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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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2
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Mehdi F, Galani S, Wickramasinghe KP, Zhao P, Lu X, Lin X, Xu C, Liu H, Li X, Liu X. Current perspectives on the regulatory mechanisms of sucrose accumulation in sugarcane. Heliyon 2024; 10:e27277. [PMID: 38463882 PMCID: PMC10923725 DOI: 10.1016/j.heliyon.2024.e27277] [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: 08/03/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/12/2024] Open
Abstract
Sugars transported from leaves (source) to stems (sink) energize cell growth, elongation, and maintenance. which are regulated by a variety of genes. This review reflects progress and prospects in the regulatory mechanism for maximum sucrose accumulation, including the role of sucrose metabolizing enzymes, sugar transporters and the elucidation of post-transcriptional control of sucrose-induced regulation of translation (SIRT) in the accumulation of sucrose. The current review suggests that SIRT is emerging as a significant mechanism controlling Scbzip44 activities in response to endogenous sugar signals (via the negative feedback mechanism). Sucrose-controlled upstream open reading frame (SC-uORF) exists at the 5' leader region of Scbzip44's main ORF, which inhibits sucrose accumulation through post-transcriptional regulatory mechanisms. Sucrose transporters (SWEET1a/4a/4b/13c, TST, SUT1, SUT4 and SUT5) are crucial for sucrose translocation from source to sink. Particularly, SWEET13c was found to be a major contributor to the efflux in the transportation of stems. Tonoplast sugar transporters (TSTs), which import sucrose into the vacuole, suggest their tissue-specific role from source to sink. Sucrose cleavage has generally been linked with invertase isozymes, whereas sucrose synthase (SuSy)-catalyzed metabolism has been associated with biosynthetic processes such as UDP-Glc, cellulose, hemicellulose and other polymers. However, other two key sucrose-metabolizing enzymes, such as sucrose-6-phosphate phosphohydrolase (S6PP) and sucrose phosphate synthase (SPS) isoforms, have been linked with sucrose biosynthesis. These findings suggest that manipulation of genes, such as overexpression of SPS genes and sucrose transporter genes, silencing of the SC-uORF of Scbzip44 (removing the 5' leader region of the main ORF that is called SIRT-Insensitive) and downregulation of the invertase genes, may lead to maximum sucrose accumulation. This review provides an overview of sugarcane sucrose-regulating systems and baseline information for the development of cultivars with higher sucrose accumulation.
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Affiliation(s)
- Faisal Mehdi
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Saddia Galani
- Dr.A. Q. Khan Institute of Biotechnology and Genetic Engineering, University of Karachi, Karachi Pakistan
| | - Kamal Priyananda Wickramasinghe
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
- Sugarcane Research Institute, Uda Walawa, 70190, Sri Lanka
| | - Peifang Zhao
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Xin Lu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Xiuqin Lin
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Chaohua Xu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Hongbo Liu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Xujuan Li
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Xinlong Liu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
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3
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Wang J, Liu J, Guo Z. Natural uORF variation in plants. TRENDS IN PLANT SCIENCE 2024; 29:290-302. [PMID: 37640640 DOI: 10.1016/j.tplants.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/04/2023] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
Abstract
Taking advantage of natural variation promotes our understanding of phenotypic diversity and trait evolution, ultimately accelerating plant breeding, in which the identification of causal variations is critical. To date, sequence variations in the coding region and transcription level polymorphisms caused by variations in the promoter have been prioritized. An upstream open reading frame (uORF) in the 5' untranslated region (5' UTR) regulates gene expression at the post-transcription or translation level. In recent years, studies have demonstrated that natural uORF variations shape phenotypic diversity. This opinion article highlights recent researches and speculates on future directions for natural uORF variation in plants.
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Affiliation(s)
- Jiangen Wang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Juhong Liu
- Fuzhou Institute for Data Technology Co., Ltd., Fuzhou 350207, China
| | - Zilong Guo
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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4
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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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5
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Lim MN, Lee SE, Jeon JS, Yoon IS, Hwang YS. OsbZIP38/87-mediated activation of OsHXK7 improves the viability of rice cells under hypoxic conditions. JOURNAL OF PLANT PHYSIOLOGY 2024; 293:154182. [PMID: 38277982 DOI: 10.1016/j.jplph.2024.154182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/28/2024]
Abstract
Maintenance of energy metabolism is critical for rice (Oryza sativa) tolerance under submerged cultivation. Here, OsHXK7 was the most actively induced hexokinase gene in the embryos of hypoxically germinating rice seeds. Suspension-cultured cells established from seeds of T-DNA null mutants for the OsHXK7 locus did not regrow after 3-d-hypoxic stress and showed increased susceptibility to low-oxygen stress-in terms of viability-and decreased alcoholic fermentation activities compared to those of the wild-type. The promoter element containing the TGACG-motif, a well-known target site for the basic leucine zipper (bZIP) transcription factors, was responsible for sugar regulation of the OsHXK7 promoter activity. Systematic screening of the OsbZIP genes showing the similar expression patterns to that of OsHXK7 in the transcriptomic datasets produced two bZIP genes, OsbZIP38 and 87, belonging to the S1 bZIP subfamily as the candidate for the activator for this gene expression. Gain- and loss-of-function experiments through transient expression assays have demonstrated that these two bZIP proteins are indeed involved in the induction of OsHXK7 expression under starvation or low-energy conditions. Our finding suggests that C/S1 bZIP network-mediated hypoxic deregulation of sugar-responsive genes may work in concert for the molecular adaptation of rice cells to submergence.
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Affiliation(s)
- Mi-Na Lim
- Department of Biotechnology, CHA University, Seongnam, 13488, South Korea
| | - Sung-Eun Lee
- Department of Systems Biotechnology, Konkuk University, Seoul, 143-701, South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, South Korea
| | - In Sun Yoon
- Molecular Breeding Division, National Academy of Agricultural Science, Jeonju, 565-851, South Korea
| | - Yong-Sic Hwang
- Department of Systems Biotechnology, Konkuk University, Seoul, 143-701, South Korea.
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6
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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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7
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Yang MY, Yang X, Yan Z, Chao Q, Shen J, Shui GH, Guo PM, Wang BC. OsTST1, a key tonoplast sugar transporter from source to sink, plays essential roles in affecting yields and height of rice (Oryza sativa L.). PLANTA 2023; 258:4. [PMID: 37219719 DOI: 10.1007/s00425-023-04160-w] [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: 02/08/2023] [Accepted: 05/14/2023] [Indexed: 05/24/2023]
Abstract
MAIN CONCLUSION OsTST1 affects yield and development and mediates sugar transportation of plants from source to sink in rice, which influences the accumulation of intermediate metabolites from tricarboxylic acid cycle indirectly. Tonoplast sugar transporters (TSTs) are essential for vacuolar sugar accumulation in plants. Carbohydrate transport across tonoplasts maintains the metabolic balance in plant cells, and carbohydrate distribution is crucial to plant growth and productivity. Large plant vacuoles store high concentrations of sugars to meet plant requirements for energy and other biological processes. The abundance of sugar transporter affects crop biomass and reproductive growth. However, it remains unclear whether the rice (Oryza sativa L.) sugar transport protein OsTST1 affects yield and development. In this study, we found that OsTST1 knockout mutants generated via CRISPR/Cas9 exhibited slower development, smaller seeds, and lower yield than wild type (WT) rice plants. Notably, plants overexpressing OsTST1 showed the opposite effects. Changes in rice leaves at 14 days after germination (DAG) and at 10 days after flowering (DAF) suggested that OsTST1 affected the accumulation of intermediate metabolites from the glycolytic pathway and the tricarboxylic acid (TCA) cycle. The modification of the sugar transport between cytosol and vacuole mediated by OsTST1 induces deregulation of several genes including transcription factors (TFs). In summary, no matter the location of sucrose and sink is, these preliminary results revealed that OsTST1 was important for sugar transport from source to sink tissues, thus affecting plant growth and development.
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Affiliation(s)
- Man-Yu Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiu Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Yan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- College of Life Sciences, National Demonstration Center for Experimental Biology Education, Sichuan University, Chengdu, 610064, China
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Shen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Guang-Hou Shui
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Peng-Mei Guo
- LipidALL Technologies Company Limited, Changzhou, 213022, Jiangsu, China
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Medina-Chávez L, Camacho C, Martínez-Rodríguez JA, Barrera-Figueroa BE, Nagel DH, Juntawong P, Peña-Castro JM. Submergence Stress Alters the Expression of Clock Genes and Configures New Zeniths and Expression of Outputs in Brachypodium distachyon. Int J Mol Sci 2023; 24:ijms24108555. [PMID: 37239900 DOI: 10.3390/ijms24108555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Plant networks of oscillating genes coordinate internal processes with external cues, contributing to increased fitness. We hypothesized that the response to submergence stress may dynamically change during different times of the day. In this work, we determined the transcriptome (RNA sequencing) of the model monocotyledonous plant, Brachypodium distachyon, during a day of submergence stress, low light, and normal growth. Two ecotypes of differential tolerance, Bd21 (sensitive) and Bd21-3 (tolerant), were included. We submerged 15-day-old plants under a long-day diurnal cycle (16 h light/8 h dark) and collected samples after 8 h of submergence at ZT0 (dawn), ZT8 (midday), ZT16 (dusk), ZT20 (midnight), and ZT24 (dawn). Rhythmic processes were enriched both with up- and down-regulated genes, and clustering highlighted that the morning and daytime oscillator components (PRRs) show peak expression in the night, and a decrease in the amplitude of the clock genes (GI, LHY, RVE) was observed. Outputs included photosynthesis-related genes losing their known rhythmic expression. Up-regulated genes included oscillating suppressors of growth, hormone-related genes with new late zeniths (e.g., JAZ1, ZEP), and mitochondrial and carbohydrate signaling genes with shifted zeniths. The results highlighted genes up-regulated in the tolerant ecotype such as METALLOTHIONEIN3 and ATPase INHIBITOR FACTOR. Finally, we show by luciferase assays that Arabidopsis thaliana clock genes are also altered by submergence changing their amplitude and phase. This study can guide the research of chronocultural strategies and diurnal-associated tolerance mechanisms.
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Affiliation(s)
- Lucisabel Medina-Chávez
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
- Programa de Doctorado en Biotecnología, División de Estudios de Posgrado, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
| | - Christian Camacho
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Jorge Arturo Martínez-Rodríguez
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
| | - Blanca Estela Barrera-Figueroa
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
| | - Dawn H Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Piyada Juntawong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Julián Mario Peña-Castro
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
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Ji X, Xin Z, Yuan Y, Wang M, Lu X, Li J, Zhang Y, Niu L, Jiang CZ, Sun D. A petunia transcription factor, PhOBF1, regulates flower senescence by modulating gibberellin biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad022. [PMID: 37786859 PMCID: PMC10541524 DOI: 10.1093/hr/uhad022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/06/2023] [Indexed: 10/04/2023]
Abstract
Flower senescence is commonly enhanced by the endogenous hormone ethylene and suppressed by the gibberellins (GAs) in plants. However, the detailed mechanisms for the antagonism of these hormones during flower senescence remain elusive. In this study, we characterized one up-regulated gene PhOBF1, belonging to the basic leucine zipper transcription factor family, in senescing petals of petunia (Petunia hybrida). Exogenous treatments with ethylene and GA3 provoked a dramatic increase in PhOBF1 transcripts. Compared with wild-type plants, PhOBF1-RNAi transgenic petunia plants exhibited shortened flower longevity, while overexpression of PhOBF1 resulted in delayed flower senescence. Transcript abundances of two senescence-related genes PhSAG12 and PhSAG29 were higher in PhOBF1-silenced plants but lower in PhOBF1-overexpressing plants. Silencing and overexpression of PhOBF1 affected expression levels of a few genes involved in the GA biosynthesis and signaling pathways, as well as accumulation levels of bioactive GAs GA1 and GA3. Application of GA3 restored the accelerated petal senescence to normal levels in PhOBF1-RNAi transgenic petunia lines, and reduced ethylene release and transcription of three ethylene biosynthetic genes PhACO1, PhACS1, and PhACS2. Moreover, PhOBF1 was observed to specifically bind to the PhGA20ox3 promoter containing a G-box motif. Transient silencing of PhGA20ox3 in petunia plants through tobacco rattle virus-based virus-induced gene silencing method led to accelerated corolla senescence. Our results suggest that PhOBF1 functions as a negative regulator of ethylene-mediated flower senescence by modulating the GA production.
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Affiliation(s)
- Xiaotong Ji
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ziwei Xin
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanping Yuan
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meiling Wang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinyi Lu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiaqi Li
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanlong Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lixin Niu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
- Crops Pathology and Genetics Research Unit, USDA-ARS, Davis, CA 95616, USA
| | - Daoyang Sun
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
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10
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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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11
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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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12
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Causier B, Hopes T, McKay M, Paling Z, Davies B. Plants utilise ancient conserved peptide upstream open reading frames in stress-responsive translational regulation. PLANT, CELL & ENVIRONMENT 2022; 45:1229-1241. [PMID: 35128674 PMCID: PMC9305500 DOI: 10.1111/pce.14277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 05/08/2023]
Abstract
The regulation of protein synthesis plays an important role in the growth and development of all organisms. Upstream open reading frames (uORFs) are commonly found in eukaryotic messenger RNA transcripts and typically attenuate the translation of associated downstream main ORFs (mORFs). Conserved peptide uORFs (CPuORFs) are a rare subset of uORFs, some of which have been shown to conditionally regulate translation by ribosome stalling. Here, we show that Arabidopsis CPuORF19, CPuORF46 and CPuORF47, which are ancient in origin, regulate translation of any downstream ORF, in response to the agriculturally significant environmental signals, heat stress and water limitation. Consequently, these CPuORFs represent a versatile toolkit for inducible gene expression with broad applications. Finally, we note that different classes of CPuORFs may operate during distinct phases of translation, which has implications for the bioengineering of these regulatory factors.
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Affiliation(s)
- Barry Causier
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Mary McKay
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Zachary Paling
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Brendan Davies
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
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13
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Ai G, Liu J, Fu X, Li T, Zhu H, Zhai Y, Xia C, Pan W, Li J, Jing M, Shen D, Xia A, Dou D. Making Use of Plant uORFs to Control Transgene Translation in Response to Pathogen Attack. BIODESIGN RESEARCH 2022; 2022:9820540. [PMID: 37850142 PMCID: PMC10521741 DOI: 10.34133/2022/9820540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/06/2022] [Indexed: 10/19/2023] Open
Abstract
Reducing crop loss to diseases is urgently needed to meet increasing food production challenges caused by the expanding world population and the negative impact of climate change on crop productivity. Disease-resistant crops can be created by expressing endogenous or exogenous genes of interest through transgenic technology. Nevertheless, enhanced resistance by overexpressing resistance-produced genes often results in adverse developmental affects. Upstream open reading frames (uORFs) are translational control elements located in the 5' untranslated region (UTR) of eukaryotic mRNAs and may repress the translation of downstream genes. To investigate the function of three uORFs from the 5' -UTR of ACCELERATED CELL 11 (uORFsACD11), we develop a fluorescent reporter system and find uORFsACD11 function in repressing downstream gene translation. Individual or simultaneous mutations of the three uORFsACD11 lead to repression of downstream translation efficiency at different levels. Importantly, uORFsACD11-mediated translational inhibition is impaired upon recognition of pathogen attack of plant leaves. When coupled with the PATHOGENESIS-RELATED GENE 1 (PR1) promoter, the uORFsACD11 cassettes can upregulate accumulation of Arabidopsis thaliana LECTIN RECEPTOR KINASE-VI.2 (AtLecRK-VI.2) during pathogen attack and enhance plant resistance to Phytophthora capsici. These findings indicate that the uORFsACD11 cassettes can be a useful toolkit that enables a high level of protein expression during pathogen attack, while for ensuring lower levels of protein expression at normal conditions.
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Affiliation(s)
- Gan Ai
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin Liu
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowei Fu
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianli Li
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai Zhu
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Zhai
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Chuyan Xia
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiye Pan
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Jialu Li
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Maofeng Jing
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai Xia
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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14
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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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15
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Li W, Huang L, Liu N, Pandey MK, Chen Y, Cheng L, Guo J, Yu B, Luo H, Zhou X, Huai D, Chen W, Yan L, Wang X, Lei Y, Varshney RK, Liao B, Jiang H. Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts. Int J Mol Sci 2021; 22:ijms22147266. [PMID: 34298903 PMCID: PMC8306169 DOI: 10.3390/ijms22147266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/02/2022] Open
Abstract
Sucrose content is a crucial indicator of quality and flavor in peanut seed, and there is a lack of clarity on the molecular basis of sucrose metabolism in peanut seed. In this context, we performed a comprehensive comparative transcriptome study on the samples collected at seven seed development stages between a high-sucrose content variety (ICG 12625) and a low-sucrose content variety (Zhonghua 10). The transcriptome analysis identified a total of 8334 genes exhibiting significantly different abundances between the high- and low-sucrose varieties. We identified 28 differentially expressed genes (DEGs) involved in sucrose metabolism in peanut and 12 of these encoded sugars will eventually be exported transporters (SWEETs). The remaining 16 genes encoded enzymes, such as cell wall invertase (CWIN), vacuolar invertase (VIN), cytoplasmic invertase (CIN), cytosolic fructose-bisphosphate aldolase (FBA), cytosolic fructose-1,6-bisphosphate phosphatase (FBP), sucrose synthase (SUS), cytosolic phosphoglucose isomerase (PGI), hexokinase (HK), and sucrose-phosphate phosphatase (SPP). The weighted gene co-expression network analysis (WGCNA) identified seven genes encoding key enzymes (CIN, FBA, FBP, HK, and SPP), three SWEET genes, and 90 transcription factors (TFs) showing a high correlation with sucrose content. Furthermore, upon validation, six of these genes were successfully verified as exhibiting higher expression in high-sucrose recombinant inbred lines (RILs). Our study suggested the key roles of the high expression of SWEETs and enzymes in sucrose synthesis making the genotype ICG 12625 sucrose-rich. This study also provided insights into the molecular basis of sucrose metabolism during seed development and facilitated exploring key candidate genes and molecular breeding for sucrose content in peanuts.
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Affiliation(s)
- Weitao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (M.K.P.); (R.K.V.)
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Liangqiang Cheng
- Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural Science, Guiyang 550006, China;
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (M.K.P.); (R.K.V.)
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch 6150, Australia
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (W.L.); (L.H.); (N.L.); (Y.C.); (J.G.); (B.Y.); (H.L.); (X.Z.); (D.H.); (W.C.); (L.Y.); (X.W.); (Y.L.); (B.L.)
- Correspondence: ; Tel.: +86-27-8671-1550; Fax: +86-27-8681-6451
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16
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Prior MJ, Selvanayagam J, Kim JG, Tomar M, Jonikas M, Mudgett MB, Smeekens S, Hanson J, Frommer WB. Arabidopsis bZIP11 Is a Susceptibility Factor During Pseudomonas syringae Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:439-447. [PMID: 33400562 DOI: 10.1094/mpmi-11-20-0310-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Matthew J Prior
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92507, U.S.A
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, U.S.A
- Department of Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Jebasingh Selvanayagam
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, U.S.A
- Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Jung-Gun Kim
- Department of Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Monika Tomar
- Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Martin Jonikas
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, U.S.A
- Department of Molecular Biology, Princeton University, 119 Lewis Thomas Laboratory, Washington Road, Princeton, NJ, U.S.A
| | - Mary Beth Mudgett
- Department of Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Sjef Smeekens
- Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Johannes Hanson
- Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, U.S.A
- Department of Biology, Stanford University, Stanford, CA 94305, U.S.A
- Molecular Physiology, Heinrich Heine Universität, 40225 Düsseldorf, Germany
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17
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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: 64] [Impact Index Per Article: 16.0] [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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van der Horst S, Filipovska T, Hanson J, Smeekens S. Metabolite Control of Translation by Conserved Peptide uORFs: The Ribosome as a Metabolite Multisensor. PLANT PHYSIOLOGY 2020; 182:110-122. [PMID: 31451550 PMCID: PMC6945846 DOI: 10.1104/pp.19.00940] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/16/2019] [Indexed: 05/19/2023]
Abstract
Ribosomes translate the mRNA code into protein, and this process can be controlled by metabolites that bind to the translating ribosome in interaction with the nascent protein.
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Affiliation(s)
- Sjors van der Horst
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Teodora Filipovska
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Johannes Hanson
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umea, Sweden
| | - Sjef Smeekens
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
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19
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Broad RC, Bonneau JP, Beasley JT, Roden S, Philips JG, Baumann U, Hellens RP, Johnson AAT. Genome-wide identification and characterization of the GDP-L-galactose phosphorylase gene family in bread wheat. BMC PLANT BIOLOGY 2019; 19:515. [PMID: 31771507 PMCID: PMC6878703 DOI: 10.1186/s12870-019-2123-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/07/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Ascorbate is a powerful antioxidant in plants and an essential micronutrient for humans. The GDP-L-galactose phosphorylase (GGP) gene encodes the rate-limiting enzyme of the L-galactose pathway-the dominant ascorbate biosynthetic pathway in plants-and is a promising gene candidate for increasing ascorbate in crops. In addition to transcriptional regulation, GGP production is regulated at the translational level through an upstream open reading frame (uORF) in the long 5'-untranslated region (5'UTR). The GGP genes have yet to be identified in bread wheat (Triticum aestivum L.), one of the most important food grain sources for humans. RESULTS Bread wheat chromosomal groups 4 and 5 were found to each contain three homoeologous TaGGP genes on the A, B, and D subgenomes (TaGGP2-A/B/D and TaGGP1-A/B/D, respectively) and a highly conserved uORF was present in the long 5'UTR of all six genes. Phylogenetic analyses demonstrated that the TaGGP genes separate into two distinct groups and identified a duplication event of the GGP gene in the ancestor of the Brachypodium/Triticeae lineage. A microsynteny analysis revealed that the TaGGP1 and TaGGP2 subchromosomal regions have no shared synteny suggesting that TaGGP2 may have been duplicated via a transposable element. The two groups of TaGGP genes have distinct expression patterns with the TaGGP1 homoeologs broadly expressed across different tissues and developmental stages and the TaGGP2 homoeologs highly expressed in anthers. Transient transformation of the TaGGP coding sequences in Nicotiana benthamiana leaf tissue increased ascorbate concentrations more than five-fold, confirming their functional role in ascorbate biosynthesis in planta. CONCLUSIONS We have identified six TaGGP genes in the bread wheat genome, each with a highly conserved uORF. Phylogenetic and microsynteny analyses highlight that a transposable element may have been responsible for the duplication and specialized expression of GGP2 in anthers in the Brachypodium/Triticeae lineage. Transient transformation of the TaGGP coding sequences in N. benthamiana demonstrated their activity in planta. The six TaGGP genes and uORFs identified in this study provide a valuable genetic resource for increasing ascorbate concentrations in bread wheat.
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Affiliation(s)
- Ronan C Broad
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Julien P Bonneau
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Jesse T Beasley
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Sally Roden
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Joshua G Philips
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Ute Baumann
- School of Agriculture, The University of Adelaide, Adelaide, South Australia, 5064, Australia
| | - Roger P Hellens
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Alexander A T Johnson
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia.
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20
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van der Horst S, Snel B, Hanson J, Smeekens S. Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs in Arabidopsis thaliana. RNA (NEW YORK, N.Y.) 2019; 25:292-304. [PMID: 30567971 PMCID: PMC6380273 DOI: 10.1261/rna.067983.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/10/2018] [Indexed: 05/10/2023]
Abstract
Eukaryotic mRNAs contain a 5' leader sequence preceding the main open reading frame (mORF) and, depending on the species, 20%-50% of eukaryotic mRNAs harbor an upstream ORF (uORF) in the 5' leader. An unknown fraction of these uORFs encode sequence conserved peptides (conserved peptide uORFs, CPuORFs). Experimentally validated CPuORFs demonstrated to regulate the translation of downstream mORFs often do so in a metabolite concentration-dependent manner. Previous research has shown that most CPuORFs possess a start codon context suboptimal for translation initiation, which turns out to be favorable for translational regulation. The suboptimal initiation context may even include non-AUG start codons, which makes CPuORFs hard to predict. For this reason, we developed a novel pipeline to identify CPuORFs unbiased of start codon using well-annotated sequence data from 31 eudicot plant species and rice. Our new pipeline was able to identify 29 novel Arabidopsis thaliana (Arabidopsis) CPuORFs, conserved across a wide variety of eudicot species of which 15 do not initiate with an AUG start codon. In addition to CPuORFs, the pipeline was able to find 14 conserved coding regions directly upstream and in frame with the mORF, which likely initiate translation on a non-AUG start codon. Altogether, our pipeline identified highly conserved coding regions in the 5' leaders of Arabidopsis transcripts, including in genes with proven functional importance such as LHY, a key regulator of the circadian clock, and the RAPTOR1 subunit of the target of rapamycin (TOR) kinase.
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Affiliation(s)
- Sjors van der Horst
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Johannes Hanson
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Sjef Smeekens
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
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21
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Sakr S, Wang M, Dédaldéchamp F, Perez-Garcia MD, Ogé L, Hamama L, Atanassova R. The Sugar-Signaling Hub: Overview of Regulators and Interaction with the Hormonal and Metabolic Network. Int J Mol Sci 2018; 57:2367-2379. [PMID: 30149541 DOI: 10.1093/pcp/pcw157] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/07/2018] [Accepted: 09/05/2016] [Indexed: 05/25/2023] Open
Abstract
Plant growth and development has to be continuously adjusted to the available resources. Their optimization requires the integration of signals conveying the plant metabolic status, its hormonal balance, and its developmental stage. Many investigations have recently been conducted to provide insights into sugar signaling and its interplay with hormones and nitrogen in the fine-tuning of plant growth, development, and survival. The present review emphasizes the diversity of sugar signaling integrators, the main molecular and biochemical mechanisms related to the sugar-signaling dependent regulations, and to the regulatory hubs acting in the interplay of the sugar-hormone and sugar-nitrogen networks. It also contributes to compiling evidence likely to fill a few knowledge gaps, and raises new questions for the future.
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Affiliation(s)
- Soulaiman Sakr
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Ming Wang
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Fabienne Dédaldéchamp
- Equipe "Sucres & Echanges Végétaux-Environnement", Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS 7267 EBI, Bâtiment B31, 3 rue Jacques Fort, TSA 51106, 86073 Poitiers CEDEX 9, France.
| | - Maria-Dolores Perez-Garcia
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Laurent Ogé
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Latifa Hamama
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Rossitza Atanassova
- Equipe "Sucres & Echanges Végétaux-Environnement", Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS 7267 EBI, Bâtiment B31, 3 rue Jacques Fort, TSA 51106, 86073 Poitiers CEDEX 9, France.
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Sakr S, Wang M, Dédaldéchamp F, Perez-Garcia MD, Ogé L, Hamama L, Atanassova R. The Sugar-Signaling Hub: Overview of Regulators and Interaction with the Hormonal and Metabolic Network. Int J Mol Sci 2018; 19:ijms19092506. [PMID: 30149541 PMCID: PMC6165531 DOI: 10.3390/ijms19092506] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/07/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022] Open
Abstract
Plant growth and development has to be continuously adjusted to the available resources. Their optimization requires the integration of signals conveying the plant metabolic status, its hormonal balance, and its developmental stage. Many investigations have recently been conducted to provide insights into sugar signaling and its interplay with hormones and nitrogen in the fine-tuning of plant growth, development, and survival. The present review emphasizes the diversity of sugar signaling integrators, the main molecular and biochemical mechanisms related to the sugar-signaling dependent regulations, and to the regulatory hubs acting in the interplay of the sugar-hormone and sugar-nitrogen networks. It also contributes to compiling evidence likely to fill a few knowledge gaps, and raises new questions for the future.
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Affiliation(s)
- Soulaiman Sakr
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Ming Wang
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Fabienne Dédaldéchamp
- Equipe "Sucres & Echanges Végétaux-Environnement", Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS 7267 EBI, Bâtiment B31, 3 rue Jacques Fort, TSA 51106, 86073 Poitiers CEDEX 9, France.
| | - Maria-Dolores Perez-Garcia
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Laurent Ogé
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Latifa Hamama
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Rossitza Atanassova
- Equipe "Sucres & Echanges Végétaux-Environnement", Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS 7267 EBI, Bâtiment B31, 3 rue Jacques Fort, TSA 51106, 86073 Poitiers CEDEX 9, France.
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23
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Luang S, Sornaraj P, Bazanova N, Jia W, Eini O, Hussain SS, Kovalchuk N, Agarwal PK, Hrmova M, Lopato S. The wheat TabZIP2 transcription factor is activated by the nutrient starvation-responsive SnRK3/CIPK protein kinase. PLANT MOLECULAR BIOLOGY 2018; 96:543-561. [PMID: 29564697 DOI: 10.1007/s11103-018-0713-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/23/2018] [Indexed: 05/09/2023]
Abstract
The understanding of roles of bZIP factors in biological processes during plant development and under abiotic stresses requires the detailed mechanistic knowledge of behaviour of TFs. Basic leucine zipper (bZIP) transcription factors (TFs) play key roles in the regulation of grain development and plant responses to abiotic stresses. We investigated the role and molecular mechanisms of function of the TabZIP2 gene isolated from drought-stressed wheat plants. Molecular characterisation of TabZIP2 and derived protein included analyses of gene expression and its target promoter, and the influence of interacting partners on the target promoter activation. Two interacting partners of TabZIP2, the 14-3-3 protein, TaWIN1 and the bZIP transcription factor TaABI5L, were identified in a Y2H screen. We established that under elevated ABA levels the activity of TabZIP2 was negatively regulated by the TaWIN1 protein and positively regulated by the SnRK3/CIPK protein kinase WPK4, reported previously to be responsive to nutrient starvation. The physical interaction between the TaWIN1 and the WPK4 was detected. We also compared the influence of homo- and hetero-dimerisation of TabZIP2 and TaABI5L on DNA binding. TabZIP2 gene functional analyses were performed using drought-inducible overexpression of TabZIP2 in transgenic wheat. Transgenic plants grown under moderate drought during flowering, were smaller than control plants, and had fewer spikes and seeds per plant. However, a single seed weight was increased compared to single seed weights of control plants in three of four evaluated transgenic lines. The observed phenotypes of transgenic plants and the regulation of TabZIP2 activity by nutrient starvation-responsive WPK4, suggest that the TabZIP2 could be the part of a signalling pathway, which controls the rearrangement of carbohydrate and nutrient flows in plant organs in response to drought.
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Affiliation(s)
- Sukanya Luang
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Pradeep Sornaraj
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Natalia Bazanova
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Commonwealth Scientific and Industrial Research Organisation, Glen Osmond, SA, 5064, Australia
| | - Wei Jia
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Omid Eini
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Department of Plant Protection, School of Agriculture, University of Zanjan, Zanjan, Iran
| | - Syed Sarfraz Hussain
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Forman Christian College, Lahore, 54600, Pakistan
| | - Nataliya Kovalchuk
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Pradeep K Agarwal
- CSIR-Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, India
| | - Maria Hrmova
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia.
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
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24
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Ghan R, Petereit J, Tillett RL, Schlauch KA, Toubiana D, Fait A, Cramer GR. The common transcriptional subnetworks of the grape berry skin in the late stages of ripening. BMC PLANT BIOLOGY 2017; 17:94. [PMID: 28558655 PMCID: PMC5450095 DOI: 10.1186/s12870-017-1043-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/22/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. RESULTS To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26 °Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock. CONCLUSIONS A common set of differentially expressed genes and gene subnetworks from seven different cultivars were examined in the skin of the late stages of grapevine berry ripening. A densely connected gene subnetwork was elucidated involving a complex interaction of berry senescent processes (autophagy), catabolism, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. Hypotheses were induced from these data sets involving sugar accumulation, light, autophagy, epigenetic regulation, and fruit development. This work provides a better understanding of berry development and the transcriptional processes involved in the late stages of ripening.
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Affiliation(s)
- Ryan Ghan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
| | - Juli Petereit
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - Richard L. Tillett
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - Karen A. Schlauch
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - David Toubiana
- Telekom Innovation, Laboratories and Cyber Security Research Center, Department of Information, Systems Engineering, Ben Gurion University, Beer Sheva, Israel
| | - Aaron Fait
- Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, 84990 Midreshet Ben-Gurion, Israel
| | - Grant R. Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
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Merchante C, Stepanova AN, Alonso JM. Translation regulation in plants: an interesting past, an exciting present and a promising future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:628-653. [PMID: 28244193 DOI: 10.1111/tpj.13520] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 05/19/2023]
Abstract
Changes in gene expression are at the core of most biological processes, from cell differentiation to organ development, including the adaptation of the whole organism to the ever-changing environment. Although the central role of transcriptional regulation is solidly established and the general mechanisms involved in this type of regulation are relatively well understood, it is clear that regulation at a translational level also plays an essential role in modulating gene expression. Despite the large number of examples illustrating the critical role played by translational regulation in determining the expression levels of a gene, our understanding of the molecular mechanisms behind such types of regulation has been slow to emerge. With the recent development of high-throughput approaches to map and quantify different critical parameters affecting translation, such as RNA structure, protein-RNA interactions and ribosome occupancy at the genome level, a renewed enthusiasm toward studying translation regulation is warranted. The use of these new powerful technologies in well-established and uncharacterized translation-dependent processes holds the promise to decipher the likely complex and diverse, but also fascinating, mechanisms behind the regulation of translation.
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Affiliation(s)
- Catharina Merchante
- Departamento de Biologia Molecular y Bioquimica, Universidad de Malaga-Instituto de Hortofruticultura Subtropical y Mediterranea, IHSM-UMA-CSIC, Malaga, Andalucía, Spain
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC, 27607, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC, 27607, USA
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Sun D, Li S, Niu L, Reid MS, Zhang Y, Jiang CZ. PhOBF1, a petunia ocs element binding factor, plays an important role in antiviral RNA silencing. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:915-930. [PMID: 28053190 PMCID: PMC6055658 DOI: 10.1093/jxb/erw490] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/09/2016] [Indexed: 05/09/2023]
Abstract
Virus-induced gene silencing (VIGS) is a common reverse genetics strategy for characterizing the function of genes in plants. The detailed mechanism governing RNA silencing efficiency triggered by viruses is largely unclear. Here, we reveal that a petunia (Petunia hybrida) ocs element binding factor, PhOBF1, one of the basic leucine zipper (bZIP) transcription factors, was up-regulated by Tobacco rattle virus (TRV) infection. Simultaneous silencing of PhOBF1 and a reporter gene, phytoene desaturase (PDS) or chalcone synthase (CHS), by TRV-based VIGS led to a failure of the development of leaf photobleaching or the white-corollas phenotype. PhOBF1 silencing caused down-regulation of RNA silencing-related genes, including RNA-dependent RNA polymerases (RDRs), Dicer-like RNase III enzymes (DCLs), and Argonautes (AGOs). After inoculation with the TRV-PhPDS, PhOBF1-RNAi lines exhibited a substantially impaired PDS silencing efficiency, whereas overexpression of PhOBF1 resulted in a recovery of the silencing phenotype (photobleaching) in systemic leaves. A compromised resistance to TRV and Tobacco mosaic virus was found in PhOBF1-RNAi lines, while PhOBF1-overexpressing lines displayed an enhanced resistance to their infections. Compared with wild-type plants, PhOBF1-silenced plants accumulated lower levels of free salicylic acid (SA), salicylic acid glucoside, and phenylalanine, contrarily to higher levels of those in plants overexpressing PhOBF1. Furthermore, transcripts of a number of genes associated with the shikimate and phenylpropanoid pathways were decreased or increased in PhOBF1-RNAi or PhOBF1-overexpressing lines, respectively. Taken together, the data suggest that PhOBF1 regulates TRV-induced RNA silencing efficiency through modulation of RDRs, DCLs, and AGOs mediated by the SA biosynthesis pathway.
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Affiliation(s)
- Daoyang Sun
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Shaohua Li
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Lixin Niu
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Michael S Reid
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Yanlong Zhang
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
- Crops Pathology and Genetic Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, USA
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27
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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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28
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Broeckx T, Hulsmans S, Rolland F. The plant energy sensor: evolutionary conservation and divergence of SnRK1 structure, regulation, and function. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6215-6252. [PMID: 27856705 DOI: 10.1093/jxb/erw416] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The SnRK1 (SNF1-related kinase 1) kinases are the plant cellular fuel gauges, activated in response to energy-depleting stress conditions to maintain energy homeostasis while also gatekeeping important developmental transitions for optimal growth and survival. Similar to their opisthokont counterparts (animal AMP-activated kinase, AMPK, and yeast Sucrose Non-Fermenting 1, SNF), they function as heterotrimeric complexes with a catalytic (kinase) α subunit and regulatory β and γ subunits. Although the overall configuration of the kinase complexes is well conserved, plant-specific structural modifications (including a unique hybrid βγ subunit) and associated differences in regulation reflect evolutionary divergence in response to fundamentally different lifestyles. While AMP is the key metabolic signal activating AMPK in animals, the plant kinases appear to be allosterically inhibited by sugar-phosphates. Their function is further fine-tuned by differential subunit expression, localization, and diverse post-translational modifications. The SnRK1 kinases act by direct phosphorylation of key metabolic enzymes and regulatory proteins, extensive transcriptional regulation (e.g. through bZIP transcription factors), and down-regulation of TOR (target of rapamycin) kinase signaling. Significant progress has been made in recent years. New tools and more directed approaches will help answer important fundamental questions regarding their structure, regulation, and function, as well as explore their potential as targets for selection and modification for improved plant performance in a changing environment.
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Affiliation(s)
- Tom Broeckx
- Laboratory for Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
| | - Sander Hulsmans
- Laboratory for Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
| | - Filip Rolland
- Laboratory for Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
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Czedik-Eysenberg A, Arrivault S, Lohse MA, Feil R, Krohn N, Encke B, Nunes-Nesi A, Fernie AR, Lunn JE, Sulpice R, Stitt M. The Interplay between Carbon Availability and Growth in Different Zones of the Growing Maize Leaf. PLANT PHYSIOLOGY 2016; 172:943-967. [PMID: 27582314 PMCID: PMC5047066 DOI: 10.1104/pp.16.00994] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/26/2016] [Indexed: 05/18/2023]
Abstract
Plants assimilate carbon in their photosynthetic tissues in the light. However, carbon is required during the night and in nonphotosynthetic organs. It is therefore essential that plants manage their carbon resources spatially and temporally and coordinate growth with carbon availability. In growing maize (Zea mays) leaf blades, a defined developmental gradient facilitates analyses in the cell division, elongation, and mature zones. We investigated the responses of the metabolome and transcriptome and polysome loading, as a qualitative proxy for protein synthesis, at dusk, dawn, and 6, 14, and 24 h into an extended night, and tracked whole-leaf elongation over this time course. Starch and sugars are depleted by dawn in the mature zone, but only after an extension of the night in the elongation and division zones. Sucrose (Suc) recovers partially between 14 and 24 h into the extended night in the growth zones, but not the mature zone. The global metabolome and transcriptome track these zone-specific changes in Suc. Leaf elongation and polysome loading in the growth zones also remain high at dawn, decrease between 6 and 14 h into the extended night, and then partially recover, indicating that growth processes are determined by local carbon status. The level of Suc-signaling metabolite trehalose-6-phosphate, and the trehalose-6-phosphate:Suc ratio are much higher in growth than mature zones at dusk and dawn but fall in the extended night. Candidate genes were identified by searching for transcripts that show characteristic temporal response patterns or contrasting responses to carbon starvation in growth and mature zones.
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Affiliation(s)
- Angelika Czedik-Eysenberg
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Stéphanie Arrivault
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Marc A Lohse
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Regina Feil
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Nicole Krohn
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Beatrice Encke
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Adriano Nunes-Nesi
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Alisdair R Fernie
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - John E Lunn
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Ronan Sulpice
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Mark Stitt
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
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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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Sagor GHM, Berberich T, Tanaka S, Nishiyama M, Kanayama Y, Kojima S, Muramoto K, Kusano T. A novel strategy to produce sweeter tomato fruits with high sugar contents by fruit-specific expression of a single bZIP transcription factor gene. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1116-26. [PMID: 26402509 DOI: 10.1111/pbi.12480] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/27/2015] [Accepted: 08/26/2015] [Indexed: 05/19/2023]
Abstract
Enhancement of sugar content and sweetness is desirable in some vegetables and in almost all fruits; however, biotechnological methods to increase sugar content are limited. Here, a completely novel methodological approach is presented that produces sweeter tomato fruits but does not have any negative effects on plant growth. Sucrose-induced repression of translation (SIRT), which is mediated by upstream open reading frames (uORFs), was initially reported in Arabidopsis AtbZIP11, a class S basic region leucine zipper (bZIP) transcription factor gene. Here, two AtbZIP11 orthologous genes, SlbZIP1 and SlbZIP2, were identified in tomato (Solanum lycopersicum). SlbZIP1 and SlbZIP2 contained four and three uORFs, respectively, in the cDNA 5'-leader regions. The second uORFs from the 5' cDNA end were conserved and involved in SIRT. Tomato plants were transformed with binary vectors in which only the main open reading frames (ORFs) of SlbZIP1 and SlbZIP2, without the SIRT-responsive uORFs, were placed under the control of the fruit-specific E8 promoter. Growth and morphology of the resulting transgenic tomato plants were comparable to those of wild-type plants. Transgenic fruits were approximately 1.5-fold higher in sugar content (sucrose/glucose/fructose) than nontransgenic tomato fruits. In addition, the levels of several amino acids, such as asparagine and glutamine, were higher in transgenic fruits than in wild-type fruits. This was expected because SlbZIP transactivates the asparagine synthase and proline dehydrogenase genes. This 'sweetening' technology is broadly applicable to other plants that utilize sucrose as a major translocation sugar.
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Affiliation(s)
- G H M Sagor
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan
| | - Thomas Berberich
- Laboratory Center, Biodiversity and Climate Research Center, Frankfurt am Main, Germany
| | - Shun Tanaka
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan
| | - Manabu Nishiyama
- Graduate School of Agricultural Science, Tohoku University, Aoba, Sendai, Japan
| | - Yoshinori Kanayama
- Graduate School of Agricultural Science, Tohoku University, Aoba, Sendai, Japan
| | - Seiji Kojima
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aoba, Sendai, Japan
| | - Koji Muramoto
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan
| | - Tomonobu Kusano
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan
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32
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Wu L, Tian L, Wang S, Zhang J, Liu P, Tian Z, Zhang H, Liu H, Chen Y. Comparative Proteomic Analysis of the Response of Maize (Zea mays L.) Leaves to Long Photoperiod Condition. FRONTIERS IN PLANT SCIENCE 2016; 7:752. [PMID: 27313588 PMCID: PMC4889979 DOI: 10.3389/fpls.2016.00752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/17/2016] [Indexed: 05/11/2023]
Abstract
Maize (Zea mays L.), an important industrial material and food source, shows an astonishing environmental adaptation. A remarkable feature of its post-domestication adaptation from tropical to temperate environments is adaptation to a long photoperiod (LP). Many photoperiod-related genes have been identified in previous transcriptomics analysis, but proteomics shows less evidence for this mechanism of photoperiod response. In this study, we sampled newly expanded leaves of maize at the three- and six-leaf stages from an LP-sensitive introgression line H496, the donor CML288, LP-insensitive inbred line, and recurrent parent Huangzao4 (HZ4) grown under long days (15 h light and 9 h dark). To characterize the proteomic changes in response to LP, the iTRAQ-labeling method was used to determine the proteome profiles of plants exposed to LP. A total of 943 proteins differentially expressed at the three- and six-leaf stages in HZ4 and H496 were identified. Functional analysis was performed by which the proteins were classified into stress defense, signal transduction, carbohydrate metabolism, protein metabolism, energy production, and transport functional groups using the WEGO online tool. The enriched gene ontology categories among the identified proteins were identified statistically with the Cytoscape plugin ClueGO + Cluepedia. Twenty Gene Ontology terms showed the highest significance, including those associated with protein processing in the endoplasmic reticulum, splicesome, ribosome, glyoxylate, dicarboxylate metabolism, L-malate dehydrogenase activity, and RNA transport. In addition, for subcellular location, all proteins showed significant enrichment of the mitochondrial outer membrane. The sugars producted by photosynthesis in plants are also a pivotal metabolic output in the circadian regulation. The results permit the prediction of several crucial proteins to photoperiod response and provide a foundation for further study of the influence of LP treatments on the circadian response in short-day plants.
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Affiliation(s)
- Liuji Wu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain CropsZhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan ProvinceZhengzhou, China
| | - Lei Tian
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain CropsZhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan ProvinceZhengzhou, China
| | - Shunxi Wang
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain CropsZhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan ProvinceZhengzhou, China
| | - Jun Zhang
- Food Crops Research Institute, Henan Academy of Agricultural ScienceZhengzhou, China
| | - Ping Liu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain CropsZhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan ProvinceZhengzhou, China
| | - Zhiqiang Tian
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain CropsZhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan ProvinceZhengzhou, China
| | - Huimin Zhang
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain CropsZhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan ProvinceZhengzhou, China
| | - Haiping Liu
- Department of Biological Science, Michigan Technological UniversityMichigan, MI, USA
| | - Yanhui Chen
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain CropsZhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan ProvinceZhengzhou, China
- *Correspondence: Yanhui Chen
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Liu W, Cheng C, Lai G, Lin Y, Lai Z. Molecular cloning and expression analysis of KIN10 and cold-acclimation related genes in wild banana 'Huanxi' (Musa itinerans). SPRINGERPLUS 2015; 4:829. [PMID: 26753116 PMCID: PMC4695468 DOI: 10.1186/s40064-015-1617-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/13/2015] [Indexed: 12/20/2022]
Abstract
Banana cultivars may experience chilling or freezing injury in some of their cultivated regions, where wild banana can still grow very well. The clarification of the cold-resistant mechanism of wild banana is vital for cold-resistant banana breeding. In this study, the central stress integrator gene KIN10 and some cold-acclimation related genes (HOS1 and ICE1s) from the cold-resistant wild banana ‘Huanxi’ (Musa itinerans) were cloned and their expression patterns under different temperature treatments were analyzed. Thirteen full-length cDNA transcripts including 6 KIN10s, 1 HOS1 and 6 ICE1s were successfully cloned. Quantitative real-time PCR (qRT-PCR) results showed that all these genes had the highest expression levels at the critical temperature of banana (13 °C). Under chilling temperature (4 °C), the expression level of KIN10 reduced significantly but the expression of HOS1 was still higher than that at the optimal temperature (28 °C, control). Both KIN10 and HOS1 showed the lowest expression levels at 0 °C, the expression level of ICE1, however, was higher than control. As sucrose plays role in plant cold-acclimation and in regulation of KIN10 and HOS1 bioactivities, the sucrose contents of wild banana under different temperatures were detected. Results showed that the sucrose content increased as temperature lowered. Our result suggested that KIN10 may participate in cold stress response via regulating sucrose biosynthesis, which is helpful in regulating cold acclimation pathway in wild banana.
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Affiliation(s)
- Weihua Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Gongti Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
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Zhang L, Zhang L, Xia C, Zhao G, Liu J, Jia J, Kong X. A novel wheat bZIP transcription factor, TabZIP60, confers multiple abiotic stress tolerances in transgenic Arabidopsis. PHYSIOLOGIA PLANTARUM 2015; 153:538-54. [PMID: 25135325 DOI: 10.1111/ppl.12261] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/30/2014] [Accepted: 06/09/2014] [Indexed: 05/03/2023]
Abstract
The basic region/leucine zipper (bZIP) transcription factors (TFs) play vital roles in the response to abiotic stress. However, little is known about the function of bZIP genes in wheat abiotic stress. In this study, we report the isolation and functional characterization of the TabZIP60 gene. Three homologous genome sequences of TabZIP60 were isolated from hexaploid wheat and mapped to the wheat homoeologous group 6. A subcellular localization analysis indicated that TabZIP60 is a nuclear-localized protein that activates transcription. Furthermore, TabZIP60 gene transcripts were strongly induced by polyethylene glycol, salt, cold and exogenous abscisic acid (ABA) treatments. Further analysis showed that the overexpression of TabZIP60 in Arabidopsis resulted in significantly improved tolerances to drought, salt, freezing stresses and increased plant sensitivity to ABA in seedling growth. Meanwhile, the TabZIP60 was capable of binding ABA-responsive cis-elements that are present in promoters of many known ABA-responsive genes. A subsequent analysis showed that the overexpression of TabZIP60 led to enhanced expression levels of some stress-responsive genes and changes in several physiological parameters. Taken together, these results suggest that TabZIP60 enhances multiple abiotic stresses through the ABA signaling pathway and that modifications of its expression may improve multiple stress tolerances in crop plants.
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Affiliation(s)
- Lina Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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35
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Hwang I, Jung HJ, Park JI, Yang TJ, Nou IS. Transcriptome analysis of newly classified bZIP transcription factors of Brassica rapa in cold stress response. Genomics 2014; 104:194-202. [PMID: 25075938 DOI: 10.1016/j.ygeno.2014.07.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/24/2014] [Accepted: 07/17/2014] [Indexed: 10/25/2022]
Abstract
Plant bZIP transcription factors play crucial roles in biological processes. In this study, 136 putative bZIP transcription members were identified in Brassica rapa. The bZIP family can be divided into nine groups according to the specific amino acid rich domain in B. rapa and Arabidopsis thaliana. To screen the cold stress responsive BrbZIP genes, we evaluated whether the transcription patterns of the BrbZIP genes were enhanced by cold treatment in the inbred lines, Chiifu and Kenshin, by microarray data analysis and qRT-PCR. The expression level of six genes increased significantly in Kenshin, but these genes were unchanged in Chiifu. These findings suggest that the six genes that encoded proteins containing N-rich regions might be involved in cold stress response. The results presented herein provide valuable information regarding the molecular basis of the bZIP transcription factors and their potential function in regulation growth and development, particularly in cold stress response.
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Affiliation(s)
- Indeok Hwang
- Department of Horticulture, Sunchon National University, 255 Jungangro, Suncheon, Jeonnam 540-950, Republic of Korea.
| | - Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, 255 Jungangro, Suncheon, Jeonnam 540-950, Republic of Korea.
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungangro, Suncheon, Jeonnam 540-950, Republic of Korea.
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungangro, Suncheon, Jeonnam 540-950, Republic of Korea.
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36
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Lastdrager J, Hanson J, Smeekens S. Sugar signals and the control of plant growth and development. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:799-807. [PMID: 24453229 DOI: 10.1093/jxb/ert474] [Citation(s) in RCA: 318] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Sugars have a central regulatory function in steering plant growth. This review focuses on information presented in the past 2 years on key players in sugar-mediated plant growth regulation, with emphasis on trehalose 6-phosphate, target of rapamycin kinase, and Snf1-related kinase 1 regulatory systems. The regulation of protein synthesis by sugars is fundamental to plant growth control, and recent advances in our understanding of the regulation of translation by sugars will be discussed.
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Affiliation(s)
- Jeroen Lastdrager
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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von Arnim AG, Jia Q, Vaughn JN. Regulation of plant translation by upstream open reading frames. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 214:1-12. [PMID: 24268158 DOI: 10.1016/j.plantsci.2013.09.006] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 05/08/2023]
Abstract
We review the evidence that upstream open reading frames (uORFs) function as RNA sequence elements for post-transcriptional control of gene expression, specifically translation. uORFs are highly abundant in the genomes of angiosperms. Their negative effect on translation is often attenuated by ribosomal translation reinitiation, a process whose molecular biochemistry is still being investigated. Certain uORFs render translation responsive to small molecules, thus offering a path for metabolic control of gene expression in evolution and synthetic biology. In some cases, uORFs form modular logic gates in signal transduction. uORFs thus provide eukaryotes with a functionality analogous to, or comparable to, riboswitches and attenuators in prokaryotes. uORFs exist in many genes regulating development and point toward translational control of development. While many uORFs appear to be poorly conserved, and the number of genes with conserved-peptide uORFs is modest, many mRNAs have a conserved pattern of uORFs. Evolutionarily, the gain and loss of uORFs may be a widespread mechanism that diversifies gene expression patterns. Last but not least, this review includes a dedicated uORF database for Arabidopsis.
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Affiliation(s)
- Albrecht G von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840, USA; Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840, USA.
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Roy B, von Arnim AG. Translational Regulation of Cytoplasmic mRNAs. THE ARABIDOPSIS BOOK 2013; 11:e0165. [PMID: 23908601 PMCID: PMC3727577 DOI: 10.1199/tab.0165] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Translation of the coding potential of a messenger RNA into a protein molecule is a fundamental process in all living cells and consumes a large fraction of metabolites and energy resources in growing cells. Moreover, translation has emerged as an important control point in the regulation of gene expression. At the level of gene regulation, translational control is utilized to support the specific life histories of plants, in particular their responses to the abiotic environment and to metabolites. This review summarizes the diversity of translational control mechanisms in the plant cytoplasm, focusing on specific cases where mechanisms of translational control have evolved to complement or eclipse other levels of gene regulation. We begin by introducing essential features of the translation apparatus. We summarize early evidence for translational control from the pre-Arabidopsis era. Next, we review evidence for translation control in response to stress, to metabolites, and in development. The following section emphasizes RNA sequence elements and biochemical processes that regulate translation. We close with a chapter on the role of signaling pathways that impinge on translation.
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Affiliation(s)
- Bijoyita Roy
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
- Current address: University of Massachussetts Medical School, Worcester, MA 01655-0122, USA
| | - Albrecht G. von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840
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The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 2012. [PMID: 23179023 DOI: 10.1038/ng.2470] [Citation(s) in RCA: 526] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.
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