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Wu J, Zhou M, Cheng Y, Chen X, Yan S, Deng S. Genome-Wide Analysis of C/S1-bZIP Subfamilies in Populus tomentosa and Unraveling the Role of PtobZIP55/21 in Response to Low Energy. Int J Mol Sci 2024; 25:5163. [PMID: 38791204 PMCID: PMC11120861 DOI: 10.3390/ijms25105163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
C/S1 basic leucine zipper (bZIP) transcription factors are essential for plant survival under energy deficiency. However, studies on the responses of C/S1-bZIPs to low energy in woody plants have not yet been reported. In this study, members of C/S1-bZIP subfamilies in Populus tomentosa were systematically analyzed using bioinformatic approaches. Four C-bZIPs and 10 S1-bZIPs were identified, and their protein properties, phylogenetic relationships, gene structures, conserved motifs, and uORFs were systematically investigated. In yeast two-hybrid assays, direct physical interactions between C-bZIP and S1-bZIP members were observed, highlighting their potential functional synergy. Moreover, expression profile analyses revealed that low energy induced transcription levels of most C/S1-bZIP members, with bZIP55 and bZIP21 (a homolog of bZIP55) exhibiting particularly significant upregulation. When the expression of bZIP55 and bZIP21 was co-suppressed using artificial microRNA mediated gene silencing in transgenic poplars, root growth was promoted. Further analyses revealed that bZIP55/21 negatively regulated the root development of P. tomentosa in response to low energy. These findings provide insights into the molecular mechanisms by which C/S1-bZIPs regulate poplar growth and development in response to energy deprivation.
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Affiliation(s)
| | | | | | | | | | - Shurong Deng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (J.W.); (M.Z.); (Y.C.); (X.C.); (S.Y.)
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Cao X, Guo Z, Wang P, Lu S, Li W, Ma Z, Mao J, Chen B. MdbZIP44-MdCPRF2-like- Mdα-GP2 regulate starch and sugar metabolism in apple under nitrogen supply. HORTICULTURE RESEARCH 2024; 11:uhae072. [PMID: 38725457 PMCID: PMC11079487 DOI: 10.1093/hr/uhae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/28/2024] [Indexed: 05/12/2024]
Abstract
Nitrogen (N) is regarded as an essential macronutrient and is tightly associated with carbon (C) metabolism in plants. The transcriptome data obtained from this study showed that the expression level of the apple basic leucine zipper (bZIP) transcription factor (TF) MdbZIP44 was up-regulated in 'Oregon Spur Delicious' (Malus domestica Borkh.) apple fruits under nitrogen supply. MdbZIP44 bound to the promoter of Mdα-GP2 gene and inhibited its expression, thereby promoting starch accumulation and decreasing glucose content in apple and tomato fruits. Besides, overexpression of MdbZIP44 promoted sucrose accumulation by regulating the activities of sucrose metabolism-related enzymes and the expression of sugar metabolism-related genes in apple callus and tomato fruits. Furthermore, biochemical assays indicated that MdbZIP44 directly interacted with MdCPRF2-like, another bZIP gene in apple. Meanwhile, this study found that MdCPRF2-like, along with the MdbZIP44 and MdCPRF2-like complex, could activate the expression of Mdα-GP2, respectively. In conclusion, this study provides a new reference for potential mechanisms underlying that MdbZIP44-MdCPRF2-like-Mdα-GP2 regulates starch and sugar metabolism under nitrogen supply.
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Affiliation(s)
- Xuejing Cao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhigang Guo
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui 741000, China
| | - Ping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Wenfang Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
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Wu HYL, Jen J, Hsu PY. What, where, and how: Regulation of translation and the translational landscape in plants. THE PLANT CELL 2024; 36:1540-1564. [PMID: 37437121 PMCID: PMC11062462 DOI: 10.1093/plcell/koad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, transfer RNAs, and the ribosome machinery through both cis- and trans-regulation while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a "primer" that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through 3 conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs; translation in organelles and viruses is not covered in this review.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Joey Jen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Qanmber G, You Q, Yang Z, Fan L, Zhang Z, Chai M, Gao B, Li F, Yang Z. Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton. J Adv Res 2024; 58:13-30. [PMID: 37207930 PMCID: PMC10982868 DOI: 10.1016/j.jare.2023.05.004] [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: 03/04/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/21/2023] Open
Abstract
INTRODUCTION The unavailability of intergenic region annotation in whole genome sequencing and pan-genomics hinders efforts to enhance crop improvement. OBJECTIVES Despite advances in research, the impact of post-transcriptional regulation on fiber development and translatome profiling at different stages of fiber growth in cotton (G. hirsutum) remains unexplored. METHODS We utilized a combination of reference-guided de novo transcriptome assembly and ribosome profiling techniques to uncover the hidden mechanisms of translational control in eight distinct tissues of upland cotton. RESULTS Our study identified P-site distribution at three-nucleotide periodicity and dominant ribosome footprint at 27 nucleotides. Specifically, we have detected 1,589 small open reading frames (sORFs), including 1,376 upstream ORFs (uORFs) and 213 downstream ORFs (dORFs), as well as 552 long non-coding RNAs (lncRNAs) with potential coding functions, which fine-tune the annotation of the cotton genome. Further, we have identified novel genes and lncRNAs with strong translation efficiency (TE), while sORFs were found to affect mRNA transcription levels during fiber elongation. The reliability of these findings was confirmed by the high consistency in correlation and synergetic fold change between RNA-sequencing (RNA-seq) and Ribosome-sequencing (Ribo-seq) analyses. Additionally, integrated omics analysis of the normal fiber ZM24 and short fiber pag1 cotton mutant revealed several differentially expressed genes (DEGs), and fiber-specific expressed (high/low) genes associated with sORFs (uORFs and dORFs). These findings were further supported by the overexpression and knockdown of GhKCS6, a gene associated with sORFs in cotton, and demonstrated the potential regulation of the mechanism governing fiber elongation on both the transcriptional and post-transcriptional levels. CONCLUSION Reference-guided transcriptome assembly and the identification of novel transcripts fine-tune the annotation of the cotton genome and predicted the landscape of fiber development. Our approach provided a high-throughput method, based on multi-omics, for discovering unannotated ORFs, hidden translational control, and complex regulatory mechanisms in crop plants.
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Affiliation(s)
- Ghulam Qanmber
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Qi You
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Liqiang Fan
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhibin Zhang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Mao Chai
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Baibai Gao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Zuoren Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
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Jia L, Zhang X, Zhang Z, Luo W, Nambeesan SU, Li Q, Qiao X, Yang B, Wang L, Zhang S. PbrbZIP15 promotes sugar accumulation in pear via activating the transcription of the glucose isomerase gene PbrXylA1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1392-1412. [PMID: 38044792 DOI: 10.1111/tpj.16569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/01/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
The composition and abundance of soluble sugars in mature pear (Pyrus) fruit are important for its acceptance by consumers. However, our understanding of the genes responsible for soluble sugar accumulation remains limited. In this study, a S1-group member of bZIP gene family, PbrbZIP15, was characterized from pear genome through the combined analyses of metabolite and transcriptome data followed by experimental validation. PbrbZIP15, located in nucleus, was found to function in fructose, sucrose, and total soluble sugar accumulation in pear fruit and calli. After analyzing the expression profiles of sugar-metabolism-related genes and the distribution of cis-acting elements in their promoters, the glucose isomerase 1 gene (PbrXylA1), whose corresponding protein catalyzed the isomerization of glucose and fructose in vitro, was identified as a downstream target gene of PbrbZIP15. PbrbZIP15 could directly bind to the G-box element in PbrXylA1 promoter and activate its transcription, as evidenced by chromatin immunoprecipitation-quantitative PCR, yeast one-hybrid, electrophoretic mobility shift assay, and dual-luciferase assay. PbrXylA1, featuring a leucine-rich signal peptide in its N-terminal, was localized to the endoplasmic reticulum. It was validated to play a significant role in fructose, sucrose, and total soluble sugar accumulation in pear fruit and calli, which was associated with the upregulated fructose/glucose ratio. Further studies revealed a positive correlation between the sucrose content and the expression levels of several sucrose-biosynthesis-related genes (PbrFRK3/8, PbrSPS1/3/4/8, and PbrSPP1) in PbrbZIP15-/PbrXylA1-transgenic fruit/calli. In conclusion, our results suggest that PbrbZIP15-induced soluble sugar accumulation during pear development is at least partly attributed to the activation of PbrXylA1 transcription.
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Affiliation(s)
- Luting Jia
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xu Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zan Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Weiqi Luo
- U.S. Horticultural Research Laboratory, ARS-USDA, Ft. Pierce, Florida, 34945, USA
- CIPM, NC State University, Raleigh, North Carolina, 27606, USA
| | | | - Qionghou Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xin Qiao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Bing Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Libin Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shaoling Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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6
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Kreisz P, Hellens AM, Fröschel C, Krischke M, Maag D, Feil R, Wildenhain T, Draken J, Braune G, Erdelitsch L, Cecchino L, Wagner TC, Ache P, Mueller MJ, Becker D, Lunn JE, Hanson J, Beveridge CA, Fichtner F, Barbier FF, Weiste C. S 1 basic leucine zipper transcription factors shape plant architecture by controlling C/N partitioning to apical and lateral organs. Proc Natl Acad Sci U S A 2024; 121:e2313343121. [PMID: 38315839 PMCID: PMC10873608 DOI: 10.1073/pnas.2313343121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/21/2023] [Indexed: 02/07/2024] Open
Abstract
Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant's nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.
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Affiliation(s)
- Philipp Kreisz
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Alicia M. Hellens
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
| | - Christian Fröschel
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Markus Krischke
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Daniel Maag
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Regina Feil
- Group System Regulation, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm14476, Germany
| | - Theresa Wildenhain
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Jan Draken
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Gabriel Braune
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Leon Erdelitsch
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Laura Cecchino
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Tobias C. Wagner
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Peter Ache
- Department of Molecular Plant Physiology and Biophysics, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Martin J. Mueller
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Dirk Becker
- Department of Molecular Plant Physiology and Biophysics, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - John E. Lunn
- Group System Regulation, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm14476, Germany
| | - Johannes Hanson
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, UmeåSE-901 87, Sweden
| | - Christine A. Beveridge
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
| | - Franziska Fichtner
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- Department of Plant Biochemistry, Institute for Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Francois F. Barbier
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- Institute for Plant Sciences of Montpellier, University of Montpellier, CNRS, INRAe, Institut Agro, Montpellier34060, France
| | - Christoph Weiste
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
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7
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Chen Y, Wu X, Wang X, Li Q, Yin H, Zhang S. bZIP transcription factor PubZIP914 enhances production of fatty acid-derived volatiles in pear. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111905. [PMID: 37884080 DOI: 10.1016/j.plantsci.2023.111905] [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: 07/13/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 10/28/2023]
Abstract
'Nanguo' pear emitted a rich aroma when entirely ripe. The six-carbon (C6) volatiles, including the aldehydes, 2-hexenal, and hexanal, as well as their corresponding alcohols and esters which are derived from lipoxygenase pathway are the important volatile components in 'Nanguo' pears. However, the transcriptional regulation mechanism of aroma synthesis of 'Nanguo' pears remains largely unknown. bZIP transcription factors (TFs) mediate different developmental processes in plants. In this study, we identified and characterized a bZIP TF that is highly expressed and induced in 'Nanguo' pear fruits at the mature stage. The content of fatty acid-derived volatiles increased significantly in transgenic pears and tomatoes of PubZIP914 overexpression. Meanwhile, PubZIP914 could regulate PuLOX3.1 by binding directly to PuLOX3.1 promoter. The results of this study provide evidence demonstrating how bZIP transcription factors regulate fatty acid-derived volatiles biosynthesis during pear fruit ripening.
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Affiliation(s)
- Yangyang Chen
- Jiangsu Engineering Research Center for Pear, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Wu
- Jiangsu Engineering Research Center for Pear, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohua Wang
- Jiangsu Engineering Research Center for Pear, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qionghou Li
- Jiangsu Engineering Research Center for Pear, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Yin
- Jiangsu Engineering Research Center for Pear, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shaoling Zhang
- Jiangsu Engineering Research Center for Pear, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.
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8
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Liu Z, Liang T, Kang C. Molecular bases of strawberry fruit quality traits: Advances, challenges, and opportunities. PLANT PHYSIOLOGY 2023; 193:900-914. [PMID: 37399254 DOI: 10.1093/plphys/kiad376] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/25/2023] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
The strawberry is one of the world's most popular fruits, providing humans with vitamins, fibers, and antioxidants. Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid and highly heterozygous, making it a challenge for breeding, quantitative trait locus (QTL) mapping, and gene discovery. Some wild strawberry relatives, such as Fragaria vesca, have diploid genomes and are becoming laboratory models for the cultivated strawberry. Recent advances in genome sequencing and CRISPR-mediated genome editing have greatly improved the understanding of various aspects of strawberry growth and development in both cultivated and wild strawberries. This review focuses on fruit quality traits that are most relevant to the consumers, including fruit aroma, sweetness, color, firmness, and shape. Recently available phased-haplotype genomes, single nucleotide polymorphism (SNP) arrays, extensive fruit transcriptomes, and other big data have made it possible to locate key genomic regions or pinpoint specific genes that underlie volatile synthesis, anthocyanin accumulation for fruit color, and sweetness intensity or perception. These new advances will greatly facilitate marker-assisted breeding, the introgression of missing genes into modern varieties, and precise genome editing of selected genes and pathways. Strawberries are poised to benefit from these recent advances, providing consumers with fruit that is tastier, longer-lasting, healthier, and more beautiful.
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Affiliation(s)
- Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Tong Liang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chunying Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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9
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Wang H, Xu K, Li X, Blanco-Ulate B, Yang Q, Yao G, Wei Y, Wu J, Sheng B, Chang Y, Jiang CZ, Lin J. A pear S1-bZIP transcription factor PpbZIP44 modulates carbohydrate metabolism, amino acid, and flavonoid accumulation in fruits. HORTICULTURE RESEARCH 2023; 10:uhad140. [PMID: 37575657 PMCID: PMC10421730 DOI: 10.1093/hr/uhad140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/08/2023] [Indexed: 08/15/2023]
Abstract
Fruit quality is defined by attributes that give value to a commodity. Flavor, texture, nutrition, and shelf life are key quality traits that ensure market value and consumer acceptance. In pear fruit, soluble sugars, organic acids, amino acids, and total flavonoids contribute to flavor and overall quality. Transcription factors (TFs) regulate the accumulation of these metabolites during development or in response to the environment. Here, we report a novel TF, PpbZIP44, as a positive regulator of primary and secondary metabolism in pear fruit. Analysis of the transient overexpression or RNAi-transformed pear fruits and stable transgenic tomato fruits under the control of the fruit-specific E8 promoter demonstrated that PpZIP44 substantially affected the contents of soluble sugar, organic acids, amino acids, and flavonoids. In E8::PpbZIP44 tomato fruit, genes involved in carbohydrate metabolism, amino acid, and flavonoids biosynthesis were significantly induced. Furthermore, in PpbZIP44 overexpression or antisense pear fruits, the expression of genes in the related pathways was significantly impacted. PpbZIP44 directly interacted with the promoter of PpSDH9 and PpProDH1 to induce their expression, thereby depleting sorbitol and proline, decreasing citrate and malate, and enhancing fructose contents. PpbZIP44 also directly bound to the PpADT and PpF3H promoters, which led to the carbon flux toward phenylalanine metabolites and enhanced phenylalanine and flavonoid contents. These findings demonstrate that PpbZIP44 mediates multimetabolism reprogramming by regulating the gene expression related to fruit quality compounds.
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Affiliation(s)
- Hong Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Kexin Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xiaogang Li
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Bárbara Blanco-Ulate
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Qingsong Yang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Gaifang Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yiduo Wei
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Jun Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
| | - Baolong Sheng
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Youhong Chang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, California, 95616, USA
| | - Jing Lin
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
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10
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Wang W, Wang Y, Chen T, Qin G, Tian S. Current insights into posttranscriptional regulation of fleshy fruit ripening. PLANT PHYSIOLOGY 2023; 192:1785-1798. [PMID: 36250906 PMCID: PMC10315313 DOI: 10.1093/plphys/kiac483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/27/2022] [Indexed: 05/26/2023]
Abstract
Fruit ripening is a complicated process that is accompanied by the formation of fruit quality. It is not only regulated at the transcriptional level via transcription factors or DNA methylation but also fine-tuned after transcription occurs. Here, we review recent advances in our understanding of key regulatory mechanisms of fleshy fruit ripening after transcription. We mainly highlight the typical mechanisms by which fruit ripening is controlled, namely, alternative splicing, mRNA N6-methyladenosine RNA modification methylation, and noncoding RNAs at the posttranscriptional level; regulation of translation efficiency and upstream open reading frame-mediated translational repression at the translational level; and histone modifications, protein phosphorylation, and protein ubiquitination at the posttranslational level. Taken together, these posttranscriptional regulatory mechanisms, along with transcriptional regulation, constitute the molecular framework of fruit ripening. We also critically discuss the potential usage of some mechanisms to improve fruit traits.
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Affiliation(s)
- Weihao Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuying Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Yan C, Yang T, Wang B, Yang H, Wang J, Yu Q. Genome-Wide Identification of the WD40 Gene Family in Tomato ( Solanum lycopersicum L.). Genes (Basel) 2023; 14:1273. [PMID: 37372453 DOI: 10.3390/genes14061273] [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: 04/19/2023] [Revised: 06/01/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
WD40 proteins are a superfamily of regulatory proteins widely found in eukaryotes that play an important role in regulating plant growth and development. However, the systematic identification and characterization of WD40 proteins in tomato (Solanum lycopersicum L.) have not been reported. In the present study, we identified 207 WD40 genes in the tomatoes genome and analyzed their chromosomal location, gene structure and evolutionary relationships. A total of 207 tomato WD40 genes were classified by structural domain and phylogenetic tree analyses into five clusters and 12 subfamilies and were found to be unevenly distributed across the 12 tomato chromosomes. We identified six tandem duplication gene pairs and 24 segmental duplication pairs in the WD40 gene family, with segmental duplication being the major mode of expansion in tomatoes. Ka/Ks analysis revealed that paralogs and orthologs of WD40 family genes underwent mainly purifying selection during the evolutionary process. RNA-seq data from different tissues and developmental periods of tomato fruit development showed tissue-specific expression of WD40 genes. In addition, we constructed four coexpression networks according to the transcriptome and metabolome data for WD40 proteins involved in fruit development that may be related to total soluble solid formation. The results provide a comprehensive overview of the tomato WD40 gene family and will provide valuable information for the validation of the function of tomato WD40 genes in fruit development.
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Affiliation(s)
- Cunyao Yan
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830000, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830000, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830000, China
| | - Haitao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830000, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830000, China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830000, China
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12
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Wang L, Zheng X, Ye Z, Su M, Zhang X, Du J, Li X, Zhou H, Huan C. Transcriptome Co-Expression Network Analysis of Peach Fruit with Different Sugar Concentrations Reveals Key Regulators in Sugar Metabolism Involved in Cold Tolerance. Foods 2023; 12:foods12112244. [PMID: 37297487 DOI: 10.3390/foods12112244] [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: 05/04/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Peach fruits are known to be highly susceptible to chilling injury (CI) during low-temperature storage, which has been linked to the level of sugar concentration in the fruit. In order to better understand the relationship between sugar metabolism and CI, we conducted a study examining the concentration of sucrose, fructose, and glucose in peach fruit with different sugar concentrations and examined their relationship with CI. Through transcriptome sequencing, we screened the functional genes and transcription factors (TFs) involved in the sugar metabolism pathway that may cause CI in peach fruit. Our results identified five key functional genes (PpSS, PpINV, PpMGAM, PpFRK, and PpHXK) and eight TFs (PpMYB1/3, PpMYB-related1, PpWRKY4, PpbZIP1/2/3, and PpbHLH2) that are associated with sugar metabolism and CI development. The analysis of co-expression network mapping and binding site prediction identified the most likely associations between these TFs and functional genes. This study provides insights into the metabolic and molecular mechanisms regulating sugar changes in peach fruit with different sugar concentrations and presents potential targets for breeding high-sugar and cold-tolerant peach varieties.
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Affiliation(s)
- Lufan Wang
- Forestry and Fruit Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Xiaolin Zheng
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Zhengwen Ye
- Forestry and Fruit Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210000, China
| | - Mingshen Su
- Forestry and Fruit Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xianan Zhang
- Forestry and Fruit Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jihong Du
- Forestry and Fruit Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xiongwei Li
- Forestry and Fruit Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Huijuan Zhou
- Forestry and Fruit Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210000, China
| | - Chen Huan
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210000, China
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13
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Eom SH, Lim HB, Hyun TK. Overexpression of the Brassica rapa bZIP Transcription Factor, BrbZIP-S, Increases the Stress Tolerance in Nicotiana benthamiana. BIOLOGY 2023; 12:biology12040517. [PMID: 37106717 PMCID: PMC10136179 DOI: 10.3390/biology12040517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023]
Abstract
In higher plants, S1-basic region-leucine zipper (S1-bZIP) transcription factors fulfill crucial roles in the physiological homeostasis of carbon and amino acid metabolisms and stress responses. However, very little is known about the physiological role of S1-bZIP in cruciferous vegetables. Here, we analyzed the physiological function of S1-bZIP from Brassica rapa (BrbZIP-S) in modulating proline and sugar metabolism. Overexpression of BrbZIP-S in Nicotiana benthamiana resulted in delayed chlorophyll degradation during the response to dark conditions. Under heat stress or recovery conditions, the transgenic lines exhibited a lower accumulation of H2O2, malondialdehyde, and protein carbonyls compared to the levels in transgenic control plants. These results strongly indicate that BrbZIP-S regulates plant tolerance against dark and heat stress. We propose that BrbZIP-S is a modulator of proline and sugar metabolism, which are required for energy homeostasis in response to environmental stress conditions.
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14
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Nguyen NH, Bui TP, Le NT, Nguyen CX, Le MTT, Dao NT, Phan Q, Van Le T, To HMT, Pham NB, Chu HH, Do PT. Disrupting Sc-uORFs of a transcription factor bZIP1 using CRISPR/Cas9 enhances sugar and amino acid contents in tomato (Solanum lycopersicum). PLANTA 2023; 257:57. [PMID: 36795295 DOI: 10.1007/s00425-023-04089-0] [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] [Received: 11/09/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Induced mutations in the SC-uORF of the tomato transcription factor gene SlbZIP1 by the CRISPR/Cas9 system led to the high accumulation of sugar and amino acid contents in tomato fruits. Tomato (Solanum lycopersicum) is one of the most popular and consumed vegetable crops in the world. Among important traits for tomato improvement such as yield, biotic and abiotic resistances, appearance, post-harvest shelf life and fruit quality, the last one seems to face more challenges because of its genetic and biochemical complexities. In this study, a dual-gRNAs CRISPR/Cas9 system was developed to induce targeted mutations in uORF regions of the SlbZIP1, a gene involved in the sucrose-induced repression of translation (SIRT) mechanism. Different induced mutations in the SlbZIP1-uORF region were identified at the T0 generation, stably transferred to the offspring, and no mutation was found at potential off-target sites. The induced mutations in the SlbZIP1-uORF region affected the transcription of SlbZIP1 and related genes in sugar and amino acid biosynthesis. Fruit component analysis showed significant increases in soluble solid, sugar and total amino acid contents in all SlbZIP1-uORF mutant lines. The accumulation of sour-tasting amino acids, including aspartic and glutamic acids, raised from 77 to 144%, while the accumulation of sweet-tasting amino acids such as alanine, glycine, proline, serine, and threonine increased from 14 to 107% in the mutant plants. Importantly, the potential SlbZIP1-uORF mutant lines with desirable fruit traits and no impaired effect on plant phenotype, growth and development were identified under the growth chamber condition. Our result indicates the potential utility of the CRISPR/Cas9 system for fruit quality improvement in tomato and other important crops.
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Affiliation(s)
- Nhung Hong Nguyen
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thao Phuong Bui
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ngoc Thu Le
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Cuong Xuan Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - My Tra Thi Le
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nhan Trong Dao
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Quyen Phan
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Trong Van Le
- National Center for Food Analysis and Assessment, Food Industries Research Institute, Hanoi, Vietnam
| | - Huong Mai Thi To
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ngoc Bich Pham
- Laboratory of Applied DNA Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang Chu
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
| | - Phat Tien Do
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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15
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Transcriptome Analysis and Screening of Genes Associated with Flower Size in Tomato ( Solanum lycopersicum). Int J Mol Sci 2022; 23:ijms232415624. [PMID: 36555271 PMCID: PMC9778759 DOI: 10.3390/ijms232415624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Flower development is not only an important way for tomato reproduction but also an important guarantee for tomato fruit production. Although more and more attention has been paid to the study of flower development, there are few studies on the molecular mechanism and gene expression level of tomato flower development. In this study, RNA-seq analysis was performed on two stages of tomato flower development using the Illumina sequencing platform. A total of 8536 DEGs were obtained by sequencing, including 3873 upregulated DEGs and 4663 down-regulated DEGs. These differentially expressed genes are related to plant hormone signaling, starch and sucrose metabolism. The pathways such as pentose, glucuronate interconversion, and Phenylpropanoid biosynthesis are closely related and mainly involved in plant cellular and metabolic processes. According to the enrichment analysis results of DEGs, active energy metabolism can be inferred during flower development, indicating that flower development requires a large amount of energy and material supply. In addition, some plant hormones, such as GA, may also have effects on flower development. Combined with previous studies, the expression levels of Solyc02g087860 and three of bZIPs were significantly increased in the full flowering stage compared with the flower bud stage, indicating that these genes may be closely related to flower development. These genes were previously reported in Arabidopsis but not in tomatoes. Our next work will conduct a detailed functional analysis of the identified bZIP family genes to characterize their association with tomato flower size. This study will provide new genetic resources for flower formation and provide a basis for tomato yield breeding.
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16
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Fine Mapping and Functional Analysis of Major Regulatory Genes of Soluble Solids Content in Wax Gourd (Benincasa hispida). Int J Mol Sci 2022; 23:ijms23136999. [PMID: 35806004 PMCID: PMC9266771 DOI: 10.3390/ijms23136999] [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: 06/06/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Soluble solids content (SSC) is an important quality trait of wax gourd, but reports about its regulatory genes are scarce. In this study, the SSC regulatory gene BhSSC2.1 in wax gourd was mined via quantitative trait locus (QTL) mapping based on high-density genetic mapping containing 12 linkage groups (LG) and bulked segregant analysis (BSA)-seq. QTL mapping and BSA-seq revealed for the first time that the SSC QTL (107.658–108.176 cM) of wax gourd was on Chr2 (LG2). The interpretable phenotypic variation rate and maximum LOD were 16.033% and 6.454, respectively. The QTL interval contained 13 genes. Real-time fluorescence quantitative expression analysis, functional annotation, and sequence analysis suggested that Bch02G016960, named BhSSC2.1, was a candidate regulatory gene of the SSC in wax gourd. Functional annotation of this gene showed that it codes for a NADP-dependent malic enzyme. According to BhSSC2.1 sequence variation, an InDel marker was developed for molecular marker-assisted breeding of wax gourd. This study will lay the foundation for future studies regarding breeding and understanding genetic mechanisms of wax gourd.
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17
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Wu CJ, Shan W, Liu XC, Zhu LS, Wei W, Yang YY, Guo YF, Bouzayen M, Chen JY, Lu WJ, Kuang JF. Phosphorylation of transcription factor bZIP21 by MAP kinase MPK6-3 enhances banana fruit ripening. PLANT PHYSIOLOGY 2022; 188:1665-1685. [PMID: 34792564 PMCID: PMC8896643 DOI: 10.1093/plphys/kiab539] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Ripening of fleshy fruits involves both diverse post-translational modifications (PTMs) and dynamic transcriptional reprogramming, but the interconnection between PTMs, such as protein phosphorylation and transcriptional regulation, in fruit ripening remains to be deciphered. Here, we conducted a phosphoproteomic analysis during banana (Musa acuminata) ripening and identified 63 unique phosphopeptides corresponding to 49 proteins. Among them, a Musa acuminata basic leucine zipper transcription factor21 (MabZIP21) displayed elevated phosphorylation level in the ripening stage. MabZIP21 transcript and phosphorylation abundance increased during banana ripening. Genome-wide MabZIP21 DNA binding assays revealed MabZIP21-regulated functional genes contributing to banana ripening, and electrophoretic mobility shift assay, chromatin immunoprecipitation coupled with quantitative polymerase chain reaction, and dual-luciferase reporter analyses demonstrated that MabZIP21 stimulates the transcription of a subset of ripening-related genes via directly binding to their promoters. Moreover, MabZIP21 can be phosphorylated by MaMPK6-3, which plays a role in banana ripening, and T318 and S436 are important phosphorylation sites. Protein phosphorylation enhanced MabZIP21-mediated transcriptional activation ability, and transient overexpression of the phosphomimetic form of MabZIP21 accelerated banana fruit ripening. Additionally, MabZIP21 enlarges its role in transcriptional regulation by activating the transcription of both MaMPK6-3 and itself. Taken together, this study reveals an important machinery of protein phosphorylation in banana fruit ripening in which MabZIP21 is a component of the complex phosphorylation pathway linking the upstream signal mediated by MaMPK6-3 with transcriptional controlling of a subset of ripening-associated genes.
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Affiliation(s)
- Chao-Jie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education/Guangdong Laboratory of Lingnan Modern Agriculture, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education/Guangdong Laboratory of Lingnan Modern Agriculture, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Xun-Cheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Li-Sha Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education/Guangdong Laboratory of Lingnan Modern Agriculture, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education/Guangdong Laboratory of Lingnan Modern Agriculture, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education/Guangdong Laboratory of Lingnan Modern Agriculture, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Yu-Fan Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education/Guangdong Laboratory of Lingnan Modern Agriculture, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Mondher Bouzayen
- Génomique et Biotechnologie des Fruits, Université de Toulouse, INRA, Castanet-Tolosan 31320, France
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education/Guangdong Laboratory of Lingnan Modern Agriculture, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education/Guangdong Laboratory of Lingnan Modern Agriculture, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education/Guangdong Laboratory of Lingnan Modern Agriculture, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
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18
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Zhu F, Wen W, Cheng Y, Fernie AR. The metabolic changes that effect fruit quality during tomato fruit ripening. MOLECULAR HORTICULTURE 2022; 2:2. [PMID: 37789428 PMCID: PMC10515270 DOI: 10.1186/s43897-022-00024-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/12/2022] [Indexed: 10/05/2023]
Abstract
As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.
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Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Weiwei Wen
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany.
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19
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Wang H, Zhang Y, Norris A, Jiang CZ. S1-bZIP Transcription Factors Play Important Roles in the Regulation of Fruit Quality and Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 12:802802. [PMID: 35095974 PMCID: PMC8795868 DOI: 10.3389/fpls.2021.802802] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Sugar metabolism not only determines fruit sweetness and quality but also acts as signaling molecules to substantially connect with other primary metabolic processes and, therefore, modulates plant growth and development, fruit ripening, and stress response. The basic region/leucine zipper motif (bZIP) transcription factor family is ubiquitous in eukaryotes and plays a diverse array of biological functions in plants. Among the bZIP family members, the smallest bZIP subgroup, S1-bZIP, is a unique one, due to the conserved upstream open reading frames (uORFs) in the 5' leader region of their mRNA. The translated small peptides from these uORFs are suggested to mediate Sucrose-Induced Repression of Translation (SIRT), an important mechanism to maintain sucrose homeostasis in plants. Here, we review recent research on the evolution, sequence features, and biological functions of this bZIP subgroup. S1-bZIPs play important roles in fruit quality, abiotic and biotic stress responses, plant growth and development, and other metabolite biosynthesis by acting as signaling hubs through dimerization with the subgroup C-bZIPs and other cofactors like SnRK1 to coordinate the expression of downstream genes. Direction for further research and genetic engineering of S1-bZIPs in plants is suggested for the improvement of quality and safety traits of fruit.
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Affiliation(s)
- Hong Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States
| | - Yunting Zhang
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ayla Norris
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, United States
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, United States
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20
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Zhou Z, Ford R, Bar I, Kanchana-udomkan C. Papaya ( Carica papaya L.) Flavour Profiling. Genes (Basel) 2021; 12:1416. [PMID: 34573398 PMCID: PMC8471406 DOI: 10.3390/genes12091416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
A major challenge to the papaya industry is inconsistency in fruit quality and, in particular, flavour, which is a complex trait that comprises taste perception in the mouth (sweetness, acidity, or bitterness) and aroma produced by several volatile compounds. Current commercial varieties vary greatly in their taste, likely due to historical prioritised selection for fruit appearance as well as large environmental effects. Therefore, it is important to better understand the genetic and biochemical mechanisms and biosynthesis pathways underpinning preferable flavour in order to select and breed for better tasting new commercial papaya varieties. As an initial step, objectively measurable standards of the compound profiles that provide papaya's taste and aroma, together with 'mouth feel', are required. This review presents an overview of the approaches to characterise the flavour profiles of papaya through sugar component determination, volatile compound detection, sensory panel testing, as well as genomics-based studies to identify the papaya flavour.
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Affiliation(s)
| | - Rebecca Ford
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia; (Z.Z.); (I.B.); (C.K.)
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21
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Chen T, Zhang Z, Li B, Qin G, Tian S. Molecular basis for optimizing sugar metabolism and transport during fruit development. ABIOTECH 2021; 2:330-340. [PMID: 36303881 PMCID: PMC9590571 DOI: 10.1007/s42994-021-00061-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022]
Abstract
Sugars are fundamental metabolites synthesized in leaves and further delivered to fruit in fruit crops. They not only provide "sweetness" as fruit quality traits, but also function as signaling molecules to modulate the responses of fruit to environmental stimuli. Therefore, the understanding to the molecular basis for sugar metabolism and transport is crucial for improving fruit quality and dissecting responses to abiotic/biotic factors. Here, we provide a review for molecular components involved in sugar metabolism and transport, crosstalk with hormone signaling, and the roles of sugars in responses to abiotic and biotic stresses. Moreover, we also envisage the strategies for optimizing sugar metabolism during fruit quality maintenance.
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Affiliation(s)
- Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
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22
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Zhang X, Feng C, Wang M, Li T, Liu X, Jiang J. Plasma membrane-localized SlSWEET7a and SlSWEET14 regulate sugar transport and storage in tomato fruits. HORTICULTURE RESEARCH 2021; 8:186. [PMID: 34333539 PMCID: PMC8325691 DOI: 10.1038/s41438-021-00624-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/22/2021] [Accepted: 04/19/2021] [Indexed: 05/25/2023]
Abstract
Sugars, especially glucose and fructose, contribute to the taste and quality of tomato fruits. These compounds are translocated from the leaves to the fruits and then unloaded into the fruits by various sugar transporters at the plasma membrane. SWEETs, are sugar transporters that regulate sugar efflux independently of energy or pH. To date, the role of SWEETs in tomato has received very little attention. In this study, we performed functional analysis of SlSWEET7a and SlSWEET14 to gain insight into the regulation of sugar transport and storage in tomato fruits. SlSWEET7a and SlSWEET14 were mainly expressed in peduncles, vascular bundles, and seeds. Both SlSWEET7a and SlSWEET14 are plasma membrane-localized proteins that transport fructose, glucose, and sucrose. Apart from the resulting increase in mature fruit sugar content, silencing SlSWEET7a or SlSWEET14 resulted in taller plants and larger fruits (in SlSWEET7a-silenced lines). We also found that invertase activity and gene expression of some SlSWEET members increased, which was consistent with the increased availability of sucrose and hexose in the fruits. Overall, our results demonstrate that suppressing SlSWEET7a and SlSWEET14 could be a potential strategy for enhancing the sugar content of tomato fruits.
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Affiliation(s)
- Xinsheng Zhang
- College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, Liaoning, China
| | - Chaoyang Feng
- College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, Liaoning, China
| | - Manning Wang
- College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, Liaoning, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, Liaoning, China
- Key Laboratory of Protected Horticulture of Education Ministry, 110866, Shenyang, Liaoning, China
| | - Xin Liu
- College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, Liaoning, China.
- Key Laboratory of Protected Horticulture of Education Ministry, 110866, Shenyang, Liaoning, China.
| | - Jing Jiang
- College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, Liaoning, China.
- Key Laboratory of Protected Horticulture of Education Ministry, 110866, Shenyang, Liaoning, China.
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23
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Wang P, Jin S, Chen X, Wu L, Zheng Y, Yue C, Guo Y, Zhang X, Yang J, Ye N. Chromatin accessibility and translational landscapes of tea plants under chilling stress. HORTICULTURE RESEARCH 2021; 8:96. [PMID: 33931606 PMCID: PMC8087716 DOI: 10.1038/s41438-021-00529-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 05/03/2023]
Abstract
Plants have evolved regulatory mechanisms at multiple levels to regulate gene expression in order to improve their cold adaptability. However, limited information is available regarding the stress response at the chromatin and translational levels. Here, we characterize the chromatin accessibility, transcriptional, and translational landscapes of tea plants in vivo under chilling stress for the first time. Chilling stress significantly affected both the transcription and translation levels as well as the translation efficiency of tea plants. A total of 3010 genes that underwent rapid and independent translation under chilling stress were observed, and they were significantly enriched in the photosynthesis-antenna protein and phenylpropanoid biosynthesis pathways. A set of genes that were significantly responsive to cold at the transcription and translation levels, including four (+)-neomenthol dehydrogenases (MNDs) and two (E)-nerolidol synthases (NESs) arranged in tandem on the chromosomes, were also found. We detected potential upstream open reading frames (uORFs) on 3082 genes and found that tea plants may inhibit the overall expression of genes by enhancing the translation of uORFs under chilling stress. In addition, we identified distal transposase hypersensitive sites (THSs) and proximal THSs and constructed a transcriptional regulatory network for tea plants under chilling stress. We also identified 13 high-confidence transcription factors (TFs) that may play a crucial role in cold regulation. These results provide valuable information regarding the potential transcriptional regulatory network in plants and help to clarify how plants exhibit flexible responses to chilling stress.
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Affiliation(s)
- Pengjie Wang
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Shan Jin
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Xuejin Chen
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Liangyu Wu
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Yucheng Zheng
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Chuan Yue
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Yongchun Guo
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jiangfan Yang
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China.
| | - Naixing Ye
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China.
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24
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Fichtner F, Dissanayake IM, Lacombe B, Barbier F. Sugar and Nitrate Sensing: A Multi-Billion-Year Story. TRENDS IN PLANT SCIENCE 2021; 26:352-374. [PMID: 33281060 DOI: 10.1016/j.tplants.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/23/2020] [Accepted: 11/04/2020] [Indexed: 05/03/2023]
Abstract
Sugars and nitrate play a major role in providing carbon and nitrogen in plants. Understanding how plants sense these nutrients is crucial, most notably for crop improvement. The mechanisms underlying sugar and nitrate sensing are complex and involve moonlighting proteins such as the nitrate transporter NRT1.1/NFP6.3 or the glycolytic enzyme HXK1. Major components of nutrient signaling, such as SnRK1, TOR, and HXK1, are relatively well conserved across eukaryotes, and the diversification of components such as the NRT1 family and the SWEET sugar transporters correlates with plant terrestrialization. In plants, Tre6P plays a hormone-like role in plant development. In addition, nutrient signaling has evolved to interact with the more recent hormone signaling, allowing fine-tuning of physiological and developmental responses.
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Affiliation(s)
- Franziska Fichtner
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Benoit Lacombe
- Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Francois Barbier
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
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25
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Pramanik D, Shelake RM, Kim MJ, Kim JY. CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement. MOLECULAR PLANT 2021; 14:127-150. [PMID: 33152519 DOI: 10.1016/j.molp.2020.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/14/2020] [Accepted: 11/02/2020] [Indexed: 05/03/2023]
Abstract
The central dogma (CD) of molecular biology is the transfer of genetic information from DNA to RNA to protein. Major CD processes governing genetic flow include the cell cycle, DNA replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation. Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population. CRISPR technology enables programmable editing of CD processes to alter DNA, RNA, or protein, which would have been impossible in the past. Here, an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided. Furthermore, CRISPR applications in major thriving areas of research, such as gene discovery (allele mining and cryptic gene activation), introgression (de novo domestication and haploid induction), and application of desired traits beneficial to farmers or consumers (biotic/abiotic stress-resilient crops, plant cell factories, and delayed senescence), are described. Finally, the global regulatory policies, challenges, and prospects for CRISPR-mediated crop improvement are discussed.
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Affiliation(s)
- Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| | - Mi Jung Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
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26
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Shipman EN, Yu J, Zhou J, Albornoz K, Beckles DM. Can gene editing reduce postharvest waste and loss of fruit, vegetables, and ornamentals? HORTICULTURE RESEARCH 2021; 8:1. [PMID: 33384412 PMCID: PMC7775472 DOI: 10.1038/s41438-020-00428-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 05/22/2023]
Abstract
Postharvest waste and loss of horticultural crops exacerbates the agricultural problems facing humankind and will continue to do so in the next decade. Fruits and vegetables provide us with a vast spectrum of healthful nutrients, and along with ornamentals, enrich our lives with a wide array of pleasant sensory experiences. These commodities are, however, highly perishable. Approximately 33% of the produce that is harvested is never consumed since these products naturally have a short shelf-life, which leads to postharvest loss and waste. This loss, however, could be reduced by breeding new crops that retain desirable traits and accrue less damage over the course of long supply chains. New gene-editing tools promise the rapid and inexpensive production of new varieties of crops with enhanced traits more easily than was previously possible. Our aim in this review is to critically evaluate gene editing as a tool to modify the biological pathways that determine fruit, vegetable, and ornamental quality, especially after storage. We provide brief and accessible overviews of both the CRISPR-Cas9 method and the produce supply chain. Next, we survey the literature of the last 30 years, to catalog genes that control or regulate quality or senescence traits that are "ripe" for gene editing. Finally, we discuss barriers to implementing gene editing for postharvest, from the limitations of experimental methods to international policy. We conclude that in spite of the hurdles that remain, gene editing of produce and ornamentals will likely have a measurable impact on reducing postharvest loss and waste in the next 5-10 years.
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Affiliation(s)
- Emma N Shipman
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA.
| | - Jingwei Yu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA.
| | - Jiaqi Zhou
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA.
| | - Karin Albornoz
- Departamento de Produccion Vegetal, Universidad de Concepcion, Region del BioBio, Concepcion, Chile.
| | - Diane M Beckles
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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27
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Leszczuk A, Kalaitzis P, Blazakis KN, Zdunek A. The role of arabinogalactan proteins (AGPs) in fruit ripening-a review. HORTICULTURE RESEARCH 2020; 7:176. [PMID: 33328442 PMCID: PMC7603502 DOI: 10.1038/s41438-020-00397-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/10/2020] [Accepted: 08/18/2020] [Indexed: 05/21/2023]
Abstract
Arabinogalactan proteins (AGPs) are proteoglycans challenging researchers for decades. However, despite the extremely interesting polydispersity of their structure and essential application potential, studies of AGPs in fruit are limited, and only a few groups deal with this scientific subject. Here, we summarise the results of pioneering studies on AGPs in fruit tissue with their structure, specific localization pattern, stress factors influencing their presence, and a focus on recent advances. We discuss the properties of AGPs, i.e., binding calcium ions, ability to aggregate, adhesive nature, and crosslinking with other cell wall components that may also be implicated in fruit metabolism. The aim of this review is an attempt to associate well-known features and properties of AGPs with their putative roles in fruit ripening. The putative physiological significance of AGPs might provide additional targets of regulation for fruit developmental programme. A comprehensive understanding of the AGP expression, structure, and untypical features may give new information for agronomic, horticulture, and renewable biomaterial applications.
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Affiliation(s)
- Agata Leszczuk
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland.
| | - Panagiotis Kalaitzis
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania, Chania, P.O. Box 85, Chania, 73100, Greece
| | - Konstantinos N Blazakis
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania, Chania, P.O. Box 85, Chania, 73100, Greece
| | - Artur Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland
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28
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Wang L, Li Y, Jin X, Liu L, Dai X, Liu Y, Zhao L, Zheng P, Wang X, Liu Y, Lin D, Qin Y. Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development. Commun Biol 2020; 3:500. [PMID: 32913289 PMCID: PMC7483743 DOI: 10.1038/s42003-020-01235-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/12/2020] [Indexed: 11/12/2022] Open
Abstract
Proper flower development is essential for sexual reproductive success and the setting of fruits and seeds. The availability of a high quality genome sequence for pineapple makes it an excellent model for studying fruit and floral organ development. In this study, we sequenced 27 different pineapple floral samples and integrated nine published RNA-seq datasets to generate tissue- and stage-specific transcriptomic profiles. Pairwise comparisons and weighted gene co-expression network analysis successfully identified ovule-, stamen-, petal- and fruit-specific modules as well as hub genes involved in ovule, fruit and petal development. In situ hybridization confirmed the enriched expression of six genes in developing ovules and stamens. Mutant characterization and complementation analysis revealed the important role of the subtilase gene AcSBT1.8 in petal development. This work provides an important genomic resource for functional analysis of pineapple floral organ growth and fruit development and sheds light on molecular networks underlying pineapple reproductive organ growth. Wang et al. perform RNA-Seq on pineapple floral samples and also use previously published RNA-Seq datasets to generate tissue- and stage-specific transcriptomic profiles. The authors use weighted gene co-expression network analysis to identify gene networks, bringing insight to underlying pineapple reproductive organ growth.
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Affiliation(s)
- Lulu Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yi Li
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xingyue Jin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liping Liu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaozhuan Dai
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanhui Liu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lihua Zhao
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ping Zheng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, 530007, China
| | - Yeqiang Liu
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, 530007, China
| | - Deshu Lin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuan Qin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China.
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29
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Xing S, Chen K, Zhu H, Zhang R, Zhang H, Li B, Gao C. Fine-tuning sugar content in strawberry. Genome Biol 2020; 21:230. [PMID: 32883370 PMCID: PMC7470447 DOI: 10.1186/s13059-020-02146-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/17/2020] [Indexed: 01/30/2023] Open
Abstract
Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33.9-83.6% higher than that of the wild-type. We also recover a series of transgene-free mutants with 35 novel genotypes containing a continuum of sugar content. All the novel genotypes could be immediately fixed in subsequent generations by asexual reproduction. Genome editing coupled with asexual reproduction offers tremendous opportunities for quantitative trait improvement.
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Affiliation(s)
- Sinian Xing
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Haocheng Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Huawei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Bingbing Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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Çolak NG, Eken NT, Ülger M, Frary A, Doğanlar S. Exploring wild alleles from Solanum pimpinellifolium with the potential to improve tomato flavor compounds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110567. [PMID: 32771168 DOI: 10.1016/j.plantsci.2020.110567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/09/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
Most consumers complain about the flavor of current tomato cultivars and many pay a premium for alternatives such as heirloom varieties. Breeding for fruit flavor is difficult because it is a quantitatively inherited trait influenced by taste, aroma and environmental factors. A lack of genetic diversity in modern tomato cultivars also necessitates exploration of new sources for flavor alleles. Wild tomato S. pimpinellifolium and inbred backcross lines were assessed for individual sugars and organic acids which are two of the main components of tomato flavor. S. pimpinellifolium was found to harbor alleles that could be used to increase glucose and fructose content and adjust acidity by altering malic and citric acid levels. Single nucleotide polymorphism markers were used to detect 14 quantitative trait loci (QTLs) for sugars and 71 for organic acids. Confirmation was provided by comparing map locations with previously identified loci. Thus, seven (50 %) of the sugar QTLs and 22 (31 %) of the organic acids loci were supported by analyses in other tomato populations. Examination of the genomic sequence containing the QTLs allowed identification of potential candidate genes for several flavor components.
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Affiliation(s)
- Nergiz Gürbüz Çolak
- Department of Molecular Biology and Genetics, Faculty of Science, Izmir Institute of Technology, İzmir 35433, Turkey.
| | - Neslihan Tek Eken
- Department of Molecular Biology and Genetics, Faculty of Science, Izmir Institute of Technology, İzmir 35433, Turkey.
| | | | - Anne Frary
- Department of Molecular Biology and Genetics, Faculty of Science, Izmir Institute of Technology, İzmir 35433, Turkey.
| | - Sami Doğanlar
- Department of Molecular Biology and Genetics, Faculty of Science, Izmir Institute of Technology, İzmir 35433, Turkey.
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Characterization and Expression Analysis of the Ca 2+/Cation Antiporter Gene Family in Tomatoes. PLANTS 2019; 9:plants9010025. [PMID: 31878106 PMCID: PMC7020160 DOI: 10.3390/plants9010025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023]
Abstract
The Ca2+/cation antiporter (CaCA) superfamily plays an important role in the regulation of the essential element Ca2+ and cation concentrations. Characterization and expression analyses of CaCA superfamily genes were performed in the tomato (Solanum lycopersicum) as a representative of dicotyledonous plants and fruit crops. Sixteen CaCA candidate genes were found and identified as tomato CaCA, SlCaCA, by a domain search. In a phylogenetic analysis of the SlCaCA superfamily, the 16 genes were classified into SlCAX, SlNCL, SlCCX, and SlMHX families. Among them, Solyc12g011070, belonging to the SlCAX family, had four splice variants, three of which were predicted to be nonfunctional because of a lack of important motifs. EF-hand domains were only found in SlNCL, in addition to consensus Na_Ca_ex domains, and the region containing EF-hand domains was characteristically long in some members of SlNCL. Furthermore, four genes of the SlCCX family were found to be intronless. As for intracellular localization, one SlCCX member was predicted to be localized to the plasma membrane, while other SlCCXs, SlCAXs, and SlMHXs were predicted to be localized to the vacuolar membrane. The expression patterns of SlCaCAs in various organs, including during several developmental stages of fruit, were classified into four groups. Genes involved in each of the SlCAX, SlNCL, and SlCCX gene families were categorized into three or four groups according to expression patterns, suggesting role sharing within each family. The main member in each subfamily and the members with characteristic fruit expression patterns included genes whose expression was regulated by sugar or auxin and that were highly expressed in a line having metabolite-rich fruit.
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Quinet M, Angosto T, Yuste-Lisbona FJ, Blanchard-Gros R, Bigot S, Martinez JP, Lutts S. Tomato Fruit Development and Metabolism. FRONTIERS IN PLANT SCIENCE 2019; 10:1554. [PMID: 31850035 PMCID: PMC6895250 DOI: 10.3389/fpls.2019.01554] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/07/2019] [Indexed: 05/20/2023]
Abstract
Tomato (Solanum lycopersicum L.) belongs to the Solanaceae family and is the second most important fruit or vegetable crop next to potato (Solanum tuberosum L.). It is cultivated for fresh fruit and processed products. Tomatoes contain many health-promoting compounds including vitamins, carotenoids, and phenolic compounds. In addition to its economic and nutritional importance, tomatoes have become the model for the study of fleshy fruit development. Tomato is a climacteric fruit and dramatic metabolic changes occur during its fruit development. In this review, we provide an overview of our current understanding of tomato fruit metabolism. We begin by detailing the genetic and hormonal control of fruit development and ripening, after which we document the primary metabolism of tomato fruits, with a special focus on sugar, organic acid, and amino acid metabolism. Links between primary and secondary metabolic pathways are further highlighted by the importance of pigments, flavonoids, and volatiles for tomato fruit quality. Finally, as tomato plants are sensitive to several abiotic stresses, we briefly summarize the effects of adverse environmental conditions on tomato fruit metabolism and quality.
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Affiliation(s)
- Muriel Quinet
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Trinidad Angosto
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
| | - Fernando J. Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
| | - Rémi Blanchard-Gros
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Servane Bigot
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Stanley Lutts
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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Timerbaev V, Dolgov S. Functional characterization of a strong promoter of the early light-inducible protein gene from tomato. PLANTA 2019; 250:1307-1323. [PMID: 31270599 DOI: 10.1007/s00425-019-03227-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/27/2019] [Indexed: 06/09/2023]
Abstract
The tomato ELIP gene promoter is mainly active in the ripening fruit. Considering its high activity, the promoter could be used for molecular breeding of plants in the future. The ability to obtain new varieties of transgenic plants with economically valuable traits relies on a high level of target gene expression, which is largely controlled by a gene promoter. Hence, research aimed at finding and characterizing new tissue-specific promoters that direct gene expression in specific plant tissues or at certain developmental stages has become the most important field of plant biotechnology. Here, we cloned and characterized the promoter of the early light-inducible protein (ELIP) gene from tomato (Solanum lycopersicum cv. Yalf). ELIPs are produced in the presence of light and putatively function in the chloroplast-to-chromoplast conversion, playing a photorepairing role in the photosynthetic system. Analysis of the promoter sequence revealed multiple cis-acting elements related to light responsiveness, and other motifs involved in plant hormone response and circadian control. To determine the functionality of the promoter, seven 5'-deletion variants were fused with the β-glucuronidase (GUS) reporter gene and introduced into tomato. Histochemical analysis of transgenic tomato plants revealed different levels of GUS activity in most analyzed tissues, depending on the promoter fragment used. The intensity of staining was considerably higher in ripening fruits than in unripe and non-fruit tissues. Quantitative analysis indicated that the level of GUS activity with the longest (full-length) version of the ELIP promoter in ripened fruits was comparable to that in plants expressing the constitutive CaMV35S promoter. Further, the location of both negative and positive regulatory motifs was identified. The described ELIP promoter is a potential tool for various applications in plant biotechnology.
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Affiliation(s)
- Vadim Timerbaev
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, 142290, Russia.
- Nikita Botanical Gardens-National Scientific Center, Russian Academy of Sciences, Yalta, 298648, Russia.
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127550, Russia.
| | - Sergey Dolgov
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, 142290, Russia
- Nikita Botanical Gardens-National Scientific Center, Russian Academy of Sciences, Yalta, 298648, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127550, Russia
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Jian W, Cao H, Yuan S, Liu Y, Lu J, Lu W, Li N, Wang J, Zou J, Tang N, Xu C, Cheng Y, Gao Y, Xi W, Bouzayen M, Li Z. SlMYB75, an MYB-type transcription factor, promotes anthocyanin accumulation and enhances volatile aroma production in tomato fruits. HORTICULTURE RESEARCH 2019; 6:22. [PMID: 30729012 PMCID: PMC6355774 DOI: 10.1038/s41438-018-0098-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/01/2018] [Accepted: 09/17/2018] [Indexed: 05/18/2023]
Abstract
Genetic manipulation of genes to upregulate specific branches of metabolic pathways is a method that is commonly used to improve fruit quality. However, the use of a single gene to impact several metabolic pathways is difficult. Here, we show that overexpression of the single gene SlMYB75 (SlMYB75-OE) is effective at improving multiple fruit quality traits. In these engineered fruits, the anthocyanin content reached 1.86 mg g-1 fresh weight at the red-ripe stage, and these SlMYB75-OE tomatoes displayed a series of physiological changes, including delayed ripening and increased ethylene production. In addition to anthocyanin, the total contents of phenolics, flavonoids and soluble solids in SlMYB75-OE fruits were enhanced by 2.6, 4, and 1.2 times, respectively, compared to those of wild-type (WT) fruits. Interestingly, a number of aroma volatiles, such as aldehyde, phenylpropanoid-derived and terpene volatiles, were significantly increased in SlMYB75-OE fruits, with some terpene volatiles showing more than 10 times higher levels than those in WT fruits. Consistent with the metabolic assessment, transcriptomic profiling indicated that the genes involved in the ethylene signaling, phenylpropanoid and isoprenoid pathways were greatly upregulated in SlMYB75-OE fruits. Yeast one-hybrid and transactivation assays revealed that SlMYB75 is able to directly bind to the MYBPLANT and MYBPZM cis-regulatory elements and to activate the promoters of the LOXC, AADC2 and TPS genes. The identification of SlMYB75 as a key regulator of fruit quality attributes through the transcriptional regulation of downstream genes involved in several metabolic pathways opens new avenues towards engineering fruits with a higher sensory and nutritional quality.
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Affiliation(s)
- Wei Jian
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
| | - Haohao Cao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, 611130 Chengdu, China
| | - Yudong Liu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
| | - Juanfang Lu
- College of Horticulture and Landscape Architecture, Southwest University, 400716 Chongqing, China
| | - Wang Lu
- College of Horticulture and Landscape Architecture, Southwest University, 400716 Chongqing, China
| | - Ning Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
| | - Jianhui Wang
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, 610066 Chengdu, China
| | - Jian Zou
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
| | - Ning Tang
- Institute of Special Plants, Chongqing University of Arts and Sciences, 402160 Yongchuan, China
| | - Chan Xu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
| | - Yulin Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
| | - Yanqiang Gao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
| | - Wanpeng Xi
- College of Horticulture and Landscape Architecture, Southwest University, 400716 Chongqing, China
| | - Mondher Bouzayen
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
- INRA, Genomique et Biotechnologie des Fruits, Chemin de Borde Rouge, F-31326 Castanet-Tolosan, France
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
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Zhou D, Shen Y, Zhou P, Fatima M, Lin J, Yue J, Zhang X, Chen LY, Ming R. Papaya CpbHLH1/2 regulate carotenoid biosynthesis-related genes during papaya fruit ripening. HORTICULTURE RESEARCH 2019; 6:80. [PMID: 31263564 PMCID: PMC6588581 DOI: 10.1038/s41438-019-0162-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/22/2019] [Accepted: 04/26/2019] [Indexed: 05/03/2023]
Abstract
The ripening of papaya is a physiological and metabolic process associated with accumulation of carotenoids, alternation of flesh color and flavor, which depending on genotype and external factors such as light and hormone. Transcription factors regulating carotenoid biosynthesis have not been analyzed during papaya fruit ripening. RNA-Seq experiments were implemented using different ripening stages of papaya fruit from two papaya varieties. Cis-elements in lycopene β-cyclase genes (CpCYC-B and CpLCY-B) were identified, and followed by genome-wide analysis to identify transcription factors binding to these cis-elements, resulting in the identification of CpbHLH1 and CpbHLH2, two bHLH genes. The expressions of CpbHLH1/2 were changed during fruit development, coupled with transcript increase of carotenoid biosynthesis-related genes including CpCYC-B, CpLCY-B, CpPDS2, CpZDS, CpLCY-E, and CpCHY-B. Yeast one-hybrid (Y1H) and transient expression assay revealed that CpbHLH1/2 could bind to the promoters of CpCYC-B and CpLCY-B, and regulate their transcriptions. In response to strong light, the results of elevated expression of carotenoid biosynthesis-related genes and the changed expression of CpbHLH1/2 indicated that CpbHLH1/2 were involved in light-mediated mechanisms of regulating critical genes in the carotenoid biosynthesis pathway. Collectively, our findings demonstrated several TF family members participating in the regulation of carotenoid genes and proved that CpbHLH1 and CpbHLH2 individually regulated the transcription of lycopene β-cyclase genes (CpCYC-B and CpLCY-B). This study yielded novel findings on regulatory mechanism of carotenoid biosynthesis during papaya fruit ripening.
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Affiliation(s)
- Dong Zhou
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Yanhong Shen
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Ping Zhou
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Mahpara Fatima
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Jishan Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Jingjing Yue
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Xingtan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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Wang Q, Zeng S, Wu X, Lei H, Wang Y, Tang H. Interspecies Developmental Differences in Metabonomic Phenotypes of Lycium ruthenicum and L. barbarum Fruits. J Proteome Res 2018; 17:3223-3236. [DOI: 10.1021/acs.jproteome.8b00349] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qi Wang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, China
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Xiangyu Wu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Hehua Lei
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, China
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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Beauvoit B, Belouah I, Bertin N, Cakpo CB, Colombié S, Dai Z, Gautier H, Génard M, Moing A, Roch L, Vercambre G, Gibon Y. Putting primary metabolism into perspective to obtain better fruits. ANNALS OF BOTANY 2018; 122:1-21. [PMID: 29718072 PMCID: PMC6025238 DOI: 10.1093/aob/mcy057] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/29/2017] [Indexed: 05/18/2023]
Abstract
Background One of the key goals of fruit biology is to understand the factors that influence fruit growth and quality, ultimately with a view to manipulating them for improvement of fruit traits. Scope Primary metabolism, which is not only essential for growth but is also a major component of fruit quality, is an obvious target for improvement. However, metabolism is a moving target that undergoes marked changes throughout fruit growth and ripening. Conclusions Agricultural practice and breeding have successfully improved fruit metabolic traits, but both face the complexity of the interplay between development, metabolism and the environment. Thus, more fundamental knowledge is needed to identify further strategies for the manipulation of fruit metabolism. Nearly two decades of post-genomics approaches involving transcriptomics, proteomics and/or metabolomics have generated a lot of information about the behaviour of fruit metabolic networks. Today, the emergence of modelling tools is providing the opportunity to turn this information into a mechanistic understanding of fruits, and ultimately to design better fruits. Since high-quality data are a key requirement in modelling, a range of must-have parameters and variables is proposed.
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Affiliation(s)
| | - Isma Belouah
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | | | - Sophie Colombié
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Zhanwu Dai
- UMR 1287 EGFV, INRA, Univ. Bordeaux, Bordeaux Sci Agro, F-Villenave d’Ornon, France
| | | | | | - Annick Moing
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Léa Roch
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | - Yves Gibon
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
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Guo YF, Zhang YL, Shan W, Cai YJ, Liang SM, Chen JY, Lu WJ, Kuang JF. Identification of Two Transcriptional Activators MabZIP4/5 in Controlling Aroma Biosynthetic Genes during Banana Ripening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6142-6150. [PMID: 29809003 DOI: 10.1021/acs.jafc.8b01435] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The transcriptional regulation of aroma formation genes remains poorly understood in the banana. In this work, we found that the expressions of a subset of aroma biosynthetic genes including MaOMT1, MaMT1, MaGT1, MaBCAT1, MaACY1, MaAGT1, and BanAAT, as well as two bZIP genes, MabZIP4 and MabZIP5, were down-regulated when prestored at 7 °C compared to those prestored at 22 °C during the ripening process of banana. Furthermore, MabZIP4 and MabZIP5 were shown to be able to activate the transcription of these aroma biosynthetic genes. Importantly, MabZIP4 directly binds to BanAAT promoter, while MabZIP5 binds to the promoters of MaMT1, MaACY1, MaAGT1, and BanAAT via the G-box motif, implicating the diverse functional significances of MabZIPs in controlling aroma biosynthesis in banana. Overall, this work sheds new insights on the understanding of transcriptional regulatory mechanisms associated with aroma formation during banana ripening.
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Affiliation(s)
- Yu-Fan Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science , South China Agricultural University , Guangzhou 510642 , PR China
| | - Yun-Liang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science , South China Agricultural University , Guangzhou 510642 , PR China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science , South China Agricultural University , Guangzhou 510642 , PR China
| | - Yong-Jian Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science , South China Agricultural University , Guangzhou 510642 , PR China
| | - Shu-Min Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science , South China Agricultural University , Guangzhou 510642 , PR China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science , South China Agricultural University , Guangzhou 510642 , PR China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science , South China Agricultural University , Guangzhou 510642 , PR China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science , South China Agricultural University , Guangzhou 510642 , PR China
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Asiche WO, Mitalo OW, Kasahara Y, Tosa Y, Mworia EG, Owino WO, Ushijima K, Nakano R, Yano K, Kubo Y. Comparative transcriptome analysis reveals distinct ethylene-independent regulation of ripening in response to low temperature in kiwifruit. BMC PLANT BIOLOGY 2018; 18:47. [PMID: 29562897 PMCID: PMC5863462 DOI: 10.1186/s12870-018-1264-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 03/08/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Kiwifruit are classified as climacteric since exogenous ethylene (or its analogue propylene) induces rapid ripening accompanied by ethylene production under positive feedback regulation. However, most of the ripening-associated changes (Phase 1 ripening) in kiwifruit during storage and on-vine occur largely in the absence of any detectable ethylene. This ripening behavior is often attributed to basal levels of system I ethylene, although it is suggested to be modulated by low temperature. RESULTS To elucidate the mechanisms regulating Phase 1 ripening in kiwifruit, a comparative transcriptome analysis using fruit continuously exposed to propylene (at 20 °C), and during storage at 5 °C and 20 °C was conducted. Propylene exposure induced kiwifruit softening, reduction of titratable acidity (TA), increase in soluble solids content (SSC) and ethylene production within 5 days. During storage, softening and reduction of TA occurred faster in fruit at 5 °C compared to 20 °C although no endogenous ethylene production was detected. Transcriptome analysis revealed 3761 ripening-related differentially expressed genes (DEGs), of which 2742 were up-regulated by propylene while 1058 were up-regulated by low temperature. Propylene exclusively up-regulated 2112 DEGs including those associated with ethylene biosynthesis and ripening such as AcACS1, AcACO2, AcPL1, AcXET1, Acβ-GAL, AcAAT, AcERF6 and AcNAC7. Similarly, low temperature exclusively up-regulated 467 DEGS including AcACO3, AcPL2, AcPMEi, AcADH, Acβ-AMY2, AcGA2ox2, AcNAC5 and AcbZIP2 among others. A considerable number of DEGs such as AcPG, AcEXP1, AcXET2, Acβ-AMY1, AcGA2ox1, AcNAC6, AcMADS1 and AcbZIP1 were up-regulated by either propylene or low temperature. Frequent 1-MCP treatments failed to inhibit the accelerated ripening and up-regulation of associated DEGs by low temperature indicating that the changes were independent of ethylene. On-vine kiwifruit ripening proceeded in the absence of any detectable endogenous ethylene production, and coincided with increased expression of low temperature-responsive DEGs as well as the decrease in environmental temperature. CONCLUSIONS These results indicate that kiwifruit possess both ethylene-dependent and low temperature-modulated ripening mechanisms that are distinct and independent of each other. The current work provides a foundation for elaborating the control of these two ripening mechanisms in kiwifruit.
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Affiliation(s)
- William O. Asiche
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700–8530 Japan
| | - Oscar W. Mitalo
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700–8530 Japan
| | - Yuka Kasahara
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700–8530 Japan
| | - Yasuaki Tosa
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700–8530 Japan
| | | | - Willis O. Owino
- Department of Food Science and Technology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700–8530 Japan
| | - Ryohei Nakano
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700–8530 Japan
| | - Kentaro Yano
- School of Agriculture, Meiji University, Kawasaki, 214–8571 Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700–8530 Japan
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Srivastava AK, Lu Y, Zinta G, Lang Z, Zhu JK. UTR-Dependent Control of Gene Expression in Plants. TRENDS IN PLANT SCIENCE 2018; 23:248-259. [PMID: 29223924 PMCID: PMC5828884 DOI: 10.1016/j.tplants.2017.11.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 10/25/2017] [Accepted: 11/06/2017] [Indexed: 05/22/2023]
Abstract
Throughout their lives, plants sense many developmental and environmental stimuli, and activation of optimal responses against these stimuli requires extensive transcriptional reprogramming. To facilitate this activation, plant mRNA contains untranslated regions (UTRs) that significantly increase the coding capacity of the genome by producing multiple mRNA variants from the same gene. In this review we compare UTRs of arabidopsis (Arabidopsis thaliana) and rice (Oryza sativum) at the genome scale to highlight their complexity in crop plants. We discuss different modes of UTR-based regulation with emphasis on genes that regulate multiple plant processes, including flowering, stress responses, and nutrient homeostasis. We demonstrate functional specificity in genes with variable UTR length and propose future research directions.
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Affiliation(s)
- Ashish Kumar Srivastava
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; Permanent address: Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Yuming Lu
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Gaurav Zinta
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
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Hsu PY, Benfey PN. Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. Proteomics 2017; 18:e1700038. [PMID: 28759167 DOI: 10.1002/pmic.201700038] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Indexed: 12/18/2022]
Abstract
Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics. We also examine the evidence for new peptides arising from sORFs and discuss their functions in plant development, environmental responses, and translational control.
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Affiliation(s)
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University, Durham, NC, USA
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Biotechnological Strategies to Improve Plant Biomass Quality for Bioethanol Production. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7824076. [PMID: 28951875 PMCID: PMC5603102 DOI: 10.1155/2017/7824076] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 07/13/2017] [Accepted: 07/19/2017] [Indexed: 11/17/2022]
Abstract
The transition from an economy dependent on nonrenewable energy sources to one with higher diversity of renewables will not be a simple process. It requires an important research effort to adapt to the dynamics of the changing energy market, sort costly processes, and avoid overlapping with social interest markets such as food and livestock production. In this review, we analyze the desirable traits of raw plant materials for the bioethanol industry and the molecular biotechnology strategies employed to improve them, in either plants already under use (as maize) or proposed species (large grass families). The fundamentals of these applications can be found in the mechanisms by which plants have evolved different pathways to manage carbon resources for reproduction or survival in unexpected conditions. Here, we review the means by which this information can be used to manipulate these mechanisms for commercial uses, including saccharification improvement of starch and cellulose, decrease in cell wall recalcitrance through lignin modification, and increase in plant biomass.
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Kanayama Y. Sugar Metabolism and Fruit Development in the Tomato. THE HORTICULTURE JOURNAL 2017; 86:417-425. [PMID: 0 DOI: 10.2503/hortj.okd-ir01] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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Li X, Fan S, Hu W, Liu G, Wei Y, He C, Shi H. Two Cassava Basic Leucine Zipper (bZIP) Transcription Factors (MebZIP3 and MebZIP5) Confer Disease Resistance against Cassava Bacterial Blight. FRONTIERS IN PLANT SCIENCE 2017; 8:2110. [PMID: 29276527 PMCID: PMC5727076 DOI: 10.3389/fpls.2017.02110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/27/2017] [Indexed: 05/19/2023]
Abstract
Basic domain-leucine zipper (bZIP) transcription factor, one type of conserved gene family, plays an important role in plant development and stress responses. Although 77 MebZIPs have been genome-wide identified in cassava, their in vivo roles remain unknown. In this study, we analyzed the expression pattern and the function of two MebZIPs (MebZIP3 and MebZIP5) in response to pathogen infection. Gene expression analysis indicated that MebZIP3 and MebZIP5 were commonly regulated by flg22, Xanthomonas axonopodis pv. manihotis (Xam), salicylic acid (SA), and hydrogen peroxide (H2O2). Subcellular localization analysis showed that MebZIP3 and MebZIP5 are specifically located in cell nucleus. Through overexpression in tobacco, we found that MebZIP3 and MebZIP5 conferred improved disease resistance against cassava bacterial blight, with more callose depositions. On the contrary, MebZIP3- and MebZIP5-silenced plants by virus-induced gene silencing (VIGS) showed disease sensitive phenotype, lower transcript levels of defense-related genes and less callose depositions. Taken together, this study highlights the positive role of MebZIP3 and MebZIP5 in disease resistance against cassava bacterial blight for further utilization in genetic improvement of cassava disease resistance.
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Affiliation(s)
- Xiaolin Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shuhong Fan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- *Correspondence: Haitao Shi, Chaozu He,
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- *Correspondence: Haitao Shi, Chaozu He,
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The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts. Sci Rep 2016; 6:30444. [PMID: 27457880 PMCID: PMC4960570 DOI: 10.1038/srep30444] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Abstract
Basic leucine zippers (bZIPs) form a large plant transcription factor family. C and S1 bZIP groups can heterodimerize, fulfilling crucial roles in seed development and stress response. S1 sequences also harbor a unique regulatory mechanism, termed Sucrose-Induced Repression of Translation (SIRT). The conservation of both C/S1 bZIP interactions and SIRT remains poorly characterized in non-model species, leaving their evolutionary origin uncertain and limiting crop research. In this work, we explored recently published plant sequencing data to establish a detailed phylogeny of C and S1 bZIPs, investigating their intertwined role in plant evolution, and the origin of SIRT. Our analyses clarified C and S1 bZIP orthology relationships in angiosperms, and identified S1 sequences in gymnosperms. We experimentally showed that the gymnosperm orthologs are regulated by SIRT, tracing back the origin of this unique regulatory mechanism to the ancestor of seed plants. Additionally, we discovered an earlier S ortholog in the charophyte algae Klebsormidium flaccidum, together with a C ortholog. This suggests that C and S groups originated by duplication from a single algal proto-C/S ancestor. Based on our observations, we propose a model wherein the C/S1 bZIP dimer network evolved in seed plants from pre-existing C/S bZIP interactions.
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