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Inès D, Courty PE, Wendehenne D, Rosnoblet C. CDC48 in plants and its emerging function in plant immunity. TRENDS IN PLANT SCIENCE 2024; 29:786-798. [PMID: 38218650 DOI: 10.1016/j.tplants.2023.12.013] [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: 09/06/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/15/2024]
Abstract
Protein homeostasis, namely the balance between protein synthesis and degradation, must be finely controlled to ensure cell survival, notably through the ubiquitin-proteasome system (UPS). In all species, including plants, homeostasis is disrupted by biotic and abiotic stresses. A key player in the maintenance of protein balance, the protein CDC48, shows emerging functions in plants, particularly in response to biotic stress. In this review on CDC48 in plants, we detail its highly conserved structure, describe a gene expansion that is only present in Viridiplantae, discuss its various functions and regulations, and finally highlight its recruitment, still not clear, during the plant immune response.
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Affiliation(s)
- Damien Inès
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - David Wendehenne
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - Claire Rosnoblet
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France.
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Liu L, Xu S, Zhang L, Zheng J. A Genome-Wide Analysis of the BAM Gene Family and Identification of the Cold-Responsive Genes in Pomegranate ( Punica granatum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1321. [PMID: 38794392 PMCID: PMC11125002 DOI: 10.3390/plants13101321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
Beta-amylases (BAMs, EC 3.2.1.2), belonging to a multigene family, play a pivotal role in starch breakdown and are also involved in hormonal and stress responses, notably to cold stress. Pomegranate trees (Punica granatum L.) are adapted to warm climates and are sensitive to cold temperatures. In this study, we analyzed eight PgBAM genes from the pomegranate genome dataset. These members unevenly distributed across chromosomes and were categorized into four groups based on their orthologous members. The motif composition was highly consistent among most members. In contrast, exon numbers and arrangements were conserved within groups or subgroups, whereas significant diversity was observed between different groups. A syntenic analysis revealed that three PgBAM members (PgBAM1/4/5) showed a total of 11 syntenic relationships with the BAM members from Arabidopsis, kiwifruit, and Chinese white pear, respectively. Promoter binding motif prediction suggested potential roles for PgBAMs' genes in light, stress, hormones, and development signaling. Gene expression indicated that PgBAM4 was predominantly expressed in leaves, PgBAM7 in flowers, and PgBAM8 in roots and leaves and during fruit ripening, particularly in pericarp development. A transcriptome analysis identified the starch and sucrose metabolism pathway (map00500) as a key factor in the cold stress response of cold-sensitive cultivar 'Tunisia' seedlings. PgBAM4 exhibited remarkable expression and was closely associated with the cold-responsive BAM genes, characterized by a closer phylogenetic relationship, conserved catalytic residues, and similar secondary and tertiary structures. Moreover, the differences in soluble sugar levels and PgBAM4 expression were closely associated with the varying cold stress resistance observed between 'Tunisia' and 'Sanbai' seedlings. Furthermore, yeast one-hybrid assays confirmed that PgCBF7, a critical transcription factor for enhancing freezing tolerance, binds to the promoter region of PgBAM4. Our findings provide a systematic overview of the PgBAM gene family and shed new light on the regulatory mechanisms underlying cold stress tolerance in pomegranate.
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Affiliation(s)
| | | | | | - Jie Zheng
- School of Life Science, Huaibei Normal University, Huaibei 235000, China; (L.L.); (S.X.); (L.Z.)
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Wu L, Cao L, Tao Y, Zhatova H, Hu H, Li C. Identification of the succinate-CoA ligase protein gene family reveals that TaSUCL1-1 positively regulate cadmium resistance in wheat. Int J Biol Macromol 2024; 268:131693. [PMID: 38657916 DOI: 10.1016/j.ijbiomac.2024.131693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
The Succinate-CoA ligase (SUCL1) gene family is involved in energy metabolism, phytohormone signaling, and plant growth, development, and tolerance to stress. This is the first study to analyze the SUCL1 gene family in wheat (Triticum aestivum). 17 TaSUCL1 genes were identified in the complete genome sequence and classified into five subfamilies based on related genes found in three other species. The 17 TaSUCL1 genes were unevenly distributed across 11 chromosomes, and the collinearity of these genes was further investigated. Through using real-time qPCR (RT-qPCR) analysis, we identified the expression patterns of the TaSUCL1 genes under various tissues and different heavy metal stress conditions. The functions of selected TaSUCL1-1 gene were investigated by RNA interference (RNAi). This study provided a comprehensive analysis of the TaSUCL1 gene family. Within the TaSUCL1 genes, the exon-intron structure and motif composition exhibited significant similarity among members of the same evolutionary branch. Homology analysis and phylogenetic comparison of the SUCL1 genes in different plants offered valuable insights for studying the evolutionary characteristics of the SUCL1 genes. The expression levels of the TaSUCL1 genes in different tissues and under various metal stress conditions reveal its important role in plant growth and development. Gene function analysis demonstrated that TaSUCL1-1 silenced wheat plants exhibited a decrease in the total cadmium (Cd) concentrations and gene expression levels compared to the wild type (WT). Additionally, TaSUCL1-1 belonging to class c physically interacts with the β-amylase protein TaBMY1 as verified by yeast two-hybridization. This research provides a useful resource for further study of the function and molecular genetic mechanism of the SUCL1 gene family members.
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Affiliation(s)
- Liuliu Wu
- School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China; Sumy National Agrarian University, Sumy 40021, Ukraine; Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Lifan Cao
- Henan Academy of Sciences, Zhengzhou 450000, China
| | - Ye Tao
- School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China; Sumy National Agrarian University, Sumy 40021, Ukraine; Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China
| | | | - Haiyan Hu
- School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Chengwei Li
- School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Agricultural University, Zhengzhou 450000, China; Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China.
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Fan X, Lin H, Ding F, Wang M. Jasmonates Promote β-Amylase-Mediated Starch Degradation to Confer Cold Tolerance in Tomato Plants. PLANTS (BASEL, SWITZERLAND) 2024; 13:1055. [PMID: 38674464 PMCID: PMC11055051 DOI: 10.3390/plants13081055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024]
Abstract
Cold stress severely restricts growth and development, reduces yields, and impairs quality in tomatoes (Solanum lycopersicum). Amylase-associated starch degradation and soluble sugar accumulation have been implicated in adaptation and resistance to abiotic stress. Here, we report a β-amylase (BAM) gene, SlBAM3, which plays a central role in tomato cold tolerance. The expression of SlBAM3 was triggered by cold stress. SlBAM3 knockout using the CRISPR/Cas9 system retarded starch degradation and reduced soluble sugar accumulation in tomato plants, eventually attenuating cold tolerance. Expression analysis revealed that the SlBAM3 transcript level was boosted by MeJA. Furthermore, MYC2, an essential component of the JA signaling pathway, could bind to the SlBAM3 promoter and directly activate SlBAM3 transcription, as revealed by yeast one-hybrid and dual LUC assays. In addition, the suppression of MYC2 resulted in increased starch accumulation, decreased soluble sugar content, and reduced tolerance to cold stress in tomato plants. Taken together, these findings demonstrate that JA positively regulates β-amylase-associated starch degradation through the MYC2-SlBAM3 module in tomato during cold stress. The results of the present work expand our understanding of the mechanisms underlying BAM gene activation and starch catabolism under cold stress. The regulatory module of SlBAM3 can be further utilized to breed tomato cultivars with enhanced cold tolerance.
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Affiliation(s)
| | | | - Fei Ding
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (X.F.); (H.L.)
| | - Meiling Wang
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (X.F.); (H.L.)
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Li M, Chen X, Huang W, Wu K, Bai Y, Guo D, Guo C, Shu Y. Comprehensive Identification of the β-Amylase (BAM) Gene Family in Response to Cold Stress in White Clover. PLANTS (BASEL, SWITZERLAND) 2024; 13:154. [PMID: 38256708 PMCID: PMC10820397 DOI: 10.3390/plants13020154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024]
Abstract
White clover (Trifolium repens L.) is an allopolyploid plant and an excellent perennial legume forage. However, white clover is subjected to various stresses during its growth, with cold stress being one of the major limiting factors affecting its growth and development. Beta-amylase (BAM) is an important starch-hydrolyzing enzyme that plays a significant role in starch degradation and responses to environmental stress. In this study, 21 members of the BAM gene family were identified in the white clover genome. A phylogenetic analysis using BAMs from Arabidopsis divided TrBAMs into four groups based on sequence similarity. Through analysis of conserved motifs, gene duplication, synteny analysis, and cis-acting elements, a deeper understanding of the structure and evolution of TrBAMs in white clover was gained. Additionally, a gene regulatory network (GRN) containing TrBAMs was constructed; gene ontology (GO) annotation analysis revealed close interactions between TrBAMs and AMY (α-amylase) and DPE (4-alpha-glucanotransferase). To determine the function of TrBAMs under various tissues and stresses, RNA-seq datasets were analyzed, showing that most TrBAMs were significantly upregulated in response to biotic and abiotic stresses and the highest expression in leaves. These results were validated through qRT-PCR experiments, indicating their involvement in multiple gene regulatory pathways responding to cold stress. This study provides new insights into the structure, evolution, and function of the white clover BAM gene family, laying the foundation for further exploration of the functional mechanisms through which TrBAMs respond to cold stress.
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Affiliation(s)
- Manman Li
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (M.L.); (D.G.); (C.G.)
| | - Xiuhua Chen
- International Agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
| | - Wangqi Huang
- National Engineering Research Center for Ornamental Horticulture, Yunnan Flower Breeding Key Laboratory, Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
| | - Kaiyue Wu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (M.L.); (D.G.); (C.G.)
| | - Yan Bai
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (M.L.); (D.G.); (C.G.)
| | - Donglin Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (M.L.); (D.G.); (C.G.)
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (M.L.); (D.G.); (C.G.)
| | - Yongjun Shu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (M.L.); (D.G.); (C.G.)
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Yang Y, Sun F, Wang P, Yusuyin M, Kuerban W, Lai C, Li C, Ma J, Xiao F. Genome-Wide Identification and Preliminary Functional Analysis of BAM (β-Amylase) Gene Family in Upland Cotton. Genes (Basel) 2023; 14:2077. [PMID: 38003020 PMCID: PMC10671626 DOI: 10.3390/genes14112077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
The β-amylase (BAM) gene family encodes important enzymes that catalyze the conversion of starch to maltose in various biological processes of plants and play essential roles in regulating the growth and development of multiple plants. So far, BAMs have been extensively studied in Arabidopsis thaliana (A. thaliana). However, the characteristics of the BAM gene family in the crucial economic crop, cotton, have not been reported. In this study, 27 GhBAM genes in the genome of Gossypium hirsutum L (G. hirsutum) were identified by genome-wide identification, and they were divided into three groups according to sequence similarity and phylogenetic relationship. The gene structure, chromosome distribution, and collinearity of all GhBAM genes identified in the genome of G. hirsutum were analyzed. Further sequence alignment of the core domain of glucosyl hydrolase showed that all GhBAM family genes had the glycosyl hydrolase family 14 domain. We identified the BAM gene GhBAM7 and preliminarily investigated its function by transcriptional sequencing analysis, qRT-PCR, and subcellular localization. These results suggested that the GhBAM7 gene may influence fiber strength during fiber development. This systematic analysis provides new insight into the transcriptional characteristics of BAM genes in G. hirsutum. It may lay the foundation for further study of the function of these genes.
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Affiliation(s)
- Yanlong Yang
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (M.Y.); (C.L.); (C.L.)
- Xinjiang Academy of Agricultural Sciences Kuqa County Upland Cotton Test Station, Xinjiang Academy of Agricultural Sciences, Kuqa 842000, China; (P.W.); (W.K.)
| | - Fenglei Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Penglong Wang
- Xinjiang Academy of Agricultural Sciences Kuqa County Upland Cotton Test Station, Xinjiang Academy of Agricultural Sciences, Kuqa 842000, China; (P.W.); (W.K.)
| | - Mayila Yusuyin
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (M.Y.); (C.L.); (C.L.)
| | - Wumaierjiang Kuerban
- Xinjiang Academy of Agricultural Sciences Kuqa County Upland Cotton Test Station, Xinjiang Academy of Agricultural Sciences, Kuqa 842000, China; (P.W.); (W.K.)
| | - Chengxia Lai
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (M.Y.); (C.L.); (C.L.)
| | - Chunping Li
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (M.Y.); (C.L.); (C.L.)
| | - Jun Ma
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (M.Y.); (C.L.); (C.L.)
| | - Fei Xiao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
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Wang D, Zuo J, Liu S, Wang W, Lu Q, Hao X, Fang Z, Liang T, Sun Y, Guo C, Zhao C, Tang Y. BRI1 EMS SUPPRESSOR1 genes regulate abiotic stress and anther development in wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1219856. [PMID: 37621887 PMCID: PMC10446898 DOI: 10.3389/fpls.2023.1219856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/14/2023] [Indexed: 08/26/2023]
Abstract
BRI1 EMS SUPPRESSOR1 (BES1) family members are crucial downstream regulators that positively mediate brassinosteroid signaling, playing vital roles in the regulation of plant stress responses and anther development in Arabidopsis. Importantly, the expression profiles of wheat (Triticum aestivum L.) BES1 genes have not been analyzed comprehensively and systematically in response to abiotic stress or during anther development. In this study, we identified 23 BES1-like genes in common wheat, which were unevenly distributed on 17 out of 21 wheat chromosomes. Phylogenetic analysis clustered the BES1 genes into four major clades; moreover, TaBES1-3A2, TaBES1-3B2 and TaBES1-3D2 belonged to the same clade as Arabidopsis BES1/BZR1 HOMOLOG3 (BEH3) and BEH4, which participate in anther development. The expression levels of 23 wheat BES1 genes were assessed using real-time quantitative PCR under various abiotic stress conditions (drought, salt, heat, and cold), and we found that most TaBES1-like genes were downregulated under abiotic stress, particularly during drought stress. We therefore used drought-tolerant and drought-sensitive wheat cultivars to explore TaBES1 expression patterns under drought stress. TaBES1-3B2 and TaBES1-3D2 expression was high in drought-tolerant cultivars but substantially repressed in drought-sensitive cultivars, while TaBES1-6D presented an opposite pattern. Among genes preferentially expressed in anthers, TaBES1-3B2 and TaBES1-3D2 expression was substantially downregulated in thermosensitive genic male-sterile wheat lines compared to common wheat cultivar under sterile conditions, while we detected no obvious differences under fertile conditions. This result suggests that TaBES1-3B2 and TaBES1-3D2 might not only play roles in regulating drought tolerance, but also participate in low temperature-induced male sterility.
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Affiliation(s)
- Dezhou Wang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Jinghong Zuo
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Shan Liu
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Weiwei Wang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Qing Lu
- Agriculture College, Yangtze University, Jingzhou, China
| | - Xiaocong Hao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Zhaofeng Fang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Ting Liang
- Agriculture College, Yangtze University, Jingzhou, China
| | - Yue Sun
- Agriculture College, Yangtze University, Jingzhou, China
| | - Chunman Guo
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Changping Zhao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Yimiao Tang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
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Apriyanto A, Compart J, Fettke J. Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield. FRONTIERS IN PLANT SCIENCE 2023; 14:1220237. [PMID: 37554560 PMCID: PMC10405827 DOI: 10.3389/fpls.2023.1220237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023]
Abstract
The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.
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Affiliation(s)
- Ardha Apriyanto
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- Research and Development, PT. Astra Agro Lestari Tbk, Jakarta Timur, Indonesia
| | - Julia Compart
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
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Ozcan KE, Monroe JD. Maize β-amylase7 encodes two proteins using alternative transcriptional start sites: nuclear BAM7 and plastidic BAM2. PLANT PHYSIOLOGY 2023:kiad227. [PMID: 37067898 PMCID: PMC10400034 DOI: 10.1093/plphys/kiad227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
An unusual β-amylase7 (BAM7) gene in some angiosperms, including grasses such as maize (Zea mays), appears to encode two functionally distinct proteins; a nuclear-localized transcription factor (BAM7) and a plastid-localized starch hydrolase (BAM2). In Arabidopsis (Arabidopsis thaliana), these two proteins are encoded by separate genes on different chromosomes but their physiological functions are not well established. Using the maize BAM7 gene as a model, we detected two populations of transcripts by 5'-RACE that encode the predicted proteins. The two transcripts are apparently synthesized independently using separate core promoters about 1 kb apart, the second of which is located in the first intron of the full-length gene. The N-terminus of the shorter protein, ZmBAM7-S, begins near the 3' end of the first intron of ZmBAM7-L and starts with a predicted chloroplast transit peptide. We previously showed that ZmBAM7-S is catalytically active with properties like those of AtBAM2. Here, we report that ZmBAM7-S targets green fluorescent protein to plastids. The transcript encoding the longer protein, ZmBAM7-L, encodes an additional DNA-binding domain containing a functional nuclear localization signal. This putative dual-function gene originated at least 400 Mya, prior to the emergence of ferns, and has persisted in some angiosperms that lack a separate BAM2 gene. It appears to have been duplicated and subfunctionalized in at least four lineages of land plants, resulting in two genes resembling Arabidopsis BAM2 and BAM7. Targeting of two products from a single gene to different subcellular locations is not uncommon in plants, but it is unusual when they are predicted to serve completely different functions in the two locations.
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Affiliation(s)
- Kenan E Ozcan
- Department of Biology, James Madison University, Harrisonburg, VA 22807 USA
| | - Jonathan D Monroe
- Department of Biology, James Madison University, Harrisonburg, VA 22807 USA
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Yang T, Li H, Li L, Wei W, Huang Y, Xiong F, Wei M. Genome-wide characterization and expression analysis of α-amylase and β-amylase genes underlying drought tolerance in cassava. BMC Genomics 2023; 24:190. [PMID: 37024797 PMCID: PMC10080747 DOI: 10.1186/s12864-023-09282-9] [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: 10/01/2022] [Accepted: 03/29/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Starch hydrolysates are energy sources for plant growth and development, regulate osmotic pressure and transmit signals in response to both biological and abiotic stresses. The α-amylase (AMY) and the β-amylase (BAM) are important enzymes that catalyze the hydrolysis of plant starch. Cassava (Manihot esculenta Crantz) is treated as one of the most drought-tolerant crops. However, the mechanisms of how AMY and BAM respond to drought in cassava are still unknown. RESULTS Six MeAMY genes and ten MeBAM genes were identified and characterized in the cassava genome. Both MeAMY and MeBAM gene families contain four genes with alternative splicing. Tandem and fragment replications play important roles in the amplification of MeAMY and MeBAM genes. Both MeBAM5 and MeBAM10 have a BZR1/BES1 domain at the N-terminus, which may have transcription factor functions. The promoter regions of MeAMY and MeBAM genes contain a large number of cis-acting elements related to abiotic stress. MeAMY1, MeAMY2, MeAMY5, and MeBAM3 are proven as critical genes in response to drought stress according to their expression patterns under drought. The starch content, soluble sugar content, and amylase activity were significantly altered in cassava under different levels of drought stress. CONCLUSIONS These results provide fundamental knowledge for not only further exploring the starch metabolism functions of cassava under drought stress but also offering new perspectives for understanding the mechanism of how cassava survives and develops under drought.
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Affiliation(s)
- Taiyi Yang
- College of Agronomy, Guangxi University, Nanning, 530004, China
| | - Hengrui Li
- Guangxi South Subtropical Agricultural Sciences Research Institute, Chongzuo, 532406, China
| | - Liangwu Li
- College of Agronomy, Guangxi University, Nanning, 530004, China
| | - Wanling Wei
- Guangxi South Subtropical Agricultural Sciences Research Institute, Chongzuo, 532406, China
| | - Yuanhang Huang
- College of Agronomy, Guangxi University, Nanning, 530004, China
| | - Faqian Xiong
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Maogui Wei
- College of Agronomy, Guangxi University, Nanning, 530004, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory of Agro-environment and Agro-products Safety, Guangxi University, Nanning, 530004, Guangxi, China.
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11
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Yang X, Zhang Q, Yang N, Chang M, Ge Y, Zhou H, Li G. Traits variation of acorns and cupules during maturation process in Quercus variabilis and Quercus aliena. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:531-541. [PMID: 36774909 DOI: 10.1016/j.plaphy.2023.02.011] [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: 10/17/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Quercus variabilis and Quercus aliena are two native tree species in China, which have similar habitats, and their regeneration mainly depends on acorn dispersal. This study analyzed the contents of water, soluble sugar, starch, soluble protein, and total phenolics in acorns and cupules during the whole development process to explore the difference between species. Thereinto, starch and total phenol occupied the dominant roles as their high contents. The acorn starch contents increased sharply during development in both species, but the contents in Q. variabilis were almost twice those of Q. aliena when mature. Similarly, high expression levels of starch synthase, soluble starch synthase 2 (SSS2) were also found in the acorns of Q. variabilis. The total phenol contents in Q. variabilis acorns were high at the early stages, and decreased sharply to similar contents in Q. aliena when mature. Additionally, the cupules in Q. variabilis had high contents of total phenols during the whole development period. Similar trends were also found in the expression patterns of UGT84A13 and SDH. The high total phenols in acorns and cupules of Q. variabilis probably protect the acorns from Mechoris ursulus, as only Q. aliena suffered a severe pest infestation in the early development stages. This study not only clarifies the interspecific difference between storage and defense substances during the development process in acorns and cupules, but also deepens understanding the specialized mechanisms of plant-pest/animal interactions in Quercus.
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Affiliation(s)
- Xiong Yang
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China; Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China; Research Center for Efficient Cultivation and Innovation of Deciduous Oaks of State Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, China.
| | - Qian Zhang
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China; Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China; Research Center for Efficient Cultivation and Innovation of Deciduous Oaks of State Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, China.
| | - Ning Yang
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China; Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China; Research Center for Efficient Cultivation and Innovation of Deciduous Oaks of State Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, China.
| | - Muxi Chang
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China; Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China; Research Center for Efficient Cultivation and Innovation of Deciduous Oaks of State Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, China.
| | - Yaoyao Ge
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China; Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China; Research Center for Efficient Cultivation and Innovation of Deciduous Oaks of State Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, China.
| | - Huirong Zhou
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China; Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China; Research Center for Efficient Cultivation and Innovation of Deciduous Oaks of State Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, China.
| | - Guolei Li
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China; Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China; Research Center for Efficient Cultivation and Innovation of Deciduous Oaks of State Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, China.
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12
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Wang Z, Zhou Y, Ren XY, Wei K, Fan XL, Huang LC, Zhao DS, Zhang L, Zhang CQ, Liu QQ, Li QF. Co-Overexpression of Two Key Source Genes, OsBMY4 and OsISA3, Improves Multiple Key Traits of Rice Seeds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:615-625. [PMID: 36537359 DOI: 10.1021/acs.jafc.2c06039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Optimized source-sink interactions are determinants of both rice yield and quality. However, most source genes have not been well studied in rice, a major grain crop. In this study, OsBMY4 and OsISA3, the key β-amylase and debranching enzymes that control transient starch degradation in rice leaves, were co-overexpressed in rice in order to accelerate starch degradation efficiency and increase the sugar supply for sink organs. Systematic analyses of the transgenic rice indicated that co-overexpression of OsBMY4 and OsISA3 not only promoted rice yield and quality, but also improved seed germination and stress tolerance. Moreover, since the OsBMY4 gene has not been characterized, we generated osbmy4 mutants using CRIPSR/Cas9 gene editing, which helped to reveal the roles of β-amylase in rice yield and quality. This study demonstrated that specific modulation of the expression of some key source genes improves the source-sink balance and leads to improvements in multiple key traits of rice seeds.
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Affiliation(s)
- Zhen Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yu Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xin-Yu Ren
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ke Wei
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiao-Lei Fan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Li-Chun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Dong-Sheng Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Lin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qian-Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, Jiangsu 225009, China
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13
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Liu J, Miao H, Wang Y, Zhang J, Zhang J, Zhen Y, Wang J, Jia C, Xu B, Li X, Xie J, Jin Z. Elucidating the role of MaBAM9b in starch degradation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111497. [PMID: 36244523 DOI: 10.1016/j.plantsci.2022.111497] [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: 07/22/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Banana is a typical starch conversion fruit. The high content of starch at harvest is quickly digested and converted to soluble sugars during the postharvest ripening process, ultimately contributing to fruit flavor. This process is regulated in a complex manner by genes and environmental factors. MaBAM9b is one of the main enzyme genes previously found by transcriptomic analysis to be highly expressed in banana fruit. However, its exact role in starch degradation remains unclear. Here, full-length MaBAM9b was isolated from banana fruit, and its subcellular localization, protein expression, and transient expression in banana fruit slices were investigated. In addition, sense and anti-sense MaBAM9b were transformed into rice (Oryza sativa L. japonica. cv. 'Nipponbare') to identify the function of MaBAM9b. MaBAM9b was 1599 bp and encoded 532 amino acids. It contained two conserved domains of PLN02803 and glycosyl hydrolase family 14 and was localized in the chloroplast. The protein expression pattern of MaBAM9b remained consistently high throughout banana fruit ripening and starch degradation. Transient overexpression or inhibition of MaBAM9b in banana fruit greatly improved or suppressed starch degradation. Genetic modification of rice indicated that overexpression of MaBAM9b greatly improved starch degradation and seed germination, while inhibition of its expression suppressed these biological processes. These results support the key role of MaBAM9b in starch degradation and provide a target gene for banana fruit quality improvement and biological breeding.
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Affiliation(s)
- Juhua Liu
- Sanya Research Institute; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101 Haikou, China; School of Horticulture, Hainan University, 571100 Haikou, China.
| | - Hongxia Miao
- Sanya Research Institute; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101 Haikou, China
| | - Yudi Wang
- School of Horticulture, Hainan University, 571100 Haikou, China
| | - Jianbin Zhang
- Sanya Research Institute; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101 Haikou, China
| | - Jing Zhang
- Sanya Research Institute; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101 Haikou, China
| | - Yunke Zhen
- Sanya Research Institute; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101 Haikou, China
| | - Jingyi Wang
- Sanya Research Institute; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101 Haikou, China
| | - Caihong Jia
- Sanya Research Institute; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101 Haikou, China
| | - Biyu Xu
- Sanya Research Institute; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101 Haikou, China
| | - Xinguo Li
- School of Horticulture, Hainan University, 571100 Haikou, China.
| | - Jianghui Xie
- Sanya Research Institute; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101 Haikou, China.
| | - Zhiqiang Jin
- Sanya Research Institute; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101 Haikou, China.
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14
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Kulakova A, Efremov G, Shchennikova A, Kochieva E. Dependence of the content of starch and reducing sugars on the level of expression of the genes of β-amylases StBAM1 and StBAM9 and the amylase inhibitor StAI during long-term low-temperature storage of potato tubers. Vavilovskii Zhurnal Genet Selektsii 2022; 26:507-514. [PMID: 36313822 PMCID: PMC9556308 DOI: 10.18699/vjgb-22-62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 11/06/2022] Open
Abstract
Solanum tuberosum L. is the most important non-grain starch crop with a potential yield of 38-48 t/ha and a starch content of 13.2-18.7 %. Potato tubers are stored at a low temperature (2-4 °C) in a state of physiological dormancy. A disadvantage of this type of storage is the degradation of starch and the accumulation of reducing sugars (cold-induced sweetening), including due to an increase in the activity of β-amylases that hydrolyze starch to maltose. In this study, a comparative analysis of the β-amylase (StBAM1, StBAM9) and amylase inhibitor (StAI ) gene expression, as well as starch and reducing sugar content in tubers during long-term low-temperature storage (September, February, April) was performed using potato cultivars Nadezhda, Barin, Krasavchik, Severnoe siyanie and Utro. The β-amylase genes, StBAM9 and one of the two StBAM1 homologs (with the highest degree of homology with AtBAM1), were selected based on phylogenetic analysis data. Evaluation of the expression of these genes and the amylase inhibitor gene showed a tendency to decrease in transcription for all analyzed cultivars. The starch content also significantly decreased during tuber storage. The amount of reducing sugars increased in the September-April period, while in February-April, their content did not change (Krasavchik), decreased (Barin, Severnoe siyanie) or continued to grow (Utro, Nadezhda). It can be assumed that the gene activity of StBAM1 and StBAM9 correlates with the amount of starch (positively) and monosaccharides (negatively). The level of StAI expression, in turn, may be directly dependent on the level of StBAM1 expression. At the same time, there is no relationship between the degree of cultivar predisposition to cold-induced sweetening and the expression profile of the StBAM1, StBAM9, and StAI genes.
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Affiliation(s)
- A.V. Kulakova
- Institute of Bioengineering, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russia
| | - G.I. Efremov
- Institute of Bioengineering, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russia
| | - A.V. Shchennikova
- Institute of Bioengineering, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russia
| | - E.Z. Kochieva
- Institute of Bioengineering, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russia
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15
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Shi H, Li X, Lv M, Li J. BES1/BZR1 Family Transcription Factors Regulate Plant Development via Brassinosteroid-Dependent and Independent Pathways. Int J Mol Sci 2022; 23:ijms231710149. [PMID: 36077547 PMCID: PMC9478962 DOI: 10.3390/ijms231710149] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 01/04/2023] Open
Abstract
The BES1/BZR1 family is a plant-specific small group of transcription factors possessing a non-canonical bHLH domain. Genetic and biochemical analyses within the last two decades have demonstrated that members of this family are key transcription factors in regulating the expression of brassinosteroid (BR) response genes. Several recent genetic and evolutionary studies, however, have clearly indicated that the BES1/BZR1 family transcription factors also function in regulating several aspects of plant development via BR-independent pathways, suggesting they are not BR specific. In this review, we summarize our current understanding of this family of transcription factors, the mechanisms regulating their activities, DNA binding motifs, and target genes. We selectively discuss a number of their biological functions via BR-dependent and particularly independent pathways, which were recently revealed by loss-of-function genetic analyses. We also highlight a few possible future directions.
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16
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Sun F, Palayam M, Shabek N. Structure of maize BZR1-type β-amylase BAM8 provides new insights into its noncatalytic adaptation. J Struct Biol 2022; 214:107885. [PMID: 35961473 DOI: 10.1016/j.jsb.2022.107885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 11/28/2022]
Abstract
Plant β-amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (β/α)8 barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. The noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of β-amylase domain of Zea mays BAM8/BES1/BZR1-5 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.
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Affiliation(s)
- Fuai Sun
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Malathy Palayam
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
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17
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Liao Y, Liu Z, Gichira AW, Yang M, Mbichi RW, Meng L, Wan T. Deep evaluation of the evolutionary history of the Heat Shock Factor (HSF) gene family and its expansion pattern in seed plants. PeerJ 2022; 10:e13603. [PMID: 35966928 PMCID: PMC9373977 DOI: 10.7717/peerj.13603] [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: 01/07/2021] [Accepted: 05/26/2022] [Indexed: 01/17/2023] Open
Abstract
Heat shock factor (HSF) genes are essential in some of the basic developmental pathways in plants. Despite extensive studies on the structure, functional diversification, and evolution of HSF genes, their divergence history and gene duplication pattern remain unknown. To further illustrate the probable divergence patterns in these subfamilies, we analyzed the evolutionary history of HSF genes using phylogenetic reconstruction and genomic syntenic analyses, taking advantage of the increased sampling of genomic data from pteridophytes, gymnosperms and basal angiosperms. We identified a novel clade that includes HSFA2, HSFA6, HSFA7, and HSFA9 with a complex relationship, which is very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We hypothesized that HSFA9 derives from HSFA2 through gene duplication in eudicots at the ancestral state, and then expanded in a lineage-specific way. Our findings indicate that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in the most recent common ancestors of monocots. We also presumed that HSFC2 derives from HSFC1 in ancestral monocots. This work proposes that during the radiation of flowering plants, an era during which there was a differentiation of angiosperms, the size of the HSF gene family was also being adjusted with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication, gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying the evolutionary history of this multigene family.
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Affiliation(s)
- Yiying Liao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Zhiming Liu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Andrew W. Gichira
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Min Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Ruth Wambui Mbichi
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Linping Meng
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Tao Wan
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
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18
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Ma Y, Han Y, Feng X, Gao H, Cao B, Song L. Genome-wide identification of BAM (β-amylase) gene family in jujube (Ziziphus jujuba Mill.) and expression in response to abiotic stress. BMC Genomics 2022; 23:438. [PMID: 35698031 PMCID: PMC9195466 DOI: 10.1186/s12864-022-08630-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Elevated temperature and drought stress have substantial impacts on fruit quality, especially in terms of sugar metabolism and content. β-Amylase (BAM) plays a critical role in regulating jujube fruit sugar levels and abiotic stress response. Nevertheless, little is known about the regulatory functions of the BAM genes in jujube fruit. Results Nine jujube BAM genes were identified, clustered into four groups, and characterized to elucidate their structure, function, and distribution. Multiple sequence alignment and gene structure analysis showed that all ZjBAM genes contain Glu-186 and Glu-380 residues and are highly conserved. Phylogenetic and synteny analysis further indicated that the ZjBAM gene family is evolutionarily conserved and formed collinear pairs with the BAM genes of peach, apple, poplar, Arabidopsis thaliana, and cucumber. A single tandem gene pair was found within the ZjBAM gene family and is indicative of putative gene duplication events. We also explored the physicochemical properties, conserved motifs, and chromosomal and subcellular localization of ZjBAM genes as well as the interaction networks and 3D structures of ZjBAM proteins. A promoter cis-acting element analysis suggested that ZjBAM promoters comprise elements related to growth, development, phytohormones, and stress response. Furthermore, a metabolic pathways annotation analysis showed that ZjBAMs are significantly upregulated in the starch and sucrose metabolism, thereby controlling starch-maltose interconversion and hydrolyzing starch to maltose. Transcriptome and qRT-PCR analyses revealed that ZjBAMs respond positively to elevated temperature and drought stress. Specifically, ZjBAM1, ZjBAM2, ZjBAM5, and ZjBAM6 are significantly upregulated in response to severe drought. Bimolecular fluorescence complementation analysis demonstrated ZjBAM1-ZjAMY3, ZjBAM8-ZjDPE1, and ZjBAM7-ZjDPE1 protein interactions that were mainly present in the plasma membrane and nucleus. Conclusion The jujube BAM gene family exhibits high evolutionary conservation. The various expression patterns of ZjBAM gene family members indicate that they play key roles in jujube growth, development, and abiotic stress response. Additionally, ZjBAMs interact with α-amylase and glucanotransferase. Collectively, the present study provides novel insights into the structure, evolution, and functions of the jujube BAM gene family, thus laying a foundation for further exploration of ZjBAM functional mechanisms in response to elevated temperature and drought stress, while opening up avenues for the development of economic forests in arid areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08630-5.
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Affiliation(s)
- Yaping Ma
- School of Agriculture, Ningxia University, Yinchuan, 750021, China.,College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yaru Han
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Xuerui Feng
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Handong Gao
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China. .,Southern Tree Seed Inspection Center, Nanjing, 210037, China.
| | - Bing Cao
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Lihua Song
- School of Agriculture, Ningxia University, Yinchuan, 750021, China.
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19
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Biochemical Insights into the functionality of a novel thermostable β-amylase from Dioclea reflexa. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Ravenburg CM, Riney MB, Monroe JD, Berndsen CE. The BAM7 gene in Zea mays encodes a protein with similar structural and catalytic properties to Arabidopsis BAM2. Acta Crystallogr D Struct Biol 2022; 78:560-570. [PMID: 35503205 PMCID: PMC9063847 DOI: 10.1107/s2059798322002169] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/23/2022] [Indexed: 11/10/2022] Open
Abstract
Starch accumulates in the plastids of green plant tissues during the day to provide carbon for metabolism at night. Starch hydrolysis is catalyzed by members of the β-amylase (BAM) family, which in Arabidopsis thaliana (At) includes nine structurally and functionally diverse members. One of these enzymes, AtBAM2, is a plastid-localized enzyme that is unique among characterized β-amylases since it is tetrameric and exhibits sigmoidal kinetics. Sequence alignments show that the BAM domains of AtBAM7, a catalytically inactive, nuclear-localized transcription factor with an N-terminal DNA-binding domain, and AtBAM2 are more closely related to each other than they are to any other AtBAM. Since the BAM2 gene is found in more ancient lineages, it was hypothesized that the BAM7 gene evolved from BAM2. However, analysis of the genomes of 48 flowering plants revealed 12 species that appear to possess a BAM7 gene but lack a BAM2 gene. Upon closer inspection, these BAM7 proteins have a greater percent identity to AtBAM2 than to AtBAM7, and they share all of the AtBAM2 functional residues that BAM7 proteins normally lack. It is hypothesized that these genes may encode BAM2-like proteins although they are currently annotated as BAM7-like genes. To test this hypothesis, a cDNA for the short form of corn BAM7 (ZmBAM7-S) was designed for expression in Escherichia coli. Small-angle X-ray scattering data indicate that ZmBAM7-S has a tetrameric solution structure that is more similar to that of AtBAM2 than to that of AtBAM1. In addition, partially purified ZmBAM7-S is catalytically active and exhibits sigmoidal kinetics. Together, these data suggest that some BAM7 genes may encode a functional BAM2. Exploring and understanding the β-amylase gene structure could have an impact on the current annotation of genes.
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21
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David LC, Lee SK, Bruderer E, Abt MR, Fischer-Stettler M, Tschopp MA, Solhaug EM, Sanchez K, Zeeman SC. BETA-AMYLASE9 is a plastidial nonenzymatic regulator of leaf starch degradation. PLANT PHYSIOLOGY 2022; 188:191-207. [PMID: 34662400 PMCID: PMC8774843 DOI: 10.1093/plphys/kiab468] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
β-Amylases (BAMs) are key enzymes of transitory starch degradation in chloroplasts, a process that buffers the availability of photosynthetically fixed carbon over the diel cycle to maintain energy levels and plant growth at night. However, during vascular plant evolution, the BAM gene family diversified, giving rise to isoforms with different compartmentation and biological activities. Here, we characterized BETA-AMYLASE 9 (BAM9) of Arabidopsis (Arabidopsis thaliana). Among the BAMs, BAM9 is most closely related to BAM4 but is more widely conserved in plants. BAM9 and BAM4 share features including their plastidial localization and lack of measurable α-1,4-glucan hydrolyzing capacity. BAM4 is a regulator of starch degradation, and bam4 mutants display a starch-excess phenotype. Although bam9 single mutants resemble the wild-type (WT), genetic experiments reveal that the loss of BAM9 markedly enhances the starch-excess phenotypes of mutants already impaired in starch degradation. Thus, BAM9 also regulates starch breakdown, but in a different way. Interestingly, BAM9 gene expression is responsive to several environmental changes, while that of BAM4 is not. Furthermore, overexpression of BAM9 in the WT reduced leaf starch content, but overexpression in bam4 failed to complement fully that mutant's starch-excess phenotype, suggesting that BAM9 and BAM4 are not redundant. We propose that BAM9 activates starch degradation, helping to manage carbohydrate availability in response to fluctuations in environmental conditions. As such, BAM9 represents an interesting gene target to explore in crop species.
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Affiliation(s)
- Laure C David
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich CH-8092, Switzerland
| | - Sang-Kyu Lee
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich CH-8092, Switzerland
| | - Eduard Bruderer
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich CH-8092, Switzerland
| | - Melanie R Abt
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich CH-8092, Switzerland
| | - Michaela Fischer-Stettler
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich CH-8092, Switzerland
| | - Marie-Aude Tschopp
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich CH-8092, Switzerland
| | - Erik M Solhaug
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich CH-8092, Switzerland
| | - Katarzyna Sanchez
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich CH-8092, Switzerland
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich CH-8092, Switzerland
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22
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Fang Y, Jiang J, Hou X, Guo J, Li X, Zhao D, Xie X. Plant protein-coding gene families: Their origin and evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:995746. [PMID: 36160967 PMCID: PMC9490259 DOI: 10.3389/fpls.2022.995746] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/15/2022] [Indexed: 05/13/2023]
Abstract
Steady advances in genome sequencing methods have provided valuable insights into the evolutionary processes of several gene families in plants. At the core of plant biodiversity is an extensive genetic diversity with functional divergence and expansion of genes across gene families, representing unique phenomena. The evolution of gene families underpins the evolutionary history and development of plants and is the subject of this review. We discuss the implications of the molecular evolution of gene families in plants, as well as the potential contributions, challenges, and strategies associated with investigating phenotypic alterations to explain the origin of plants and their tolerance to environmental stresses.
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Affiliation(s)
- Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiaolong Hou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Jiyuan Guo
- Department of Resources and Environment, Moutai Institute, Zunyi, China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Degang Zhao
- Key Laboratory of Mountain Plant Resources Protection and Germplasm Innovation, Ministry of Education, College of Life Sciences, Institute of Agricultural Bioengineering, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- *Correspondence: Degang Zhao,
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- Xin Xie,
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23
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Abbasi AZ, Bilal M, Khurshid G, Yiotis C, Zeb I, Hussain J, Baig A, Shah MM, Chaudhary SU, Osborne B, Ahmad R. Expression of cyanobacterial genes enhanced CO 2 assimilation and biomass production in transgenic Arabidopsis thaliana. PeerJ 2021; 9:e11860. [PMID: 34434649 PMCID: PMC8359801 DOI: 10.7717/peerj.11860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/05/2021] [Indexed: 01/01/2023] Open
Abstract
Background Photosynthesis is a key process in plants that is compromised by the oxygenase activity of Rubisco, which leads to the production of toxic compound phosphoglycolate that is catabolized by photorespiratory pathway. Transformation of plants with photorespiratory bypasses have been shown to reduce photorespiration and enhance plant biomass. Interestingly, engineering of a single gene from such photorespiratory bypasses has also improved photosynthesis and plant productivity. Although single gene transformations may not completely reduce photorespiration, increases in plant biomass accumulation have still been observed indicating an alternative role in regulating different metabolic processes. Therefore, the current study was aimed at evaluating the underlying mechanism (s) associated with the effects of introducing a single cyanobacterial glycolate decarboxylation pathway gene on photosynthesis and plant performance. Methods Transgenic Arabidopsis thaliana plants (GD, HD, OX) expressing independently cyanobacterial decarboxylation pathway genes i.e., glycolate dehydrogenase, hydroxyacid dehydrogenase, and oxalate decarboxylase, respectively, were utilized. Photosynthetic, fluorescence related, and growth parameters were analyzed. Additionally, transcriptomic analysis of GD transgenic plants was also performed. Results The GD plants exhibited a significant increase (16%) in net photosynthesis rate while both HD and OX plants showed a non-significant (11%) increase as compared to wild type plants (WT). The stomatal conductance was significantly higher (24%) in GD and HD plants than the WT plants. The quantum efficiencies of photosystem II, carbon dioxide assimilation and the chlorophyll fluorescence-based photosynthetic electron transport rate were also higher than WT plants. The OX plants displayed significant reductions in the rate of photorespiration relative to gross photosynthesis and increase in the ratio of the photosynthetic electron flow attributable to carboxylation reactions over that attributable to oxygenation reactions. GD, HD and OX plants accumulated significantly higher biomass and seed weight. Soluble sugars were significantly increased in GD and HD plants, while the starch levels were higher in all transgenic plants. The transcriptomic analysis of GD plants revealed 650 up-regulated genes mainly related to photosynthesis, photorespiratory pathway, sucrose metabolism, chlorophyll biosynthesis and glutathione metabolism. Conclusion This study revealed the potential of introduced cyanobacterial pathway genes to enhance photosynthetic and growth-related parameters. The upregulation of genes related to different pathways provided evidence of the underlying mechanisms involved particularly in GD plants. However, transcriptomic profiling of HD and OX plants can further help to identify other potential mechanisms involved in improved plant productivity.
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Affiliation(s)
- Anum Zeb Abbasi
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, KP, Pakistan
| | - Misbah Bilal
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, KP, Pakistan
| | - Ghazal Khurshid
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, KP, Pakistan
| | - Charilaos Yiotis
- School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin, Ireland.,Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Iftikhar Zeb
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, KP, Pakistan
| | - Jamshaid Hussain
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, KP, Pakistan
| | - Ayesha Baig
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, KP, Pakistan
| | - Mohammad Maroof Shah
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, KP, Pakistan
| | - Safee Ullah Chaudhary
- Department of Biology, School of Science and Engineering, Lahore University of Management Sciences, Lahore, Punjab, Pakistan
| | - Bruce Osborne
- School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Raza Ahmad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, KP, Pakistan
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24
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Zhang DL, Wang Y, Jia BC, Tian XQ, Chu J, Yin HB, Jameson PE, Chen SH, Guo SL. Genome-Wide Identification and Expression Analysis of the β-Amylase Gene Family in Chenopodium quinoa. DNA Cell Biol 2021; 40:936-948. [PMID: 34042512 DOI: 10.1089/dna.2020.5911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
β-Amylase (BAM) is an important starch hydrolase, playing a role in a variety of plant growth and development processes. In this study, 22 BAM gene family members (GFMs) were identified in quinoa (Chenopodium quinoa), an ancient crop gaining modern consumer acceptance because of its nutritional qualities. The genetic structure, phylogenetic and evolutionary relationships, and expression patterns of CqBAM GFMs in different tissues, were analyzed. Phylogenetic analyses assigned the CqBAMs, AtBAMs, and OsBAMs into four clades. The CqBAM gene family had expanded due to segmental duplication. RNA-seq analysis revealed expression of the duplicated pairs to be similar, with the expression of CqBAM GFM pairs showing a degree of tissue specificity that was confirmed by reverse transcription quantitative PCR (RT-qPCR). Several CqBAM GFMs were also responsive to abiotic stresses in shoots and/or roots. In conclusion, the BAM gene family in quinoa was identified and systematically analyzed using bioinformatics and experimental methods. These results will help to elucidate the evolutionary relationship and biological functions of the BAM gene family in quinoa.
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Affiliation(s)
| | - Yu Wang
- College of Life Sciences, Yantai University, Yantai, China
| | - Bing-Chen Jia
- College of Life Sciences, Yantai University, Yantai, China
| | - Xiao-Qin Tian
- College of Life Sciences, Yantai University, Yantai, China
| | - Jing Chu
- College of Life Sciences, Yantai University, Yantai, China
| | - Hai-Bo Yin
- College of Life Sciences, Yantai University, Yantai, China
| | - Paula E Jameson
- College of Life Sciences, Yantai University, Yantai, China.,School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Shi-Hua Chen
- College of Life Sciences, Yantai University, Yantai, China
| | - Shan-Li Guo
- College of Life Sciences, Yantai University, Yantai, China
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25
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Paul JS, Gupta N, Beliya E, Tiwari S, Jadhav SK. Aspects and Recent Trends in Microbial α-Amylase: a Review. Appl Biochem Biotechnol 2021; 193:2649-2698. [PMID: 33715051 DOI: 10.1007/s12010-021-03546-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/26/2021] [Indexed: 10/21/2022]
Abstract
α-Amylases are the oldest and versatile starch hydrolysing enzymes which can replace chemical hydrolysis of starch in industries. It cleaves the α-(1,4)-D-glucosidic linkage of starch and other related polysaccharides to yield simple sugars like glucose, maltose and limit dextrin. α-Amylase covers about 30% shares of the total enzyme market. On account of their superior features, α-amylase is the most widely used among all the existing amylases for hydrolysis of polysaccharides. Endo-acting α-amylase of glycoside hydrolase family 13 is an extensively used biocatalyst and has various biotechnological applications like in starch processing, detergent, textile, paper and pharmaceutical industries. Apart from these, it has some novel applications including polymeric material for drug delivery, bioremediating agent, biodemulsifier and biofilm inhibitor. The present review will accomplish the research gap by providing the unexplored aspects of microbial α-amylase. It will allow the readers to know about the works that have already been done and the latest trends in this field. The manuscript has covered the latest immobilization techniques and the site-directed mutagenesis approaches which are readily being performed to confer the desirable property in wild-type α-amylases. Furthermore, it will state the inadequacies and the numerous obstacles coming in the way of its production during upstream and downstream steps and will also suggest some measures to obtain stable and industrial-grade α-amylase.
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Affiliation(s)
- Jai Shankar Paul
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India
| | - Nisha Gupta
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India
| | - Esmil Beliya
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India.,Department of Botany, Govt. College, Bichhua, Chhindwara, MP, 480111, India
| | - Shubhra Tiwari
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India
| | - Shailesh Kumar Jadhav
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India.
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26
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Tsamir-Rimon M, Ben-Dor S, Feldmesser E, Oppenhimer-Shaanan Y, David-Schwartz R, Samach A, Klein T. Rapid starch degradation in the wood of olive trees under heat and drought is permitted by three stress-specific beta amylases. THE NEW PHYTOLOGIST 2021; 229:1398-1414. [PMID: 32880972 DOI: 10.1111/nph.16907] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Carbon reserve use is a major drought response in trees, enabling tree survival in conditions prohibiting photosynthesis. However, regulation of starch metabolism under drought at the whole-tree scale is still poorly understood. To this end, we combined measurements of nonstructural carbohydrates (NSCs), tree physiology and gene expression. The experiment was conducted outside on olive trees in pots under 90 d of seasonal spring to summer warming. Half of the trees were also subjected to limited water conditions for 28 d. Photosynthesis decreased in dehydrating trees from 19 to 0.5 µmol m-2 s-1 during the drought period. Starch degradation and mannitol production were a major drought response, with mannitol increasing to 71% and 41% out of total NSCs in shoots and roots, respectively. We identified the gene family members potentially relevant either to long-term or stress-induced carbon storage. Partitioning of expression patterns among β amylase and starch synthase family members was observed, with three β amylases possibly facilitating the rapid starch degradation under heat and drought. Our results suggest a group of stress-related, starch metabolism genes, correlated with NSC fluctuations during drought and recovery. The daily starch metabolism gene expression was different from the stress-mode starch metabolism pattern, where some genes are uniquely expressed during the stress-mode response.
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Affiliation(s)
- Mor Tsamir-Rimon
- Plant & Environmental Sciences Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Shifra Ben-Dor
- Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ester Feldmesser
- Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yaara Oppenhimer-Shaanan
- Plant & Environmental Sciences Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Rakefet David-Schwartz
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7505101, Israel
| | - Alon Samach
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Tamir Klein
- Plant & Environmental Sciences Department, Weizmann Institute of Science, Rehovot, 76100, Israel
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27
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Sidar A, Albuquerque ED, Voshol GP, Ram AFJ, Vijgenboom E, Punt PJ. Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms. Front Bioeng Biotechnol 2020; 8:871. [PMID: 32850729 PMCID: PMC7410926 DOI: 10.3389/fbioe.2020.00871] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.
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Affiliation(s)
- Andika Sidar
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Department of Food Science and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Erica D Albuquerque
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Sun Pharmaceutical Industries Europe BV., Hoofddorp, Netherlands
| | - Gerben P Voshol
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
| | - Arthur F J Ram
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Erik Vijgenboom
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Peter J Punt
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
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28
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Fernie AR, Wen W. Editorial overview: Evolution of metabolic diversity. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:A1-A4. [PMID: 32546303 DOI: 10.1016/j.pbi.2020.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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29
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Abt MR, Zeeman SC. Evolutionary innovations in starch metabolism. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:109-117. [PMID: 32428846 DOI: 10.1016/j.pbi.2020.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 05/23/2023]
Abstract
The traditional view of starch metabolism has focused on the multiplicity of enzymes and enzyme isoforms contributing to the production of the constituent polymers, amylopectin and amylose. However, knowledge of these enzymes has not provided a full insight into many aspects of starch biosynthesis. This enzyme-centered view has recently been augmented by the discovery and characterization of novel proteins with proposed regulatory, scaffolding, and interactive roles. This begins to reveal an unprecedented level of complexity beyond mere glucan biosynthesis, enabling us to envisage how starch granules are initiated and grow into specific forms, allowing it to serve biological roles beyond just carbohydrate storage. This review focuses on very recent findings in this vibrant field, highlighting the evolutionary novelty.
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Affiliation(s)
- Melanie R Abt
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland.
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30
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Monroe JD. Involvement of five catalytically active Arabidopsis β-amylases in leaf starch metabolism and plant growth. PLANT DIRECT 2020; 4:e00199. [PMID: 32072133 PMCID: PMC7011640 DOI: 10.1002/pld3.199] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/16/2019] [Accepted: 12/27/2019] [Indexed: 05/14/2023]
Abstract
Starch degradation in chloroplasts requires β-amylase (BAM) activity, but in Arabidopsis, there are nine BAM proteins, five of which are thought to be catalytic. Although single-gene knockouts revealed the necessity of BAM3 for starch degradation, contributions of other BAMs are poorly understood. Moreover, it is not possible to detect the contribution of individual BAMs in plants containing multiple active BAMs. Therefore, we constructed a set of five quadruple mutants each expressing only one catalytically active BAM, and a quintuple mutant missing all of these BAMs (B-Null). Using these mutants, we assessed the influence of each individual BAM on plant growth and on leaf starch degradation. Both BAM1 and BAM3 alone support wild-type (WT) levels of growth. BAM3 alone is sufficient to degrade leaf starch completely whereas BAM1 alone can only partially degrade leaf starch. In contrast, BAM2, BAM5, and BAM6 have no detectable effect on starch degradation or plant growth, being comparable with the B-Null plants. B-Null plant extracts contained no measurable amylase activity, whereas BAM3 and BAM1 contributed about 70% and 14% of the WT activity, respectively. BAM2 activity was low but detectable and BAM6 contributed no measurable activity. Interestingly, activity of BAM1 and BAM3 in the mutants varied little developmentally or diurnally, and did not increase appreciably in response to osmotic or cold stress. With these genetic lines, we now have new opportunities to investigate members of this diverse gene family.
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31
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Brodribb TJ, Sussmilch F, McAdam SAM. From reproduction to production, stomata are the master regulators. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:756-767. [PMID: 31596990 DOI: 10.1111/tpj.14561] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/14/2019] [Accepted: 10/03/2019] [Indexed: 05/22/2023]
Abstract
The best predictor of leaf level photosynthetic rate is the porosity of the leaf surface, as determined by the number and aperture of stomata on the leaf. This remarkable correlation between stomatal porosity (or diffusive conductance to water vapour gs ) and CO2 assimilation rate (A) applies to all major lineages of vascular plants (Figure 1) and is sufficiently predictable that it provides the basis for the model most widely used to predict water and CO2 fluxes from leaves and canopies. Yet the Ball-Berry formulation is only a phenomenological approximation that captures the emergent character of stomatal behaviour. Progressing to a more mechanistic prediction of plant gas exchange is challenging because of the diversity of biological components regulating stomatal action. These processes are the product of more than 400 million years of co-evolution between stomatal, vascular and photosynthetic tissues. Both molecular and structural components link the abiotic world of the whole plant with the turgor pressure of the epidermis and guard cells, which ultimately determine stomatal pore size and porosity to water and CO2 exchange (New Phytol., 168, 2005, 275). In this review we seek to simplify stomatal behaviour by using an evolutionary perspective to understand the principal selective pressures involved in stomatal evolution, thus identifying the primary regulators of stomatal aperture. We start by considering the adaptive process that has locked together the regulation of water and carbon fluxes in vascular plants, finally examining specific evidence for evolution in the proteins responsible for regulating guard cell turgor.
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Affiliation(s)
- Timothy J Brodribb
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Frances Sussmilch
- Institute for Molecular Plant Physiology and Biophysics, University of Wurzburg, Wuerzburg, Bavaria, Germany
| | - Scott A M McAdam
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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Yu X, Jin H, Fu X, Yang Q, Yuan F. Quantitative proteomic analyses of two soybean low phytic acid mutants to identify the genes associated with seed field emergence. BMC PLANT BIOLOGY 2019; 19:569. [PMID: 31856712 PMCID: PMC6921446 DOI: 10.1186/s12870-019-2201-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 12/12/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Seed germination is essential to crop growth and development, and ultimately affects its harvest. It is difficult to breed soybeans low in phytic acid with a higher seed field emergence. Although additional management and selection could overcome the phytate reduction, the mechanisms of seed germination remain unknown. RESULTS A comparative proteomic analysis was conducted between two low phytic acid (LPA) soybean mutants (TW-1-M and TW-1), both of which had a deletion of 2 bp in the GmMIPS1 gene. However, the TW-1 seeds showed a significantly lower field emergence compared to the TW-1-M. There were 282 differentially accumulated proteins (DAPs) identified between two mutants at the three stages. Among these DAPs, 80 were down-accumulated and 202 were up-accumulated. Bioinformatic analysis showed that the identified proteins were related to functional categories of oxidation reduction, response to stimulus and stress, dormancy and germination processes and catalytic activity. KEGG analysis showed that these DAPs were mainly involved in energy metabolism and anti-stress pathways. Based upon the conjoint analysis of DAPs with the differentially expressed genes (DEGs) previously published among three germination stages in two LPA mutants, 30 shared DAPs/DEGs were identified with different patterns, including plant seed protein, beta-amylase, protein disulfide-isomerase, disease resistance protein, pyrophosphate-fructose 6-phosphate 1-phosphotransferase, cysteine proteinase inhibitor, non-specific lipid-transfer protein, phosphoenolpyruvate carboxylase and acyl-coenzyme A oxidase. CONCLUSIONS Seed germination is a very complex process in LPA soybean mutants. The TW-1-M and TW-1 showed many DAPs involved in seed germination. The differential accumulation of these proteins could result in the difference of seed field emergence between the two mutants. The high germination rate in the TW-1-M might be strongly attributed to reactive oxygen species-related and plant hormone-related genes. All these findings would help us further explore the germination mechanisms in LPA crops.
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Affiliation(s)
- Xiaomin Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hangxia Jin
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xujun Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qinghua Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fengjie Yuan
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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