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Zhou P, Chen H, Dang J, Shi Z, Shao Y, Liu C, Fan L, Wu Q. Single-cell transcriptome of Nepeta tenuifolia leaves reveal differentiation trajectories in glandular trichomes. FRONTIERS IN PLANT SCIENCE 2022; 13:988594. [PMID: 36340347 PMCID: PMC9627484 DOI: 10.3389/fpls.2022.988594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
The peltate glandular trichomes (PGTs) on Nepeta tenuifolia leaves can secrete and store bioactive essential oils. ScRNA-seq is a powerful tool for uncovering heterogeneous cells and exploring the development and differentiation of specific cells. Due to leaves rich in PGTs, the young leaves were used to isolated protoplasts and successfully captured 33,254 protoplasts for sequencing purposes. After cell type annotation, all the cells were partitioned into six broad populations with 19 clusters. Cells from PGTs were identified based on the expression patterns of trichome-specific genes, monoterpene biosynthetic genes, and metabolic analysis of PGT secretions. The developmental trajectories of PGTs were delineated by pseudotime analysis. Integrative analysis of scRNA-seq data from N. tenuifolia leaves and Arabidopsis thaliana shoot revealed that PGTs were specific to N. tenuifolia. Thus, our results provide a promising basis for exploring cell development and differentiation in plants, especially glandular trichome initiation and development.
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Affiliation(s)
- Peina Zhou
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Hongyu Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Jingjie Dang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Zunrui Shi
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Yongfang Shao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Chanchan Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Qinan Wu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
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Yadav V, Arif N, Singh VP, Guerriero G, Berni R, Shinde S, Raturi G, Deshmukh R, Sandalio LM, Chauhan DK, Tripathi DK. Histochemical Techniques in Plant Science: More Than Meets the Eye. PLANT & CELL PHYSIOLOGY 2021; 62:1509-1527. [PMID: 33594421 DOI: 10.1093/pcp/pcab022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/31/2021] [Indexed: 05/12/2023]
Abstract
Histochemistry is an essential analytical tool interfacing extensively with plant science. The literature is indeed constellated with examples showing its use to decipher specific physiological and developmental processes, as well as to study plant cell structures. Plant cell structures are translucent unless they are stained. Histochemistry allows the identification and localization, at the cellular level, of biomolecules and organelles in different types of cells and tissues, based on the use of specific staining reactions and imaging. Histochemical techniques are also widely used for the in vivo localization of promoters in specific tissues, as well as to identify specific cell wall components such as lignin and polysaccharides. Histochemistry also enables the study of plant reactions to environmental constraints, e.g. the production of reactive oxygen species (ROS) can be traced by applying histochemical staining techniques. The possibility of detecting ROS and localizing them at the cellular level is vital in establishing the mechanisms involved in the sensitivity and tolerance to different stress conditions in plants. This review comprehensively highlights the additional value of histochemistry as a complementary technique to high-throughput approaches for the study of the plant response to environmental constraints. Moreover, here we have provided an extensive survey of the available plant histochemical staining methods used for the localization of metals, minerals, secondary metabolites, cell wall components, and the detection of ROS production in plant cells. The use of recent technological advances like CRISPR/Cas9-based genome-editing for histological application is also addressed. This review also surveys the available literature data on histochemical techniques used to study the response of plants to abiotic stresses and to identify the effects at the tissue and cell levels.
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Affiliation(s)
- Vaishali Yadav
- D D Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Prayagraj 211002, India
| | - Namira Arif
- D D Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Prayagraj 211002, India
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj 211002, India
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Hautcharage, Luxembourg
| | - Roberto Berni
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux 5030, Belgium
| | - Suhas Shinde
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112, USA
| | - Gaurav Raturi
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rupesh Deshmukh
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Luisa M Sandalio
- Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, Granada 18008, Spain
| | - Devendra Kumar Chauhan
- D D Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Prayagraj 211002, India
| | - Durgesh Kumar Tripathi
- Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, I 2 Block, 5th Floor, AUUP Campus Sector-125, Noida 201313, India
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Roach M, Arrivault S, Mahboubi A, Krohn N, Sulpice R, Stitt M, Niittylä T. Spatially resolved metabolic analysis reveals a central role for transcriptional control in carbon allocation to wood. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68. [PMID: 28645173 PMCID: PMC5853372 DOI: 10.1093/jxb/erx200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The contribution of transcriptional and post-transcriptional regulation to modifying carbon allocation to developing wood of trees is not well defined. To clarify the role of transcriptional regulation, the enzyme activity patterns of eight central primary metabolism enzymes across phloem, cambium, and developing wood of aspen (Populus tremula L.) were compared with transcript levels obtained by RNA sequencing of sequential stem sections from the same trees. Enzymes were selected on the basis of their importance in sugar metabolism and in linking primary metabolism to lignin biosynthesis. Existing enzyme assays were adapted to allow measurements from ~1 mm3 sections of dissected stem tissue. These experiments provided high spatial resolution of enzyme activity changes across different stages of wood development, and identified the gene transcripts probably responsible for these changes. In most cases, there was a clear positive relationship between transcripts and enzyme activity. During secondary cell wall formation, the increases in transcript levels and enzyme activities also matched with increased levels of glucose, fructose, hexose phosphates, and UDP-glucose, emphasizing an important role for transcriptional regulation in carbon allocation to developing aspen wood. These observations corroborate the efforts to increase carbon allocation to wood by engineering gene regulatory networks.
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Affiliation(s)
- Melissa Roach
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - Amir Mahboubi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Nicole Krohn
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ronan Sulpice
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Plant Systems Biology Laboratory, Plant AgriBiosciences Research Centre, School of Natural Science, Galway, Ireland
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Totte Niittylä
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Correspondence:
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Isolation and dynamic expression of four genes involving in shikimic acid pathway in Camellia sinensis 'Baicha 1' during periodic albinism. Mol Biol Rep 2016; 43:1119-27. [PMID: 27553670 DOI: 10.1007/s11033-016-4045-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
Abstract
Flavonoids are the main flavor components and functional ingredients in tea, and the shikimic acid pathway is considered as one of the most important pathways in flavonoid biosynthesis, but little was known about the function of regulatory genes in the metabolism phenolic compounds in tea plant (Camellia sinensis), especially related genes in shikimic acid pathway. The dynamic changes of catechin (predominant flavonoid) contents were analyzed in this study, and four genes (CsPPT, CsDAHPS, CsSDH and CsCS) involving in shikimic acid pathway in C. sinensis albino cultivar 'Baicha 1' were cloned and characterized. The full-length cDNA sequences of these genes were obtained using reverse transcription-PCR and rapid amplification of cDNA ends. At the albinistic stage, the amounts of all catechins decreased to the lowest levels, when epigallocatechin gallate was the highest, whereas gallocatechin-3-O-gallate the lowest. Gene expression patterns analyzed by qRT-PCR showed that CsPPT and CsDAHPS were highly expressed in flowers and buds, while CsSDH and CsCS showed high expression levels in buds and leaves. It was also found that the transcript abundance of shikimic acid biosynthetic genes followed a tightly regulated biphasic pattern, and was affected by albinism. The transcript levels of CsPPT and CsDAHPS were decreased at albinistic stage followed elevated expression, whereas CsSDH and CsCS were increased only at re-greening stage. Taken together, these findings suggested that these four genes in C. sinensis may play different roles in shikimic acid biosynthesis and these genes may have divergent functions.
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Barros J, Serk H, Granlund I, Pesquet E. The cell biology of lignification in higher plants. ANNALS OF BOTANY 2015; 115:1053-74. [PMID: 25878140 PMCID: PMC4648457 DOI: 10.1093/aob/mcv046] [Citation(s) in RCA: 334] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/23/2015] [Accepted: 03/10/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Lignin is a polyphenolic polymer that strengthens and waterproofs the cell wall of specialized plant cell types. Lignification is part of the normal differentiation programme and functioning of specific cell types, but can also be triggered as a response to various biotic and abiotic stresses in cells that would not otherwise be lignifying. SCOPE Cell wall lignification exhibits specific characteristics depending on the cell type being considered. These characteristics include the timing of lignification during cell differentiation, the palette of associated enzymes and substrates, the sub-cellular deposition sites, the monomeric composition and the cellular autonomy for lignin monomer production. This review provides an overview of the current understanding of lignin biosynthesis and polymerization at the cell biology level. CONCLUSIONS The lignification process ranges from full autonomy to complete co-operation depending on the cell type. The different roles of lignin for the function of each specific plant cell type are clearly illustrated by the multiple phenotypic defects exhibited by knock-out mutants in lignin synthesis, which may explain why no general mechanism for lignification has yet been defined. The range of phenotypic effects observed include altered xylem sap transport, loss of mechanical support, reduced seed protection and dispersion, and/or increased pest and disease susceptibility.
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Affiliation(s)
- Jaime Barros
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Henrik Serk
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Irene Granlund
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Edouard Pesquet
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
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Kong JQ. Phenylalanine ammonia-lyase, a key component used for phenylpropanoids production by metabolic engineering. RSC Adv 2015. [DOI: 10.1039/c5ra08196c] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Phenylalanine ammonia-lyase, a versatile enzyme with industrial and medical applications.
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Affiliation(s)
- Jian-Qiang Kong
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products
- Beijing
- China
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Cui K, He CY, Zhang JG, Duan AG, Zeng YF. Temporal and Spatial Profiling of Internode Elongation-Associated Protein Expression in Rapidly Growing Culms of Bamboo. J Proteome Res 2012; 11:2492-507. [DOI: 10.1021/pr2011878] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kai Cui
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, People’s
Republic of China
| | - Cai-yun He
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
| | - Jian-guo Zhang
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
| | - Ai-guo Duan
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
| | - Yan-fei Zeng
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
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