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Moradi A, Lung SC, Chye ML. Interaction of Soybean ( Glycine max (L.) Merr.) Class II ACBPs with MPK2 and SAPK2 Kinases: New Insights into the Regulatory Mechanisms of Plant ACBPs. PLANTS (BASEL, SWITZERLAND) 2024; 13:1146. [PMID: 38674555 PMCID: PMC11055065 DOI: 10.3390/plants13081146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/06/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
Plant acyl-CoA-binding proteins (ACBPs) function in plant development and stress responses, with some ACBPs interacting with protein partners. This study tested the interaction between two Class II GmACBPs (Glycine max ACBPs) and seven kinases, using yeast two-hybrid (Y2H) assays and bimolecular fluorescence complementation (BiFC). The results revealed that both GmACBP3.1 and GmACBP4.1 interact with two soybean kinases, a mitogen-activated protein kinase MPK2, and a serine/threonine-protein kinase SAPK2, highlighting the significance of the ankyrin-repeat (ANK) domain in facilitating protein-protein interactions. Moreover, an in vitro kinase assay and subsequent Phos-tag SDS-PAGE determined that GmMPK2 and GmSAPK2 possess the ability to phosphorylate Class II GmACBPs. Additionally, the kinase-specific phosphosites for Class II GmACBPs were predicted using databases. The HDOCK server was also utilized to predict the binding models of Class II GmACBPs with these two kinases, and the results indicated that the affected residues were located in the ANK region of Class II GmACBPs in both docking models, aligning with the findings of the Y2H and BiFC experiments. This is the first report describing the interaction between Class II GmACBPs and kinases, suggesting that Class II GmACBPs have potential as phospho-proteins that impact signaling pathways.
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Affiliation(s)
| | - Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China;
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China;
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2
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Ma Q, Wang Y, Li S, Wen J, Zhu L, Yan K, Du Y, Li S, Yan L, Xie Z, Lyu Y, Shen F, Li Q. Ribosome footprint profiling enables elucidating the systemic regulation of fatty acid accumulation in Acer truncatum. BMC Biol 2023; 21:68. [PMID: 37013569 PMCID: PMC10071632 DOI: 10.1186/s12915-023-01564-8] [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: 11/18/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The accumulation of fatty acids in plants covers a wide range of functions in plant physiology and thereby affects adaptations and characteristics of species. As the famous woody oilseed crop, Acer truncatum accumulates unsaturated fatty acids and could serve as the model to understand the regulation and trait formation in oil-accumulation crops. Here, we performed Ribosome footprint profiling combing with a multi-omics strategy towards vital time points during seed development, and finally constructed systematic profiling from transcription to proteomes. Additionally, we characterized the small open reading frames (ORFs) and revealed that the translational efficiencies of focused genes were highly influenced by their sequence features. RESULTS The comprehensive multi-omics analysis of lipid metabolism was conducted in A. truncatum. We applied the Ribo-seq and RNA-seq techniques, and the analyses of transcriptional and translational profiles of seeds collected at 85 and 115 DAF were compared. Key members of biosynthesis-related structural genes (LACS, FAD2, FAD3, and KCS) were characterized fully. More meaningfully, the regulators (MYB, ABI, bZIP, and Dof) were identified and revealed to affect lipid biosynthesis via post-translational regulations. The translational features results showed that translation efficiency tended to be lower for the genes with a translated uORF than for the genes with a non-translated uORF. They provide new insights into the global mechanisms underlying the developmental regulation of lipid metabolism. CONCLUSIONS We performed Ribosome footprint profiling combing with a multi-omics strategy in A. truncatum seed development, which provides an example of the use of Ribosome footprint profiling in deciphering the complex regulation network and will be useful for elucidating the metabolism of A. truncatum seed oil and the regulatory mechanisms.
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Affiliation(s)
- Qiuyue Ma
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Yuxiao Wang
- Nanjing Forestry University, Nanjing, 210037, China
| | - Shushun Li
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Jing Wen
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Lu Zhu
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Kunyuan Yan
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Yiming Du
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Shuxian Li
- Nanjing Forestry University, Nanjing, 210037, China
| | - Liping Yan
- Shandong Academy of Forestry Sciences, Jinan, 250014, China
| | - Zhijun Xie
- Xiangyang Forestry Science and Technology Extension Station, Xiangyang, 441000, China
| | - Yunzhou Lyu
- Jiangsu Academy of Forestry, Nanjing, 211153, China.
| | - Fei Shen
- Institute of Biology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100197, China.
| | - Qianzhong Li
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China.
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Zheng X, Oba BT, Wang H, Shen C, Zhao R, Zhao D, Ding H. Organo-mineral complexes alter bacterial composition and induce carbon and nitrogen cycling in the rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155671. [PMID: 35525342 DOI: 10.1016/j.scitotenv.2022.155671] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/19/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
It is widely thought that organo-mineral complexes (OMCs) stabilize organic matter via mineral adsorption. Recent studies have demonstrated that root exudates can activate OMCs, but the influence of OMCs on plant rhizosphere, which is among the most active areas for microbes, has not been thoroughly researched. In this study, a pot experiment using Brassica napus was conducted to investigate the effects of OMCs on plant rhizosphere. The result showed that OMC addition significantly promoted the growth of B. napus compared to the prevalent fertilization (PF, chemical fertilizer + chicken compost) treatment. Specifically, OMC addition increased the relative abundance (RA) of nitrogen-fixing bacteria and the bacterial α-diversity, and the operational taxonomic unit (OTU) group with RA > 0.5% in the OMC-treated rhizosphere was the result of a deterministic assembly process with homogeneous selection. Gene abundance related to nitrogen cycling and the soil chemical analysis demonstrated that the OMC-altered bacterial community induced nitrogen fixation and converted nitrate to ammonium. The upregulated carbon sequestration pathway genes and the increased soil microbial biomass carbon (23.68%) demonstrated that the bacterial-induced carbon storage in the rhizosphere was activated. This study shows that the addition of OMCs can influence the biogeochemical carbon and nitrogen cycling via regulating microorganisms in the rhizosphere. The findings provide fresh insights into the effects of OMCs on the biogeochemical cycling of important elements and suggest a promising strategy for improving soil productivity.
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Affiliation(s)
- Xuehao Zheng
- School of Environmental Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
| | - Belay Tafa Oba
- School of Environmental Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China; College of Natural Science, Arba Minch University, Arba Minch 21, Ethiopia
| | - Han Wang
- School of Environmental Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
| | - Chenbo Shen
- School of Environmental Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
| | - Rui Zhao
- School of Environmental Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
| | - Dan Zhao
- School of Environmental Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
| | - Hui Ding
- School of Environmental Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China.
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4
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Dhaka N, Jain R, Yadav A, Yadav P, Kumar N, Sharma MK, Sharma R. Transcriptome analysis reveals cell cycle-related transcripts as key determinants of varietal differences in seed size of Brassica juncea. Sci Rep 2022; 12:11713. [PMID: 35810218 PMCID: PMC9271088 DOI: 10.1038/s41598-022-15938-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/01/2022] [Indexed: 11/22/2022] Open
Abstract
Brassica juncea is an important oilseed crop, widely grown as a source of edible oil. Seed size is a pivotal agricultural trait in oilseed Brassicas. However, the regulatory mechanisms underlying seed size determination are poorly understood. To elucidate the transcriptional dynamics involved in the determination of seed size in B. juncea, we performed a comparative transcriptomic analysis using developing seeds of two varieties, small-seeded Early Heera2 (EH2) and bold-seeded Pusajaikisan (PJK), at three distinct stages (15, 30 and 45 days after pollination). We detected 112,550 transcripts, of which 27,186 and 19,522 were differentially expressed in the intra-variety comparisons and inter-variety comparisons, respectively. Functional analysis using pathway, gene ontology, and transcription factor enrichment revealed that cell cycle- and cell division-related transcripts stay upregulated during later stages of seed development in the bold-seeded variety but are downregulated at the same stage in the small-seeded variety, indicating that an extended period of cell proliferation in the later stages increased seed weight in PJK as compared to EH2. Further, k-means clustering and candidate genes-based analyses unravelled candidates for employing in seed size improvement of B. juncea. In addition, candidates involved in determining seed coat color, oil content, and other seed traits were also identified.
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Affiliation(s)
- Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
| | - Rubi Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhinandan Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Pinky Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Neeraj Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | | | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Pilani, Rajasthan, India
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Hamdan MF, Lung SC, Guo ZH, Chye ML. Roles of acyl-CoA-binding proteins in plant reproduction. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2918-2936. [PMID: 35560189 DOI: 10.1093/jxb/erab499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/11/2021] [Indexed: 06/15/2023]
Abstract
Acyl-CoA-binding proteins (ACBPs) constitute a well-conserved family of proteins in eukaryotes that are important in stress responses and development. Past studies have shown that ACBPs are involved in maintaining, transporting and protecting acyl-CoA esters during lipid biosynthesis in plants, mammals, and yeast. ACBPs show differential expression and various binding affinities for acyl-CoA esters. Hence, ACBPs can play a crucial part in maintaining lipid homeostasis. This review summarizes the functions of ACBPs during the stages of reproduction in plants and other organisms. A comprehensive understanding on the roles of ACBPs during plant reproduction may lead to opportunities in crop improvement in agriculture.
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Affiliation(s)
- Mohd Fadhli Hamdan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Ze-Hua Guo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
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6
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Transgenic manipulation of triacylglycerol biosynthetic enzymes in B. napus alters lipid-associated gene expression and lipid metabolism. Sci Rep 2022; 12:3352. [PMID: 35233071 PMCID: PMC8888550 DOI: 10.1038/s41598-022-07387-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/17/2022] [Indexed: 12/18/2022] Open
Abstract
Oilseed rape (Brassica napus) is an important crop that is cultivated for the oil (mainly triacylglycerol; TAG) it produces in its seeds. TAG synthesis is controlled mainly by key enzymes in the Kennedy pathway, such as glycerol 3-phosphate acyltransferase (GPAT), lysophosphatidate acyltransferase (LPAT) and diacylglycerol acyltransferase (DGAT) but can also be produced from phosphoglycerides such as phosphatidylcholine (PC) by the activity of the enzyme phospholipid: diacylglycerol acyltransferase (PDAT). To evaluate the potential for these enzymes to alter oil yields or composition, we analysed transgenic B. napus lines which overexpressed GPAT, LPAT or PDAT using heterologous transgenes from Arabidopsis and Nasturtium and examined lipid profiles and changes in gene expression in these lines compared to WT. Distinct changes in PC and TAG abundance and spatial distribution in embryonic tissues were observed in some of the transgenic lines, together with altered expression of genes involved generally in acyl-lipid metabolism. Overall our results show that up-regulation of these key enzymes differentially affects lipid composition and distribution as well as lipid-associated gene expression, providing important information which could be used to improve crop properties by metabolic engineering.
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7
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Interactions between plant lipid-binding proteins and their ligands. Prog Lipid Res 2022; 86:101156. [DOI: 10.1016/j.plipres.2022.101156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/05/2021] [Accepted: 01/14/2022] [Indexed: 01/11/2023]
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8
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Li J, Lin K, Zhang S, Wu J, Fang Y, Wang Y. Genome-Wide Analysis of Myeloblastosis-Related Genes in Brassica napus L. and Positive Modulation of Osmotic Tolerance by BnMRD107. FRONTIERS IN PLANT SCIENCE 2021; 12:678202. [PMID: 34220898 PMCID: PMC8248502 DOI: 10.3389/fpls.2021.678202] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/30/2021] [Indexed: 06/01/2023]
Abstract
Myeloblastosis (MYB)-related transcription factors comprise a large subfamily of the MYB family. They play significant roles in plant development and in stress responses. However, MYB-related proteins have not been comprehensively investigated in rapeseed (Brassica napus L.). In the present study, a genome-wide analysis of MYB-related transcription factors was performed in rapeseed. We identified 251 Brassica napus MYB (BnMYB)-related members, which were divided phylogenetically into five clades. Evolutionary analysis suggested that whole genome duplication and segmental duplication events have played a significant role in the expansion of BnMYB-related gene family. Selective pressure of BnMYB-related genes was estimated using the Ka/Ks ratio, which indicated that BnMYB-related genes underwent strong purifying selection during evolution. In silico analysis showed that various development-associated, phytohormone-responsive, and stress-related cis-acting regulatory elements were enriched in the promoter regions of BnMYB-related genes. Furthermore, MYB-related genes with tissue or organ-specific, stress-responsive expression patterns were identified in B. napus based on temporospatial and abiotic stress expression profiles. Among the stress-responsive MYB-related genes, BnMRD107 was strongly induced by drought stress, and was therefore selected for functional study. Rapeseed seedlings overexpressing BnMRD107 showed improved resistance to osmotic stress. Our findings not only lay a foundation for further functional characterization of BnMYB-related genes, but also provide valuable clues to determine candidate genes for future genetic improvement of B. napus.
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Affiliation(s)
- Jian Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Keyun Lin
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Shuai Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Jian Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
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Azlan NS, Guo ZH, Yung WS, Wang Z, Lam HM, Lung SC, Chye ML. In silico Analysis of Acyl-CoA-Binding Protein Expression in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:646938. [PMID: 33936134 PMCID: PMC8082252 DOI: 10.3389/fpls.2021.646938] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/12/2021] [Indexed: 05/02/2023]
Abstract
Plant acyl-CoA-binding proteins (ACBPs) form a highly conserved protein family that binds to acyl-CoA esters as well as other lipid and protein interactors to function in developmental and stress responses. This protein family had been extensively studied in non-leguminous species such as Arabidopsis thaliana (thale cress), Oryza sativa (rice), and Brassica napus (oilseed rape). However, the characterization of soybean (Glycine max) ACBPs, designated GmACBPs, has remained unreported although this legume is a globally important crop cultivated for its high oil and protein content, and plays a significant role in the food and chemical industries. In this study, 11 members of the GmACBP family from four classes, comprising Class I (small), Class II (ankyrin repeats), Class III (large), and Class IV (kelch motif), were identified. For each class, more than one copy occurred and their domain architecture including the acyl-CoA-binding domain was compared with Arabidopsis and rice. The expression profile, tertiary structure and subcellular localization of each GmACBP were predicted, and the similarities and differences between GmACBPs and other plant ACBPs were deduced. A potential role for some Class III GmACBPs in nodulation, not previously encountered in non-leguminous ACBPs, has emerged. Interestingly, the sole member of Class III ACBP in each of non-leguminous Arabidopsis and rice had been previously identified in plant-pathogen interactions. As plant ACBPs are known to play important roles in development and responses to abiotic and biotic stresses, the in silico expression profiles on GmACBPs, gathered from data mining of RNA-sequencing and microarray analyses, will lay the foundation for future studies in their applications in biotechnology.
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Affiliation(s)
- Nur Syifaq Azlan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ze-Hua Guo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wai-Shing Yung
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Zhili Wang
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
- *Correspondence: Shiu-Cheung Lung,
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
- Mee-Len Chye,
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Meng W, Xu L, Du ZY, Wang F, Zhang R, Song X, Lam SM, Shui G, Li Y, Chye ML. RICE ACYL-COA-BINDING PROTEIN6 Affects Acyl-CoA Homeostasis and Growth in Rice. RICE (NEW YORK, N.Y.) 2020; 13:75. [PMID: 33159253 PMCID: PMC7647982 DOI: 10.1186/s12284-020-00435-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/21/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUNDS Acyl-coenzyme A (CoA) esters are important intermediates in lipid metabolism with regulatory properties. Acyl-CoA-binding proteins bind and transport acyl-CoAs to fulfill these functions. RICE ACYL-COA-BINDING PROTEIN6 (OsACBP6) is currently the only one peroxisome-localized plant ACBP that has been proposed to be involved in β-oxidation in transgenic Arabidopsis. The role of the peroxisomal ACBP (OsACBP6) in rice (Oryza sativa) was investigated. RESULTS Here, we report on the function of OsACBP6 in rice. The osacbp6 mutant showed diminished growth with reduction in root meristem activity and leaf growth. Acyl-CoA profiling and lipidomic analysis revealed an increase in acyl-CoA content and a slight triacylglycerol accumulation caused by the loss of OsACBP6. Comparative transcriptomic analysis discerned the biological processes arising from the loss of OsACBP6. Reduced response to oxidative stress was represented by a decline in gene expression of a group of peroxidases and peroxidase activities. An elevation in hydrogen peroxide was observed in both roots and shoots/leaves of osacbp6. Taken together, loss of OsACBP6 not only resulted in a disruption of the acyl-CoA homeostasis but also peroxidase-dependent reactive oxygen species (ROS) homeostasis. In contrast, osacbp6-complemented transgenic rice displayed similar phenotype to the wild type rice, supporting a role for OsACBP6 in the maintenance of the acyl-CoA pool and ROS homeostasis. Furthermore, quantification of plant hormones supported the findings observed in the transcriptome and an increase in jasmonic acid level occurred in osacbp6. CONCLUSIONS In summary, OsACBP6 appears to be required for the efficient utilization of acyl-CoAs. Disruption of OsACBP6 compromises growth and led to provoked defense response, suggesting a correlation of enhanced acyl-CoAs content with defense responses.
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Affiliation(s)
- Wei Meng
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China.
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Lijian Xu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China
| | - Zhi-Yan Du
- Department of Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Fang Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Rui Zhang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Xingshun Song
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Lipidall Technologies Company Limited, Changzhou, 213000, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuhua Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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Aznar-Moreno JA, Venegas-Calerón M, Du ZY, Garcés R, Tanner JA, Chye ML, Martínez-Force E, Salas JJ. Characterization and function of a sunflower (Helianthus annuus L.) Class II acyl-CoA-binding protein. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 300:110630. [PMID: 33180709 DOI: 10.1016/j.plantsci.2020.110630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 05/13/2023]
Abstract
Acyl-CoA-binding proteins (ACBP) bind to long-chain acyl-CoA esters and phospholipids, enhancing the activity of different acyltransferases in animals and plants. Nevertheless, the role of these proteins in the synthesis of triacylglycerols (TAGs) remains unclear. Here, we cloned a cDNA encoding HaACBP1, a Class II ACBP from sunflower (Helianthus annuus), one of the world's most important oilseed crop plants. Transcriptome analysis of this gene revealed strong expression in developing seeds from 16 to 30 days after flowering. The recombinant protein (rHaACBP1) was expressed in Escherichia coli and purified to be studied by in vitro isothermal titration calorimetry and for phospholipid binding. Its high affinity for saturated palmitoyl-CoA (16:0-CoA; KD 0.11 μM) and stearoyl-CoA (18:0-CoA; KD 0.13 μM) esters suggests that rHaACBP1 could act in acyl-CoA transfer pathways that involve saturated acyl derivatives. Furthermore, rHaACBP1 also binds to both oleoyl-CoA (18:1-CoA; KD 6.4 μM) and linoleoyl-CoA (18:2-CoA; KD 21.4 μM) esters, the main acyl-CoA substrates used to synthesise the TAGs that accumulate in sunflower seeds. Interestingly, rHaACBP1 also appears to bind to different species of phosphatidylcholines (dioleoyl-PC and dilinoleoyl-PC), glycerolipids that are also involved in TAG synthesis, and while it interacts with dioleoyl-PA, this is less prominent than its binding to the PC derivative. Expression of rHaACBP in yeast alters its fatty acid composition, as well as the composition and size of the host acyl-CoA pool. These results suggest that HaACBP1 may potentially fulfil a role in the transport and trafficking of acyl-CoAs during sunflower seed development.
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Affiliation(s)
- Jose A Aznar-Moreno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Mónica Venegas-Calerón
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013, Sevilla, Spain
| | - Zhi-Yan Du
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Rafael Garcés
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013, Sevilla, Spain
| | - Julian A Tanner
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Enrique Martínez-Force
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013, Sevilla, Spain
| | - Joaquín J Salas
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013, Sevilla, Spain.
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Global Transcriptome and Correlation Analysis Reveal Cultivar-Specific Molecular Signatures Associated with Fruit Development and Fatty Acid Determination in Camellia oleifera Abel. Int J Genomics 2020; 2020:6162802. [PMID: 32953873 PMCID: PMC7481963 DOI: 10.1155/2020/6162802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/02/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
Background Oil-tea Camellia is a very important edible oil plant widely distributed in southern China. Tea oil extracted from the oil-tea Camellia seeds is beneficial to health and is considered as a health edible oil. We attempt to identify genes related to fatty acid biosynthesis in an oil-tea Camellia seed kernel, generated a comprehensive transcriptome analysis of the seed kernel at different developmental stages, and explore optimal picking time of fruit. Material and Methods. A gas chromatography-mass spectrometer was used to detect the content of various fatty acids in samples. Transcriptome analysis was performed to detect gene dynamics and corresponding functions. Results Multiple phenotypic data were counted in detail, including the oil content, oleic acid content, linoleic acid content, linolenic acid content, fruit weight, fruit height, fruit diameter, single seed weight, seed length, and seed width in different developmental stages, which indicate that a majority of indicators increased with the development of oil-tea Camellia. The transcriptomics was conducted to perform a comprehensive and system-level view on dynamic gene expression networks for different developmental stages. Short Time-series Expression Miner (STEM) analysis of XL106 (the 6 time points) and XL210 (8 time points) was performed to screen related fatty acid (FA) gene set, from which 1041 candidate genes related to FA were selected in XL106 and 202 related genes were screened in XL210 based on GO and KEGG enrichment. Then, candidate genes and trait dataset were combined to conduct correlation analysis, and 10 genes were found to be strongly connected with several key traits. Conclusions The multiple phenotypic data revealed the dynamic law of changes during the picking stage. Transcriptomic analysis identified a large number of potential key regulatory factors that can control the oil content of dried kernels, oleic acid, linoleic acid, linolenic acid, fresh seed rate, and kernel-to-seed ratio, thereby providing a new insight into the molecular networks underlying the picking stage of oil-tea Camellia, which provides a theoretical basis for the optimal fruit picking point.
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Hui WK, Zhao FY, Wang JY, Chen XY, Li JW, Zhong Y, Li HY, Zheng JX, Zhang LZ, Que QM, Wu AM, Gong W. De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism. BMC Genomics 2020; 21:81. [PMID: 31992199 PMCID: PMC6986037 DOI: 10.1186/s12864-020-6521-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species. Results Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage). Conclusions The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.
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Affiliation(s)
- Wen-Kai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fei-Yan Zhao
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing-Yan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao-Yang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Jue-Wei Li
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Zhong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hong-Yun Li
- Agricultural Technology Extension Center in Yantan District, Zigong, 643030, China
| | - Jun-Xing Zheng
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liang-Zhen Zhang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qing-Min Que
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
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Siles L, Eastmond P, Kurup S. Big data from small tissues: extraction of high-quality RNA for RNA-sequencing from different oilseed Brassica seed tissues during seed development. PLANT METHODS 2020; 16:80. [PMID: 32518582 PMCID: PMC7275424 DOI: 10.1186/s13007-020-00626-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/28/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Obtaining high-quality RNA for gene expression analyses from different seed tissues is challenging due to the presence of various contaminants, such as polyphenols, polysaccharides and lipids which interfere with RNA extraction methods. At present, the available protocols for extracting RNA from seeds require high amounts of tissue and are mainly focused on extracting RNA from whole seeds. However, extracting RNA at the tissue level enables more detailed studies regarding tissue specific transcriptomes during seed development. RESULTS Seeds from heart stage embryo to mature developmental stages of Brassica napus and B. oleracea were sampled for isolation of the embryo, endosperm and seed coat tissues. Ovules and ovary wall tissue were also collected from pre-fertilized buds. Subsequent to testing several RNA extraction methods, modifications applied to E.Z.N.A. Plant RNA and Picopure RNA Isolation kit extraction methods resulted in RNA with high yield and quality. Furthermore, the use of polyvinylpolypyrrolidone for seed coats and endosperm at green stages resulted in high-quality RNA. As a result of the introduced modifications to established RNA extraction methods, the RNA from all the above-mentioned tissues presented clear 28S and 18S bands and high RIN values, ranging from 7.0 to 10.0. The protocols reported in this study are not only suitable for different and challenging seed tissue types, but also enable the extraction of high-quality RNA using only 2 to 3 mg of starting tissue. CONCLUSIONS Here, we present efficient, reproducible and reliable high-quality RNA extraction methods for diverse oilseed Brassica spp reproductive tissue types including pre-fertilization and developing seed tissues for diploid and polyploid species. The high-quality RNA obtained is suitable for RNA-Sequencing and subsequent gene expression analysis.
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Affiliation(s)
- Laura Siles
- Department of Plant Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
| | - Peter Eastmond
- Department of Plant Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
| | - Smita Kurup
- Department of Plant Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
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