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Zhao Y, Shi J, Feng B, Yuan S, Yue X, Shi W, Yan Z, Xu D, Zuo J, Wang Q. Multi-omic analysis of the extension of broccoli quality during storage by folic acid. J Adv Res 2024; 59:65-78. [PMID: 37406731 PMCID: PMC11081962 DOI: 10.1016/j.jare.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023] Open
Abstract
INTRODUCTION Folic acid (FA) is a critical metabolite in all living organisms and an important nutritional component of broccoli. Few studies have been conducted on the impact of an exogenous application of FA on the postharvest physiology of fruits and vegetables during storage. In this regard, the mechanism by which an exogenous application of FA extends the postharvest quality of broccoli is unclear. OBJECTIVE This study utilized a multicomponent analysis to investigate how an exogenous application of FA effects the postharvest quality of broccoli. METHODS Broccoli was soaked in 5 mg/L FA for 10 min and the effect of the treatment on the appearance and nutritional quality of broccoli was evaluated. These data were combined with transcriptomic, metabolomic, and DNA methylation data to provide insight into the potential mechanism by which FA delays senescence. RESULTS The FA treatment inhibited the yellowing of broccoli during storage. CHH methylation was identified as the main type of methylation that occurs in broccoli and the FA treatment was found to inhibit DNA methylation, promote the accumulation of endogenous FA and chlorophyl, and inhibit ethylene biosynthesis in stored broccoli. The FA treatment also prevented the formation of off-odors by inhibiting the degradation of glucosinolate. CONCLUSIONS FA treatment inhibited the loss of nutrients during the storage of broccoli, delayed its yellowing, and inhibited the generation of off-odors. Our study provides deeper insight into the mechanism by which the postharvest application of FA delays postharvest senescence in broccoli and provides the foundation for further studies of postharvest metabolism in broccoli.
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Affiliation(s)
- Yaqi Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China; State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agriculture, Guangxi University, Nanning 530004, China
| | - Junyan Shi
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bihong Feng
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Shuzhi Yuan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaozhen Yue
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wenlin Shi
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China; College of Agriculture, Guangxi University, Nanning 530004, China
| | - Zhicheng Yan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Dongying Xu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Carvalho P, Gomes C, Saibo NJ. C4 Phosphoenolpyruvate Carboxylase: Evolution and transcriptional regulation. Genet Mol Biol 2024; 46:e20230190. [PMID: 38517370 PMCID: PMC10958771 DOI: 10.1590/1678-4685-gmb-2023-0190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024] Open
Abstract
Photosynthetic phosphoenolpyruvate carboxylase (PEPC) catalyses the irreversible carboxylation of phosphoenolpyruvate (PEP), producing oxaloacetate (OAA). This enzyme catalyses the first step of carbon fixation in C4 photosynthesis, contributing to the high photosynthetic efficiency of C4 plants. PEPC is also involved in replenishing tricarboxylic acid cycle intermediates, such as OAA, being involved in the C/N balance. In plants, PEPCs are classified in two types: bacterial type (BTPC) and plant-type (PTPC), which includes photosynthetic and non-photosynthetic PEPCs. During C4 evolution, photosynthetic PEPCs evolved independently. C4 PEPCs evolved to be highly expressed and active in a spatial-specific manner. Their gene expression pattern is also regulated by developmental cues, light, circadian clock as well as adverse environmental conditions. However, the gene regulatory networks controlling C4 PEPC gene expression, namely its cell-specificity, are largely unknown. Therefore, after an introduction to the evolution of PEPCs, this review aims to discuss the current knowledge regarding the transcriptional regulation of C4 PEPCs, focusing on cell-specific and developmental expression dynamics, light and circadian regulation, as well as response to abiotic stress. In conclusion, this review aims to highlight the evolution, transcriptional regulation by different signals and importance of PEPC in C4 photosynthesis and its potential as tool for crop improvement.
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Affiliation(s)
- Pedro Carvalho
- Universidade Nova de Lisboa, Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Célia Gomes
- Universidade Nova de Lisboa, Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Nelson J.M. Saibo
- Universidade Nova de Lisboa, Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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Li A, Wang F, Ding T, Li K, Liu H, Zhang Q, Mu Q, Zhao H, Shan S, Wang P. Genome-wide DNA methylation dynamics and RNA-seq analysis during grape (cv. 'Cabernet Franc') skin coloration. Genomics 2024; 116:110810. [PMID: 38402913 DOI: 10.1016/j.ygeno.2024.110810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
This study generated whole genome DNA methylation maps to characterize DNA methylomes of grape (cv. 'Cabernet Franc') skins and examine their functional significance during grape skin coloration. We sampled grape skin tissues at three key stages (the early stage of grape berry swelling, the late stage of grape berry swelling and the veraison) during which the color of grape berries changed from green to red. DNA methylation levels of grape skins at the three stages were higher in transposable element regions than in the genic regions, and the CG and CHG DNA methylation levels of the genic region were higher than the CHH DNA methylation levels. We identified differentially methylated regions (DMRs) in S2_vs_S1 and S3_vs_S1. The results indicated that DMRs predominantly occurred within the CHH context during grape skin coloration. Many gene ontology (GO)-enriched DMR-related genes were involved in "nucleotide binding," "catalytic activity" and "ribonucleotide binding" terms; however, many KEGG-enriched DMR-related genes were involved in the "flavonoid biosynthesis" pathway. Our results could provide an important foundation for future research on the development mechanism of grape berries.
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Affiliation(s)
- Ao Li
- Shandong Academy of Grape, Jinan 250100, China
| | | | | | - Ke Li
- Shandong Academy of Grape, Jinan 250100, China
| | - Huiping Liu
- Shandong Academy of Grape, Jinan 250100, China
| | | | - Qian Mu
- Shandong Academy of Grape, Jinan 250100, China
| | | | - Shouming Shan
- College of Enology and Horticulture, Ningxia University, Ningxia 750021, China.
| | - Pengfei Wang
- Shandong Academy of Grape, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture and Rural Affairs, Jinan 250100, China.
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Yu W, Pei R, Zhang Y, Tu Y, He B. Light regulation of secondary metabolism in fungi. J Biol Eng 2023; 17:57. [PMID: 37653453 PMCID: PMC10472637 DOI: 10.1186/s13036-023-00374-4] [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: 07/03/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023] Open
Abstract
Fungi have evolved unique metabolic regulation mechanisms for adapting to the changing environments. One of the key features of fungal adaptation is the production of secondary metabolites (SMs), which are essential for survival and beneficial to the organism. Many of these SMs are produced in response to the environmental cues, such as light. In all fungal species studied, the Velvet complex transcription factor VeA is a central player of the light regulatory network. In addition to growth and development, the intensity and wavelength of light affects the formation of a broad range of secondary metabolites. Recent studies, mainly on species of the genus Aspergillus, revealed that the dimer of VeA-VelB and LaeA does not only regulate gene expression in response to light, but can also be involved in regulating production of SMs. Furthermore, the complexes have a wide regulatory effect on different types of secondary metabolites. In this review, we discussed the role of light in the regulation of fungal secondary metabolism. In addition, we reviewed the photoreceptors, transcription factors, and signaling pathways that are involved in light-dependent regulation of secondary metabolism. The effects of transcription factors on the production of secondary metabolites, as well as the potential applications of light regulation for the production of pharmaceuticals and other products were discussed. Finally, we provided an overview of the current research in this field and suggested potential areas for future research.
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Affiliation(s)
- Wenbin Yu
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China
| | - Rongqiang Pei
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China
| | - Yufei Zhang
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China
| | - Yayi Tu
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China.
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China.
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El-Shehawi AM, Elseehy MA, Elseehy MM. CpG Methylation of the Proximal Promoter Region Regulates the Expression of NAC6D Gene in Response to High Temperature in Wheat (Triticum aestivum). CYTOL GENET+ 2022. [DOI: 10.3103/s009545272205005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pradhan B, Panda D, Bishi SK, Chakraborty K, Muthusamy SK, Lenka SK. Progress and prospects of C 4 trait engineering in plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:920-931. [PMID: 35727191 DOI: 10.1111/plb.13446] [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: 01/14/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Incorporating C4 photosynthetic traits into C3 crops is a rational approach for sustaining future demands for crop productivity. Using classical plant breeding, engineering this complex trait is unlikely to achieve its target. Therefore, it is critical and timely to implement novel biotechnological crop improvement strategies to accomplish this goal. However, a fundamental understanding of C3 , C4 , and C3 -C4 intermediate metabolism is crucial for the targeted use of biotechnological tools. This review assesses recent progress towards engineering C4 photosynthetic traits in C3 crops. We also discuss lessons learned from successes and failures of recent genetic engineering attempts in C3 crops, highlighting the pros and cons of using rice as a model plant for short-, medium- and long-term goals of genetic engineering. This review provides an integrated approach towards engineering improved photosynthetic efficiency in C3 crops for sustaining food, fibre and fuel production around the globe.
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Affiliation(s)
- B Pradhan
- Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Kolkata, India
| | - D Panda
- Department of Biodiversity & Conservation of Natural Resources, Central University of Odisha, Koraput, India
| | - S K Bishi
- School of Genomics and Molecular Breeding, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - K Chakraborty
- Department of Plant Physiology, ICAR-National Rice Research Institute, Cuttack, India
| | - S K Muthusamy
- Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - S K Lenka
- Department of Plant Biotechnology, Gujarat Biotechnology University, Gujarat, India
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Cui H. Challenges and Approaches to Crop Improvement Through C3-to-C4 Engineering. FRONTIERS IN PLANT SCIENCE 2021; 12:715391. [PMID: 34594351 PMCID: PMC8476962 DOI: 10.3389/fpls.2021.715391] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/06/2021] [Indexed: 05/24/2023]
Abstract
With a rapidly growing world population and dwindling natural resources, we are now facing the enormous challenge of increasing crop yields while simultaneously improving the efficiency of resource utilization. Introduction of C4 photosynthesis into C3 crops is widely accepted as a key strategy to meet this challenge because C4 plants are more efficient than C3 plants in photosynthesis and resource usage, particularly in hot climates, where the potential for productivity is high. Lending support to the feasibility of this C3-to-C4 engineering, evidence indicates that C4 photosynthesis has evolved from C3 photosynthesis in multiple lineages. Nevertheless, C3-to-C4 engineering is not an easy task, as several features essential to C4 photosynthesis must be introduced into C3 plants. One such feature is the spatial separation of the two phases of photosynthesis (CO2 fixation and carbohydrate synthesis) into the mesophyll and bundle sheath cells, respectively. Another feature is the Kranz anatomy, characterized by a close association between the mesophyll and bundle sheath (BS) cells (1:1 ratio). These anatomical features, along with a C4-specific carbon fixation enzyme (PEPC), form a CO2-concentration mechanism that ensures a high photosynthetic efficiency. Much effort has been taken in the past to introduce the C4 mechanism into C3 plants, but none of these attempts has met with success, which is in my opinion due to a lack of system-level understanding and manipulation of the C3 and C4 pathways. As a prerequisite for the C3-to-C4 engineering, I propose that not only the mechanisms that control the Kranz anatomy and cell-type-specific expression in C3 and C4 plants must be elucidated, but also a good understanding of the gene regulatory network underlying C3 and C4 photosynthesis must be achieved. In this review, I first describe the past and current efforts to increase photosynthetic efficiency in C3 plants and their limitations; I then discuss a systems approach to tackling down this challenge, some practical issues, and recent technical innovations that would help us to solve these problems.
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Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
- College of Life Science, Northwest Science University of Agriculture and Forestry, Yangling, China
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8
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S Alotaibi S, El-Shehawi AM, M Elseehy M. Heat Shock Proteins Expression Is Regulated by Promoter CpG Methylation/demethylation under Heat Stress in Wheat Varieties. Pak J Biol Sci 2021; 23:1310-1320. [PMID: 32981265 DOI: 10.3923/pjbs.2020.1310.1320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Heat shock proteins are induced by high temperature and other environmental stimuli to protect cellular proteins. Despite extensive research on the molecular response to heat stress, the effect of high temperatures on genes and pathways remains unclear. This study investigated the expression of the HSP17 gene in nine Egyptian wheat varieties and the role of HSP17 promoter CpG methylation in the regulation of HSP17 under high temperature. MATERIALS AND METHODS The HSP17 expression was investigated by using semi-quantitative PCR analysis. Methylation at the HSP17 promoter proximal region was analyzed using bisulphite sequencing and CpG viewer software. RESULTS Under normal conditions, HSP17 and methyltransferase 3 (MET3) exhibited similar expression levels in the 9 studied varieties. After exposure to high temperature, the expression level of HSP17 in Giza155 was barely detected. Among the nine varieties, the expression level of HSP17 was highest in Giza168 (11.3 folds of Giza155). Analysis of methylation of 14 CpG islands at the HSP17 proximal promoter sequence showed that methylation of 10 CpG islands differed only by 10-20%, whereas methylation at the other 4 CpGs differed by 56.7-60%. The high expression of HSP17 in Giza168 in response to high temperature was associated with low methylation of four CpGs and low MET3 expression, whereas low expression of HSP17 in Giza155 was associated with high methylation and high MET3 expression. CONCLUSION The results can aid the development of next-generation approaches to the evaluation of commercial wheat varieties and the development of next-generation approaches to plant breeding employing epiallele integration.
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Mona Mohamed Elseehy. Differential Transgeneration Methylation of Exogenous Promoters in T1 Transgenic Wheat (Triticum aestivum). CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720050151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Elseehy MM, El-Shehawi AM. Methylation of Exogenous Promoters Regulates Soybean Isoflavone Synthase (GmIFS) Transgene in T0 Transgenic Wheat (Triticum aestivum). CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720030032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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Wojtasik W, Boba A, Preisner M, Kostyn K, Szopa J, Kulma A. DNA Methylation Profile of β-1,3-Glucanase and Chitinase Genes in Flax Shows Specificity Towards Fusarium Oxysporum Strains Differing in Pathogenicity. Microorganisms 2019; 7:E589. [PMID: 31757035 PMCID: PMC6956085 DOI: 10.3390/microorganisms7120589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 11/16/2022] Open
Abstract
Most losses in flax (Linum usitatissimum L.) crops are caused by fungal infections. The new epigenetic approach to improve plant resistance requires broadening the knowledge about the influence of pathogenic and non-pathogenic Fusarium oxysporum strains on changes in the profile of DNA methylation. Two contrasting effects on the levels of methylation in flax have been detected for both types of Fusarium strain infection: Genome-wide hypermethylation and hypomethylation of resistance-related genes (β-1,3-glucanase and chitinase). Despite the differences in methylation profile, the expression of these genes increased. Plants pretreated with the non-pathogenic strain memorize the hypomethylation pattern and then react more efficiently upon pathogen infection. The peak of demethylation correlates with the alteration in gene expression induced by the non-pathogenic strain. In the case of pathogen infection, the expression peak lags behind the gene demethylation. Dynamic changes in tetramer methylation induced by both pathogenic and non-pathogenic Fusarium strains are dependent on the ratio between the level of methyltransferase and demethylase gene expression. Infection with both Fusarium strains suppressed methyltransferase expression and increased the demethylase (demeter) transcript level. The obtained results provide important new information about changes in methylation profile and thus expression regulation of pathogenesis-related genes in the flax plant response to stressors.
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Affiliation(s)
- Wioleta Wojtasik
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
| | - Aleksandra Boba
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
| | - Marta Preisner
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
- Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Plant Sciences, pl. Grunwaldzki 24A, 50-363 Wroclaw, Poland
| | - Kamil Kostyn
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
- Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Plant Sciences, pl. Grunwaldzki 24A, 50-363 Wroclaw, Poland
| | - Jan Szopa
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
- Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Plant Sciences, pl. Grunwaldzki 24A, 50-363 Wroclaw, Poland
| | - Anna Kulma
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
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Górska AM, Gouveia P, Borba AR, Zimmermann A, Serra TS, Lourenço TF, Margarida Oliveira M, Peterhänsel C, Saibo NJM. ZmbHLH80 and ZmbHLH90 transcription factors act antagonistically and contribute to regulate PEPC1 cell-specific gene expression in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:270-285. [PMID: 30900785 DOI: 10.1111/tpj.14323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/20/2018] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Compartmentation of photosynthetic reactions between mesophyll and bundle sheath cells is a key feature of C4 photosynthesis and depends on the cell-specific accumulation of major C4 enzymes, such as phosphoenolpyruvate carboxylase 1. The ZmPEPC1 upstream region, which drives light-inducible and mesophyll-specific gene expression in maize, has been shown to keep the same properties when introduced into rice (C3 plant), indicating that rice has the transcription factors (TFs) needed to confer C4 -like gene expression. Using a yeast one-hybrid approach, we identified OsbHLH112, a rice basic Helix-Loop-Helix (bHLH) TF that interacts with the maize ZmPEPC1 upstream region. Moreover, we found that maize OsbHLH112 homologues, ZmbHLH80, and ZmbHLH90, also interact with the ZmPEPC1 upstream region, suggesting that these C4 regulators were co-opted from C3 plants. A transactivation assay in maize mesophyll protoplasts revealed that ZmbHLH80 represses, whereas ZmbHLH90 activates, ZmPEPC1 expression. In addition, ZmbHLH80 was shown to impair the ZmPEPC1 promoter activation caused by ZmbHLH90. We showed that ZmbHLH80 and ZmbHLH90 bind to the same cis-element within the ZmPEPC1 upstream region either as homodimers or heterodimers. The formation of homo- and heterodimers with higher oligomeric forms promoted by ZmbHLH80 may explain its negative effect on gene transcription. Gene expression analysis revealed that ZmbHLH80 is preferentially expressed in bundle sheath cells, whereas ZmbHLH90 does not show a clear cell-specific expression pattern. Altogether, our results led us to propose a model in which ZmbHLH80 contributes to mesophyll-specific ZmPEPC1 gene expression by impairing ZmbHLH90-mediated ZmPEPC1 activation in the bundle sheath cells.
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Affiliation(s)
- Alicja M Górska
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Paulo Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Ana R Borba
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Anna Zimmermann
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
- Leibniz Universität Hannover, Institut für Botanik, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Tânia S Serra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Tiago F Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Maria Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Christoph Peterhänsel
- Leibniz Universität Hannover, Institut für Botanik, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
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14
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Wang P, Shi S, Ma J, Song H, Zhang Y, Gao C, Zhao C, Zhao S, Hou L, Lopez-Baltazar J, Fan S, Xia H, Wang X. Global Methylome and gene expression analysis during early Peanut pod development. BMC PLANT BIOLOGY 2018; 18:352. [PMID: 30545288 PMCID: PMC6293580 DOI: 10.1186/s12870-018-1546-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. RESULTS To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing. A novel mapping strategy of reads was developed and used for methylome and gene expression analysis. Differentially methylated genes, such as nodulin, cell number regulator-like protein, and senescence-associated genes, were identified during the early developmental stages of the peanut pod. The expression levels of gibberellin-related genes changed during this period of pod development. From the stage one (S1) gynophore to the stage two (S2) gynophore, the expression levels of two key methyltransferase genes, DRM2 and MET1, were up-regulated, which may lead to global DNA methylation changes between these two stages. The differentially methylated and expressed genes identified in the S1, S2, and stage 3 (S3) gynophore are involved in different biological processes such as stem cell fate determination, response to red, blue, and UV light, post-embryonic morphogenesis, and auxin biosynthesis. The expression levels of many genes were co-related by their DNA methylation levels. In addition, our results showed that the abundance of some 24-nucleotide siRNAs and miRNAs were positively associated with DNA methylation levels of their target loci in peanut pods. CONCLUSION A novel mapping strategy of reads was described and verified in this study. Our results suggest that the methylated modes of the S1, S2, and S3 gynophore are different. The methylation changes that were identified during early peanut pod development provide useful information for understanding the roles of epigenetic regulation in peanut pod development.
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Affiliation(s)
- Pengfei Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Shandong Academy of Grape, Jinan, 250100 People’s Republic of China
| | - Suhua Shi
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Junjie Ma
- Life Science College of Shandong University, Jinan, 250100 People’s Republic of China
| | - Hui Song
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Ye Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Chao Gao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | | | - Shoujin Fan
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
- Life Science College of Shandong University, Jinan, 250100 People’s Republic of China
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15
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Li X, Yu H, Jiao Y, Shahid MQ, Wu J, Liu X. Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice. PLoS One 2018; 13:e0201854. [PMID: 30080873 PMCID: PMC6078310 DOI: 10.1371/journal.pone.0201854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/23/2018] [Indexed: 12/17/2022] Open
Abstract
Autotetraploid rice is a useful germplasm with high biomass production; however, low fertility is the main barrier in commercial utilization. In our previous study, differential expression of meiosis-related miRNAs was found to be involved in the pollen sterility of autotetraploid rice. However, genome-wide DNA variations and methylomes associated with low fertility of autotetraploid rice are still poorly understood. Here, we measured both global DNA variations and the methylome and compared them with the transcriptome during pollen development in autotetraploid rice by high-throughput sequencing. A total of 34416 SNPs, 6993 InDels, 1003 SVs and 25 CNVs were detected, and 11367 and 41117 differentially methylated regions showed hypermethylation and hypomethylation in 02428-4x. In total, 1110 genes displayed differentially expression in 02428-4x during meiosis, of these six harbored CNVs, including four upregulated genes with gain CNVs, such as LOC_Os11g38620. We identified 122 genes by comparing with the previous data that might be associated with low fertility during pollen development in 02428-4x. Of the 122 gens, 98 were displayed methylation and differential expression, including OsMADS98, CYP703A3 and OsABCG26. The downregulation of these three genes were confirmed by qPCR during meiosis of 02428-4x, which played pivotal roles in pollen fertility. These results indicate that the low fertility of autotetraploid rice is not only caused by the differential expression of genes involved in pollen development, but also by sequence variation and differential methylation, suggesting that the reason for pollen sterility in autotetraploid rice is complex and might be affected by multiple factors.
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Affiliation(s)
- Xiang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yamin Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
- * E-mail:
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16
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Hsu FM, Yen MR, Wang CT, Lin CY, Wang CJR, Chen PY. Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize. Epigenetics Chromatin 2017; 10:42. [PMID: 28854962 PMCID: PMC5577757 DOI: 10.1186/s13072-017-0148-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/08/2017] [Indexed: 11/11/2022] Open
Abstract
Background
DNA methylation plays important roles in many regulatory processes in plants. It is economically infeasible to profile genome-wide DNA methylation at a single-base resolution in maize, given its genome size of ~2.5 Gb. As an alternative, we adapted region of interest (ROI)-directed reduced representation bisulfite sequencing (RRBS) to survey genome-wide methylation in maize. Results We developed a pipeline for selecting restriction enzymes in silico and experimentally showed that, in the maize genome, MseI- and CviQI-digested fragments are precisely enriched in promoters and gene bodies, respectively. We proceeded with comparisons of epigenomes and transcriptomes between shoots and tassels and found that the occurrences of highly methylated, tissue-specific, mCHH islands upstream of transcription start sites (TSSs) were positively correlated with differential gene expression. Furthermore, 5′ regulatory regions between TSS and mCHH islands often contain putative binding sites of known transcription factors (TFs) that regulate the flowering process and the timing of the transition from the vegetative to the reproductive phase. By integrating MNase-seq and siRNA-seq data, we found that regions of mCHH islands accumulate 21nt-siRNAs in a tissue-specific manner, marking the transition to open chromatin, thereby ensuring the accessibility of TFs for tissue-specific gene regulation. Conclusions Our ROI-directed RRBS pipeline is eminently applicable to DNA methylation profiling of large genomes. Our results provide novel insights into the tissue-specific epigenomic landscapes in maize, demonstrating that DNA methylation and siRNA and chromatin accessibility constitute a critical, interdependent component that orchestrates the transition from the vegetative to the reproductive phase. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0148-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fei-Man Hsu
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chi-Ting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chien-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chung-Ju Rachel Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
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17
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Turco GM, Kajala K, Kunde‐Ramamoorthy G, Ngan C, Olson A, Deshphande S, Tolkunov D, Waring B, Stelpflug S, Klein P, Schmutz J, Kaeppler S, Ware D, Wei C, Etchells JP, Brady SM. DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor. THE NEW PHYTOLOGIST 2017; 214:1213-1229. [PMID: 28186631 PMCID: PMC5655736 DOI: 10.1111/nph.14448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/19/2016] [Indexed: 05/23/2023]
Abstract
Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues. Many genes associated with vascular development in other species show enriched expression in developing vasculature. However, several transcription factor families varied in vascular expression in sorghum compared with Arabidopsis and maize. Furthermore, differential expression of genes associated with DNA methylation were identified between vascular and nonvascular tissues, implying that changes in DNA methylation are a feature of sorghum root vascularization, which we confirmed using tissue-specific DNA methylome data. Roots treated with a DNA methylation inhibitor also showed a significant decrease in root length. Tissues and organs can be discriminated based on their genomic methylation patterns and methylation context. Consequently, tissue-specific changes in DNA methylation are part of the normal developmental process.
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Affiliation(s)
- Gina M. Turco
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
| | - Kaisa Kajala
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
| | | | - Chew‐Yee Ngan
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory1 Bungtown RoadCold Spring HarborNY11724USA
| | | | - Denis Tolkunov
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Barbara Waring
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
| | - Scott Stelpflug
- Department of Agronomy and Great Lakes Bioenergy Research CenterUniversity of Wisconsin1575 Linden DriveMadisonWI53706USA
| | - Patricia Klein
- Institute for Plant Genomics and Biotechnology and Department of Horticultural SciencesTexas A and M UniversityCollege StationTX77843USA
| | - Jeremy Schmutz
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
- HudsonAlpha Institute for Biotechnology601 Genome Way NWHuntsvilleAL35806USA
| | - Shawn Kaeppler
- Department of Agronomy and Great Lakes Bioenergy Research CenterUniversity of Wisconsin1575 Linden DriveMadisonWI53706USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory1 Bungtown RoadCold Spring HarborNY11724USA
- USDA‐ARSIthacaNY14853USA
| | - Chia‐Lin Wei
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - J. Peter Etchells
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
- School of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH3 1LEUK
| | - Siobhan M. Brady
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
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18
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Liu X, Li X, Zhang C, Dai C, Zhou J, Ren C, Zhang J. Phosphoenolpyruvate carboxylase regulation in C4-PEPC-expressing transgenic rice during early responses to drought stress. PHYSIOLOGIA PLANTARUM 2017; 159:178-200. [PMID: 27592839 DOI: 10.1111/ppl.12506] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 07/14/2016] [Accepted: 08/05/2016] [Indexed: 05/11/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) has important functions in C4 photosynthesis and biosynthesis of intermediate metabolites. In this study, the drought resistance of C4-PEPC-expressing transgenic rice (Oryza sativa, line PC) plants was assessed using simulated drought conditions [i.e. polyethylene glycol (PEG)-6000 treatment]. The dry weight of PC plants was higher than that of wild-type (WT) plants following treatment with 15% PEG-6000 for 16 days. Furthermore, the water use efficiency, relative water content and proline content in PC plants were higher than those of WT plants, as were C4-PEPC activity and transcript levels following treatment with 5% PEG-6000 for 2 h. The protein kinase activities and transcript levels of sucrose non-fermenting-1-related protein kinases (SnRKs) genes, such as SnRK1a, OsK24 and OsK35 were also higher in PC plants than in WT plants following treatment with 5% PEG-6000 for 2 h. Additionally, phosphoenolpyruvate carboxylase kinase (PPCK, EC 4.1.1.32) activities and transcript levels (e.g. PPCK1 and PPCK2) increased following drought treatment. These changes were regulated by signaling molecules, such as calcium, nitric oxide and hydrogen peroxide. Furthermore, the -1095 to -416 region of the C4-PEPC promoter in PC plants was demethylated following exposure to drought conditions for 1 h. The demethylation coincided with an increase in C4-PEPC expression. Our data suggest that the demethylation of the C4-PEPC promoter and the phosphorylation catalyzed by PPCK have key roles in conferring drought tolerance to the transgenic rice plants.
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Affiliation(s)
- Xiaolong Liu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xia Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
| | - Chen Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
| | - Chuanchao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jiayu Zhou
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Chenggang Ren
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
| | - Jinfei Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
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19
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Reeves G, Grangé-Guermente MJ, Hibberd JM. Regulatory gateways for cell-specific gene expression in C4 leaves with Kranz anatomy. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:107-116. [PMID: 27940469 DOI: 10.1093/jxb/erw438] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
C4 photosynthesis is a carbon-concentrating mechanism that increases delivery of carbon dioxide to RuBisCO and as a consequence reduces photorespiration. The C4 pathway is therefore beneficial in environments that promote high photorespiration. This pathway has evolved many times, and involves restricting gene expression to either mesophyll or bundle sheath cells. Here we review the regulatory mechanisms that control cell-preferential expression of genes in the C4 cycle. From this analysis, it is clear that the C4 pathway has a complex regulatory framework, with control operating at epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels. Some genes of the C4 pathway are regulated at multiple levels, and we propose that this ensures robust expression in each cell type. Accumulating evidence suggests that multiple genes of the C4 pathway may share the same regulatory mechanism. The control systems for C4 photosynthesis gene expression appear to operate in C3 plants, and so it appears that pre-existing mechanisms form the basis of C4 photosynthesis gene expression.
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Affiliation(s)
- Gregory Reeves
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Julian M Hibberd
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
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20
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Russo MT, Annunziata R, Sanges R, Ferrante MI, Falciatore A. The upstream regulatory sequence of the light harvesting complex Lhcf2 gene of the marine diatom Phaeodactylum tricornutum enhances transcription in an orientation- and distance-independent fashion. Mar Genomics 2015; 24 Pt 1:69-79. [PMID: 26117181 DOI: 10.1016/j.margen.2015.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/31/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
Diatoms are a key phytoplankton group in the contemporary ocean, showing extraordinary adaptation capacities to rapidly changing environments. The recent availability of whole genome sequences from representative species has revealed distinct features in their genomes, like novel combinations of genes encoding distinct metabolisms and a significant number of diatom-specific genes. However, the regulatory mechanisms driving diatom gene expression are still largely uncharacterized. Considering the wide variety of fields of study orbiting diatoms, ranging from ecology, evolutionary biology to biotechnology, it is thus essential to increase our understanding of fundamental gene regulatory processes such as transcriptional regulation. To this aim, we explored the functional properties of the 5'-flanking region of the Phaeodatylum tricornutum Lhcf2 gene, encoding a member of the Light Harvesting Complex superfamily and we showed that this region enhances transcription of a GUS reporter gene in an orientation- and distance-independent fashion. This represents the first example of a cis-regulatory sequence with enhancer-like features discovered in diatoms and it is instrumental for the generation of novel genetic tools and diatom exploitation in different areas of study.
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Affiliation(s)
| | - Rossella Annunziata
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine, UMR 7238, F-75006 Paris, France; CNRS, UMR 7238, F-75006 Paris, France
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | | | - Angela Falciatore
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine, UMR 7238, F-75006 Paris, France; CNRS, UMR 7238, F-75006 Paris, France.
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21
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Wang P, Xia H, Zhang Y, Zhao S, Zhao C, Hou L, Li C, Li A, Ma C, Wang X. Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across embryo and endosperm in Maize (Zea may). BMC Genomics 2015; 16:21. [PMID: 25612809 PMCID: PMC4316406 DOI: 10.1186/s12864-014-1204-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/24/2014] [Indexed: 12/26/2022] Open
Abstract
Background Epigenetic modifications play important roles in plant and animal development. DNA methylation impacts the transposable element (TE) silencing, gene imprinting and expression regulation. Results Through a genome-wide analysis, DNA methylation peaks were characterized and mapped in maize embryo and endosperm genome, respectively. Distinct methylation level was observed across maize embryo and endosperm. The maize embryo genome contained more DNA methylation than endosperm. Totally, 985,478 CG islands (CGIs) were identified and most of them were unmethylated. More CGI shores were methylated than CGIs in maize suggested that DNA methylation level was not positively correlated with CpG density. The promoter sequence and transcriptional termination region (TTR) were more methylated than the gene body (intron and exon) region based on peak number and methylated depth. Result showed that 99% TEs were methylated in maize embryo, but a large portion of them (34.8%) were not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated region between embryo and endosperm are CGI shores. Our results indicated that DNA methylation is associated with both gene silencing and gene activation in maize. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 41.5% imprinting genes were similarly methylated and 58.5% imprinting genes were differentially methylated between embryo and endosperm. Methylation level was associated with allelic silencing of only a small number of imprinting genes. The expression of maize DEMETER-like (DME-like) gene and MBD101 gene (MBD4 homolog) were higher in endosperm than in embryo. These two genes may be associated with distinct methylation levels across maize embryo and endosperm. Conclusions Through MeDIP-seq we systematically analyzed the methylomes of maize embryo and endosperm and results indicated that the global methylation status of embryo was more than that of the endosperm. Differences could be observed at the total number of methylation peaks, DMRs and specific methylated genes which were tightly associated with development of embryo and endosperm. Our results also revealed that many DNA methylation regions didn’t affect transcription of the corresponding genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1204-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengfei Wang
- Agricultural College, Anhui Agricultural University, Hefei, 230036, PR China. .,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Han Xia
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Ye Zhang
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Shuzhen Zhao
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Chuanzhi Zhao
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Lei Hou
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Changsheng Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Aiqin Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Chuanxi Ma
- Agricultural College, Anhui Agricultural University, Hefei, 230036, PR China.
| | - Xingjun Wang
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
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22
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Dong Q, Jiang H, Xu Q, Li X, Peng X, Yu H, Xiang Y, Cheng B. Cloning and characterization of a multifunctional promoter from maize (Zea mays L.). Appl Biochem Biotechnol 2014; 175:1344-57. [PMID: 25391545 DOI: 10.1007/s12010-014-1277-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/23/2014] [Indexed: 10/24/2022]
Abstract
The use of tissue-specific promoters to drive the expression of target genes during certain developmental stages or in specific organs can prevent unnecessary gene expression caused by constitutive promoters. Utilizing heterologous promoters to regulate the expression of genes in transgenic receptors can help prevent gene silencing. Here, we engineered heterologous maize promoters that regulate gene-specific expression in rice plant receptors. We performed a histochemical and quantitative β-glucuronidase (GUS) analysis of the Zea mays legumin1 (ZM-LEGF) gene promoter and detailed detection of stably transformed rice expressing the GUS gene under the control of the promoter of ZM-LEGF (pZM-LEGF) and its truncated promoters throughout development. When the promoter sequence was truncated, the location and intensity of GUS expression changed. The results suggest that the sequence from -140 to +41 is a critical region that confers the expression of the entire promoter. Truncation of pZM-LEG (3'-deleted region of pZM-LEGF) markedly increased the GUS activity, with the core cis-elements located in the -273 to -140 regions, namely pZM-LEG6. Detailed analysis of pZM-LEG6::GUS T2 transformant rice seeds and plant tissues at different developmental stages indicated that this promoter is an ideal vegetative tissue-specific promoter that can serve as a valuable tool for transgenic rice breeding and genetic engineering studies.
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Affiliation(s)
- Qing Dong
- Key Lab of Biomass Improvement and Conversion, Anhui Agricultural University, Hefei, 230036, China
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Chen T, Zhu XG, Lin Y. Major alterations in transcript profiles between C3-C4 and C4 photosynthesis of an amphibious species Eleocharis baldwinii. PLANT MOLECULAR BIOLOGY 2014; 86:93-110. [PMID: 25008152 DOI: 10.1007/s11103-014-0215-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 06/11/2014] [Indexed: 06/03/2023]
Abstract
Engineering C4 photosynthetic metabolism into C3 crops is regarded as a major strategy to increase crop productivity, and clarification of the evolutionary processes of C4 photosynthesis can help the better use of this strategy. Here, Eleocharis baldwinii, a species in which C4 photosynthesis can be induced from a C3-C4 state under either environmental or ABA treatments, was used to identify the major transcriptional modifications during the process from C3-C4 to C4. The transcriptomic comparison suggested that in addition to the major differences in C4 core pathway, the pathways of glycolysis, citrate acid metabolism and protein synthesis were dramatically modified during the inducement of C4 photosynthetic states. Transcripts of many transporters, including not only metabolite transporters but also ion transporters, were dramatically increased in C4 photosynthetic state. Many candidate regulatory genes with unidentified functions were differentially expressed in C3-C4 and C4 photosynthetic states. Finally, it was indicated that ABA, auxin signaling and DNA methylation play critical roles in the regulation of C4 photosynthesis. In summary, by studying the different photosynthetic states of the same species, this work provides the major transcriptional differences between C3-C4 and C4 photosynthesis, and many of the transcriptional differences are potentially related to C4 development and therefore are the potential targets for reverse genetics studies.
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Affiliation(s)
- Taiyu Chen
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
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24
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Külahoglu C, Denton AK, Sommer M, Maß J, Schliesky S, Wrobel TJ, Berckmans B, Gongora-Castillo E, Buell CR, Simon R, De Veylder L, Bräutigam A, Weber APM. Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species. THE PLANT CELL 2014; 26:3243-60. [PMID: 25122153 PMCID: PMC4371828 DOI: 10.1105/tpc.114.123752] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 06/20/2014] [Accepted: 07/06/2014] [Indexed: 05/04/2023]
Abstract
C(4) photosynthesis outperforms the ancestral C(3) state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C(3) backgrounds. However, the genetic architecture of C(4) photosynthesis remains largely unknown. To define the divergence in gene expression modules between C(3) and C(4) photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C(4)) and Tarenaya hassleriana (C(3)), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C(3) and C(4) species. We found that known C(4) genes were recruited to photosynthesis from different expression domains in C(3), including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C(3) root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C(4) bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C(4) leaf.
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Affiliation(s)
- Canan Külahoglu
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Alisandra K Denton
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Manuel Sommer
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Janina Maß
- Institute of Informatics, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Simon Schliesky
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Thomas J Wrobel
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Barbara Berckmans
- Institute of Developmental Genetics, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Elsa Gongora-Castillo
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Rüdiger Simon
- Institute of Developmental Genetics, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
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25
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Candaele J, Demuynck K, Mosoti D, Beemster GT, Inzé D, Nelissen H. Differential methylation during maize leaf growth targets developmentally regulated genes. PLANT PHYSIOLOGY 2014; 164:1350-64. [PMID: 24488968 PMCID: PMC3938625 DOI: 10.1104/pp.113.233312] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/28/2014] [Indexed: 05/20/2023]
Abstract
DNA methylation is an important and widespread epigenetic modification in plant genomes, mediated by DNA methyltransferases (DMTs). DNA methylation is known to play a role in genome protection, regulation of gene expression, and splicing and was previously associated with major developmental reprogramming in plants, such as vernalization and transition to flowering. Here, we show that DNA methylation also controls the growth processes of cell division and cell expansion within a growing organ. The maize (Zea mays) leaf offers a great tool to study growth processes, as the cells progressively move through the spatial gradient encompassing the division zone, transition zone, elongation zone, and mature zone. Opposite to de novo DMTs, the maintenance DMTs were transcriptionally regulated throughout the growth zone of the maize leaf, concomitant with differential CCGG methylation levels in the four zones. Surprisingly, the majority of differentially methylated sequences mapped on or close to gene bodies and not to repeat-rich loci. Moreover, especially the 5' and 3' regions of genes, which show overall low methylation levels, underwent differential methylation in a developmental context. Genes involved in processes such as chromatin remodeling, cell cycle progression, and growth regulation, were differentially methylated. The presence of differential methylation located upstream of the gene anticorrelated with transcript expression, while gene body differential methylation was unrelated to the expression level. These data indicate that DNA methylation is correlated with the decision to exit mitotic cell division and to enter cell expansion, which adds a new epigenetic level to the regulation of growth processes.
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Horst I, Heimann L, Peterhansel C. Signal integration on plant promoters: a case study in maize. PLANT SIGNALING & BEHAVIOR 2013; 8:25389. [PMID: 23857353 PMCID: PMC4002602 DOI: 10.4161/psb.25389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Gene promoters perceive numerous signals and integrate this information into a single response, the transcriptional activity of a gene. It was speculated that covalent modification of histones on the promoters might have an important function in storage and integration of signals. Using the genes for the core proteins of C4 metabolism in maize as a model, we associated the perception of specific signals with the establishment of individual histone modifications. Core elements of the histone code defined in these studies are conserved on all C4 genes and on other maize genes that respond to similar stimuli. Moreover, the code is used in independent C4 lineages. However, our data also advise caution because interpretation of histone modifications might differ dependent on the promoter position of the modification. The model provided here constitutes a starting point for genome-wide decoding of stimulus-modification pairs in epigenetic gene regulation.
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Affiliation(s)
- Ina Horst
- Leibniz University Hannover; Institute of Botany; Hannover, Germany
- These authors contributed equally to this work
| | - Louisa Heimann
- Leibniz University Hannover; Institute of Botany; Hannover, Germany
- These authors contributed equally to this work
| | - Christoph Peterhansel
- Leibniz University Hannover; Institute of Botany; Hannover, Germany
- Correspondence to: Christoph Peterhansel,
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Denton AK, Simon R, Weber APM. C₄ photosynthesis: from evolutionary analyses to strategies for synthetic reconstruction of the trait. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:315-321. [PMID: 23510604 DOI: 10.1016/j.pbi.2013.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 02/24/2013] [Accepted: 02/25/2013] [Indexed: 06/01/2023]
Abstract
C₄ photosynthesis represents the most productive modes of photosynthesis in land plants and some of the most productive crops on the planet, such as maize and sugarcane, and many ecologically important native plants use this type of photosynthesis. Despite its ecological and economic importance, the genetic basis of C₄ photosynthesis remains largely unknown. Even many fundamental aspects of C₄ biochemistry, such as the molecular identity of solute transporters, and many aspects of C₄ plant leaf development, such as the Kranz anatomy, are currently not understood. Here, we review recent progress in gaining a mechanistic understanding of the complex C₄ trait through comparative evolutionary analyses of C₃ and C₄ species.
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Affiliation(s)
- Alisandra K Denton
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences-CEPLAS, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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28
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Heimann L, Horst I, Perduns R, Dreesen B, Offermann S, Peterhansel C. A Common histone modification code on C4 genes in maize and its conservation in Sorghum and Setaria italica. PLANT PHYSIOLOGY 2013; 162:456-69. [PMID: 23564230 PMCID: PMC3641223 DOI: 10.1104/pp.113.216721] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/04/2013] [Indexed: 05/19/2023]
Abstract
C4 photosynthesis evolved more than 60 times independently in different plant lineages. Each time, multiple genes were recruited into C4 metabolism. The corresponding promoters acquired new regulatory features such as high expression, light induction, or cell type-specific expression in mesophyll or bundle sheath cells. We have previously shown that histone modifications contribute to the regulation of the model C4 phosphoenolpyruvate carboxylase (C4-Pepc) promoter in maize (Zea mays). We here tested the light- and cell type-specific responses of three selected histone acetylations and two histone methylations on five additional C4 genes (C4-Ca, C4-Ppdk, C4-Me, C4-Pepck, and C4-RbcS2) in maize. Histone acetylation and nucleosome occupancy assays indicated extended promoter regions with regulatory upstream regions more than 1,000 bp from the transcription initiation site for most of these genes. Despite any detectable homology of the promoters on the primary sequence level, histone modification patterns were highly coregulated. Specifically, H3K9ac was regulated by illumination, whereas H3K4me3 was regulated in a cell type-specific manner. We further compared histone modifications on the C4-Pepc and C4-Me genes from maize and the homologous genes from sorghum (Sorghum bicolor) and Setaria italica. Whereas sorghum and maize share a common C4 origin, C4 metabolism evolved independently in S. italica. The distribution of histone modifications over the promoters differed between the species, but differential regulation of light-induced histone acetylation and cell type-specific histone methylation were evident in all three species. We propose that a preexisting histone code was recruited into C4 promoter control during the evolution of C4 metabolism.
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