimuli activating specific TF, stress-associated genes (SAGs) and stress-associated proteins (SAPs) linked with heat-stress tolerance and other biological functions especially size, number and quality of grains. Even, MAPKs have been reported to influence the activity of ATP-binding cassette (ABC) transporter superfamily involved in stabilizing the quality of the grains under adverse conditions. Wheat has also diverse network of MAPKs involved in transcriptional reprogramming upon sensing the terminal HS and in turn protect the plants. Current review mainly focuses on the role of MAPKs as signaling sensor and modulator of defense mechanism for mitigating the effect of heat on plants with focus on wheat. It also indirectly protects the nutrient depletion from the grains under heat stress. MAPKs, lying at pivotal positions, can be utilized for manipulating the heat-stress response (HSR) of wheat to develop plant for future (P4F).
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Affiliation(s)
- Ranjeet R Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Kirti Arora
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Suneha Goswami
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Akshay Sakhare
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Bhupinder Singh
- Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Shelly Praveen
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
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Wang Y, Liu A. Genomic Characterization and Expression Analysis of Basic Helix-Loop-Helix (bHLH) Family Genes in Traditional Chinese Herb Dendrobium officinale. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9081044. [PMID: 32824436 PMCID: PMC7463459 DOI: 10.3390/plants9081044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 05/26/2023]
Abstract
Dendrobium officinale Kimura et Migo is of great importance as a traditional Chinese herb due to its abundant metabolites. The family of basic helix-loop-helix (bHLH) transcription factors widely exists in plants and plays an essential role in plant growth and development, secondary metabolism as well as responses to environmental changes. However, there is limited information on bHLH genes in D. officinale. In the present study, a total of 98 putative DobHLH genes were identified at the genomic level, which could be classified into 18 clades. Gene structures and conserved motifs in DobHLH genes showed high conservation during their evolution. The conserved amino acids and DNA bindings of DobHLH proteins were predicted, both of which are pivotal for their function. Furthermore, gene expression from eight tissues showed that some DobHLH genes were ubiquitously expressed while other DobHLH genes were expressed in the specific tissues. Expressional changes of DobHLH genes under MeJA and ABA treatments were detected by qRT-PCR. The protein-protein interactions between DobHLHs were predicted and several interactions were confirmed by yeast two hybrid. Therefore, our results here contribute to the understanding of bHLH genes in D. officinale and lay a foundation for the further functional study of its biological processes.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan, China;
- Bio-Innovation Center of DR PLANT, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224 Yunnan, China
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27
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Genome-Wide Identification and Expression Profile Analysis of the Phospholipase C Gene Family in Wheat ( Triticum aestivum L.). PLANTS 2020; 9:plants9070885. [PMID: 32668812 PMCID: PMC7412115 DOI: 10.3390/plants9070885] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/20/2022]
Abstract
Phospholipid-hydrolyzing enzymes include members of the phospholipase C (PLC) family that play important roles in regulating plant growth and responding to stress. In the present study, a systematic in silico analysis of the wheat PLC gene family revealed a total of 26 wheat PLC genes (TaPLCs). Phylogenetic and sequence alignment analyses divided the wheat PLC genes into 2 subfamilies, TaPI-PLC (containing the typical X, Y, and C2 domains) and TaNPC (containing a phosphatase domain). TaPLC expression patterns differed among tissues, organs, and under abiotic stress conditions. The transcript levels of 8 TaPLC genes were validated through qPCR analyses. Most of the TaPLC genes were sensitive to salt stress and were up-regulated rapidly, and some were sensitive to low temperatures and drought. Overexpression of TaPI-PLC1-2B significantly improved resistance to salt and drought stress in Arabidopsis, and the primary root of P1-OE was significantly longer than that of the wild type under stress conditions. Our results not only provide comprehensive information for understanding the PLC gene family in wheat, but can also provide a solid foundation for functional characterization of the wheat PLC gene family.
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28
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Yang M, Zhou C, Yang H, Kuang R, Huang B, Wei Y. Genome-wide analysis of basic helix-loop-helix transcription factors in papaya ( Carica papaya L.). PeerJ 2020; 8:e9319. [PMID: 32704439 PMCID: PMC7341539 DOI: 10.7717/peerj.9319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/17/2020] [Indexed: 11/20/2022] Open
Abstract
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.
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Affiliation(s)
- Min Yang
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
| | - Chenping Zhou
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
| | - Hu Yang
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
| | - Ruibin Kuang
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
| | - Bingxiong Huang
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
| | - Yuerong Wei
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
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29
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Liu H, Yang Y, Liu D, Wang X, Zhang L. Transcription factor TabHLH49 positively regulates dehydrin WZY2 gene expression and enhances drought stress tolerance in wheat. BMC PLANT BIOLOGY 2020; 20:259. [PMID: 32503498 PMCID: PMC7275420 DOI: 10.1186/s12870-020-02474-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/27/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND As functional proteins, dehydrins are found in many maturing seeds and vegetable tissues under adverse environmental conditions. However, the regulation of dehydrin expression remains unclear. RESULTS In this study, a novel drought stress-related bHLH transcription factor, TabHLH49, was isolated from a wheat cDNA library treated with the drought and cold stress by using yeast one-hybrid system. TabHLH49 protein possesses a typical conserved bHLH domain and is a Myc-type bHLH transcription factor. TabHLH49 was detected in the nucleus of tobacco epidermal cells, and the amino acid sequences at the C-terminus (amino acids 323-362) is necessary for its transactivation activity. Real-time PCR analyses revealed the tissue-specific expression and drought stress-responsive expression of TabHLH49 in wheat. In addition, the verification in Y1H and electrophoretic mobility shift assays illustrated that TabHLH49 protein can bind and interact with the promoter of the wheat WZY2 dehydrin. Furthermore, the dual-luciferase assays showed that TabHLH49 can positively regulate the expression of WZY2 dehydrin. The transient expression and BSMV-mediated gene silencing of TabHLH49 also showed that TabHLH49 positively regulates the expression of WZY2 dehydrin and improves drought stress resistance in wheat. CONCLUSIONS These results provide direct evidences that TabHLH49 positively regulates expression level of dehydrin WZY2 gene and improves drought tolerance of wheat.
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Affiliation(s)
- Hao Liu
- College of Life Science/State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Ying Yang
- College of Life Science/State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
- College of Nursing, Weinan Vocational&Technical College, Weinan, 714000, China
| | - Dandan Liu
- School of Agriculture, Yunnan University, Kunming, 650000, China
| | - Xiaoyu Wang
- College of Life Science/State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266000, China
| | - Linsheng Zhang
- College of Life Science/State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China.
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Sun W, Jin X, Ma Z, Chen H, Liu M. Basic helix-loop-helix (bHLH) gene family in Tartary buckwheat (Fagopyrum tataricum): Genome-wide identification, phylogeny, evolutionary expansion and expression analyses. Int J Biol Macromol 2019; 155:1478-1490. [PMID: 31734362 DOI: 10.1016/j.ijbiomac.2019.11.126] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/25/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
Abstract
Tartary buckwheat (Fagopyrum tataricum) a kind of edible and medicinal plant, is of great nutritional value. It is difficult to remove the hull of Tartary buckwheat fruit and breeding new easy-dehulled varieties has been one of the major breeding objectives. The bHLH gene family plays a vital role in plant growth and fruit dehiscence. In order to improve Tartary buckwheat breeding, we need to study the bHLH gene family for excavating genes with potential regulation of fruit development and dehiscence. Here, 164 Fagopyrum tataricum bHLH (FtbHLH) genes were identified. Analyses of gene structure and motif composition illustrate that the members of specific FtbHLH subfamily are relatively conserved. Synteny and phylogenetic analyses of bHLH genes in Tartary buckwheat and other plants lay a foundation for further exploring the evolutionary characteristic of the FtbHLH genes (FtbHLHs). qRT-PCR experiments showed that FtbHLHs expression patterns were different in plant organs, indicating that they may perform diverse functions. In addition, some genes that potentially regulate flower and fruit development and easy dehulling were screened out. Overall, this study will be helpful for further analyzing the biological function of FtbHLHs and provides clues for improving the genetic breeding and economic value of the Tartary buckwheat.
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Affiliation(s)
- Wenjun Sun
- Shanghai Jiao Tong University, School of Agriculture and Biology, Shanghai, China; Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Xiu Jin
- Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Zhaotang Ma
- Shanghai Jiao Tong University, School of Agriculture and Biology, Shanghai, China; Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Hui Chen
- Sichuan Agricultural University, College of Life Science, Ya'an, China.
| | - Moyang Liu
- Shanghai Jiao Tong University, School of Agriculture and Biology, Shanghai, China.
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Wang M, Kawakami Y, Bhullar NK. Molecular Analysis of Iron Deficiency Response in Hexaploid Wheat. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00067] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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32
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Genome-Wide Identification, Expression Analysis, and Subcellular Localization of Carthamus tinctorius bHLH Transcription Factors. Int J Mol Sci 2019; 20:ijms20123044. [PMID: 31234449 PMCID: PMC6627405 DOI: 10.3390/ijms20123044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/16/2022] Open
Abstract
The basic helix-loop-helix (bHLH) family is the second largest superfamily of transcription factors that belongs to all three eukaryotic kingdoms. The key function of this superfamily is the regulation of growth and developmental mechanisms in plants. However, the bHLH gene family in Carthamus tinctorius has not yet been studied. Here, we identified 41 bHLH genes in Carthamus tinctorius that were classified into 23 subgroups. Further, we conducted a phylogenetic analysis and identified 10 conserved protein motifs found in the safflower bHLH family. We comprehensively analyzed a group of bHLH genes that could be associated with flavonoid biosynthesis in safflower by gene expression analysis, gene ontology annotation, protein interaction network prediction, subcellular localization of the candidate CtbHLH40 gene, and real-time quantitative expression analysis. This study provides genome-wide identification of the genes related to biochemical and physiological processes in safflower.
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Wei K, Chen H. Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat. BMC PLANT BIOLOGY 2018; 18:309. [PMID: 30497403 PMCID: PMC6267037 DOI: 10.1186/s12870-018-1529-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/15/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. Comparative functional genomics can provide powerful approaches to draw inferences about gene function and evolution among species. The comprehensive comparison of bHLH gene family in different gramineous plants has not yet been reported. RESULTS In this study, a total of 183, 231 and 571 bHLHs were identified in rice, maize and wheat genomes respectively, and 1154 bHLH genes from the three species and Arabidopsis were classified into 36 subfamilies. Of the identified genes, 110 OsbHLHs, 188 ZmbHLHs and 209 TabHLHs with relatively high mRNA abundances were detected in one or more tissues during development, and some of them exhibited tissue-specific expression such as TabHLH454-459, ZmbHLH099-101 and OsbHLH037 in root, TabHLH559-562, - 046, - 047 and ZmbHLH010, - 072, - 226 in leaf, TabHLH216-221, - 333, - 335, - 340 and OsbHLH005, - 141 in inflorescence, TabHLH081, ZmbHLH139 and OsbHLH144 in seed. Forty five, twenty nine and thirty one differentially expressed bHLHs were respectively detected in wheat, maize and rice under drought stresses using RNA-seq technology. Among them, the expressions of TabHLH046, - 047, ZmbHLH097, - 098, OsbHLH006 and - 185 were strongly induced, whereas TabHLH303, - 562, ZmbHLH155, - 154, OsbHLH152 and - 113 showed significant down-regulation. Twenty two TabHLHs were induced after stripe rust infection at 24 h and nine of them were suppressed at 72 hpi, whereas 28 and 6 TabHLHs exhibited obviously down- and up-regulation after powdery mildew attack respectively. Forty one ZmbHLHs were differentially expressed in response to F. verticillioides infection. Twenty two co-expression modules were identified by the WGCNA, some of which were associated with particular tissue types. And GO enrichment analysis for the modules showed that some TabHLHs were involved in the control of several biological processes, such as tapetal PCD, lipid metabolism, iron absorption, stress responses and signal regulation. CONCLUSION The present study identifies the bHLH family in rice, maize and wheat genomes, and detailedly discusses the evolutionary relationships, expression and function of bHLHs. This study provides some novel and detail information about bHLHs, and may facilitate understanding the molecular basis of the plant growth, development and stress physiology.
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Affiliation(s)
- Kaifa Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, 36 Xian-Qian-Zhi Street, Zhangzhou, 363000 Fujian China
| | - Huiqin Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084 China
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Cheng X, Xiong R, Liu H, Wu M, Chen F, Xiang Y. Basic helix-loop-helix gene family: Genome wide identification, phylogeny, and expression in Moso bamboo. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:104-119. [PMID: 30179736 DOI: 10.1016/j.plaphy.2018.08.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 05/26/2023]
Abstract
Studies have shown that basic helix-loop-helix (bHLH) transcription factors play important roles in plant growth and survival, and response to various biotic/abiotic stresses. We identified a total of 448 bHLH genes. These genes were classified into 21 bHLH subfamilies, and most genes in a given subfamily had similar gene structures and conserved motifs. We identified 176 homologous pairs in the three species. We calculated Ka, Ks, and Ka/Ks to analyze the replication relationships among the three species. Multiple sequence analysis revealed that the PebHLH genes had the distinct bHLH structure. The gene ontology annotation analysis showed that the PebHLH genes had many molecular functions. Promoter cis-element analysis revealed that most of the PebHLH genes contained cis-elements that can respond to various biotic/abiotic stress-related events. The tissue expression patterns of the PebHLH genes indicated that most members were expressed in leaves, roots, and stems. Quantitative real-time PCR analysis showed that 21 selected PebHLH genes were differentially regulated after abscisic acid, drought, and methyl jasmonate treatments. This study has laid the basis for studying the functions of AtbHLH, OsbHLH, and PebHLH genes, and will contribute to future studies of the functions of bHLH genes in other plant species.
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Affiliation(s)
- Xinran Cheng
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Rui Xiong
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Huanlong Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Min Wu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Feng Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China.
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35
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Li M, Wang R, Tian H, Gao Y. Transcriptome responses in wheat roots to colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis. MYCORRHIZA 2018; 28:747-759. [PMID: 30251133 DOI: 10.1007/s00572-018-0868-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/17/2018] [Indexed: 05/11/2023]
Abstract
The influence of arbuscular mycorrhizal (AM) colonization on the expression of genes in the roots of wheat (Triticum aestivum L.) at the transcriptome level is largely unknown. A pot experiment was established to study the responses of the transcriptome profile in the roots of wheat to colonization by the AM fungus Rhizophagus irregularis using high through-put sequencing methods. The results indicated that the expression of 11,746 genes was regulated by AM colonization, and 64.7% of them were up-regulated genes. 1106 genes were only expressed in roots colonized by AM fungi, and 108 genes were only expressed in non-mycorrhizal roots. The differentially expressed genes (DEGs) were primarily distributed on the 2B, 3B, 2A, 2D, and 5B chromosomes of wheat. The DEGs (including both up- and down- regulated) mainly located on membranes, and functioned in nucleotide binding and transferase activity during cellular protein modification and biosynthetic processes. The data revealed that AM colonization up-regulated genes involved in the phenylpropanoid biosynthesis pathway and transcription factors which play vital roles in protecting plants from biotic or abiotic stresses. A number of key genes involved in molecular signal biosynthesis and recognition, epidermal cell colonization and arbuscule formation, carbon and nutrients exchange during AM symbiosis were found. All the ammonium transporter (AMT), iron-phytosiderophore transporter, boron, zinc, and magnesium transporter genes found in our study were up-regulated DEGs. One new AM-specific induced AMT and three new AM-specific induced nitrate transporter (NRT) genes were found in the roots of wheat colonized by AM fungi, even though a negative growth response of wheat to AM colonization occurred. The present study provided new information which is important for understanding the mechanisms behind the development and function of the symbiosis between wheat and AM fungi.
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Affiliation(s)
- Mengjiao Li
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Runze Wang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Hui Tian
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China.
| | - Yajun Gao
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
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36
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Yanfang Y, Kaikai Z, Liying Y, Xing L, Ying W, Hongwei L, Qiang L, Duanfen C, Deyou Q. Identification and characterization of MYC transcription factors in Taxus sp. Gene 2018; 675:1-8. [DOI: 10.1016/j.gene.2018.06.065] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/22/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
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37
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Wani SH, Tripathi P, Zaid A, Challa GS, Kumar A, Kumar V, Upadhyay J, Joshi R, Bhatt M. Transcriptional regulation of osmotic stress tolerance in wheat (Triticum aestivum L.). PLANT MOLECULAR BIOLOGY 2018; 97:469-487. [PMID: 30109563 DOI: 10.1007/s11103-018-0761-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/31/2018] [Indexed: 05/24/2023]
Abstract
The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses. Recent reports have provided novel insights on the role of TFs in osmotic stress tolerance via direct molecular links. However, our knowledge on the regulatory role TFs during osmotic stress tolerance in wheat remains limited. The present review in its first part sheds light on the importance of studying the role of osmotic stress tolerance in wheat plants and second aims to decipher molecular mechanisms of TFs belonging to several classes, including DREB, NAC, MYB, WRKY and bHLH, which have been reported to engage in osmotic stress mediated gene expression in wheat and third part covers the systems biology approaches to understand the transcriptional regulation of osmotic stress and the role of long non-coding RNAs in response to osmotic stress with special emphasis on wheat. The current concept may lead to an understanding in molecular regulation and signalling interaction of TFs under osmotic stress to clarify challenges and problems for devising potential strategies to improve complex regulatory events involved in plant tolerance to osmotic stress adaptive pathways in wheat.
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Affiliation(s)
- Shabir H Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 192101, India.
| | - Prateek Tripathi
- Department of Cell & Molecular Biology, The Scripps Research Institute, Jolla, CA, 92037, USA
| | - Abbu Zaid
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Ghana S Challa
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA
| | - Anuj Kumar
- Advance Centre for Computational and Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, Uttarakhand, 248007, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule, Pune University, Pune, India
| | - Jyoti Upadhyay
- Department of Pharmaceutical Sciences, Kumaun University, Campus Bhimtal, Bhimtal, Uttarakhand, 293136, India
| | - Rohit Joshi
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manoj Bhatt
- Guru Gobind Singh Indraprastha University, New Delhi, India
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Zhang C, Feng R, Ma R, Shen Z, Cai Z, Song Z, Peng B, Yu M. Genome-wide analysis of basic helix-loop-helix superfamily members in peach. PLoS One 2018; 13:e0195974. [PMID: 29659634 PMCID: PMC5901983 DOI: 10.1371/journal.pone.0195974] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/03/2018] [Indexed: 12/24/2022] Open
Abstract
The basic helix-loop-helix (bHLH) transcription factor family is a superfamily found in all eukaryotes that plays important roles in regulating growth and development. Over the past several decades, many bHLH superfamily genes have been identified and characterized in herbaceous and woody plants. However, the genes belonging to the bHLH superfamily in peach (Prunus persica) have not yet been comprehensively identified and characterized. Here, we identified 95 members of the bHLH superfamily in the peach genome, and these genes were classified into 19 subfamilies based on a phylogenetic comparison with bHLH proteins from Arabidopsis. The members within each subfamily were highly conserved according to the analysis of motif compositions and exon/intron organizations. The 95 bHLH genes were unevenly distributed on chromosomes 1 to 8 of the peach genome. We identified 57 pairs of bHLH members that were orthologous between peach and Arabidopsis. Additionally, 48 pairs of paralogous bHLH genes were identified on the eight chromosomes of the peach genome. Coupled with relative expression analysis of bHLH genes in red-fleshed peach fruit at five developmental stages, we identified several bHLH genes that might be involved in fruit development and anthocyanin biosynthesis. This study provides insight into the molecular mechanisms through which these genes are involved in the regulation of biological and biochemical processes in peach and lays the foundation for further studies on these genes.
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Affiliation(s)
- Chunhua Zhang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Ruchao Feng
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Ruijuan Ma
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Zhijun Shen
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Zhixiang Cai
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Zhizhong Song
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Bin Peng
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Mingliang Yu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
- * E-mail:
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