1
|
Ge X, Yu X, Liu Z, Yuan J, Qin A, Wang Y, Chen Y, Qin W, Liu Y, Liu X, Zhou Y, Wang P, Yang J, Liu H, Zhao Z, Hu M, Zhang Y, Sun S, Herrera-Estrella L, Tran LSP, Sun X, Li F. Spatiotemporal transcriptome and metabolome landscapes of cotton somatic embryos. Nat Commun 2025; 16:859. [PMID: 39833155 PMCID: PMC11747644 DOI: 10.1038/s41467-025-55870-6] [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: 10/20/2022] [Accepted: 01/02/2025] [Indexed: 01/22/2025] Open
Abstract
Somatic embryogenesis (SE) is a developmental process related to the regeneration of tissue-cultured plants, which serves as a useful technique for crop breeding and improvement. However, SE in cotton is difficult and elusive due to the lack of precise cellular level information on the reprogramming of gene expression patterns involved in somatic embryogenesis. Here, we investigate the spatial and single-cell expression profiles of key genes and the metabolic patterns of key metabolites by integrated single-cell RNA-sequencing (scRNA-seq), spatial transcriptomics (ST), and spatial metabolomics (SM). To evaluate the results of these analyses, we functionally characterized the potential roles of two representative marker genes, AATP1 and DOX2, in the regulation of cotton somatic embryo development. A publicly available web-based resource database ( https://cotton.cricaas.com.cn/somaticembryo/ ) in this study provides convenience for future studies of the expression patterns of marker genes at specific developmental stages during the process of SE in cotton.
Collapse
Affiliation(s)
- Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaole Yu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Zhixin Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Jiachen Yuan
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Aizhi Qin
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Ye Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yanli Chen
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenqiang Qin
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yumeng Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xingxing Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Yaping Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Peng Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jincheng Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Hao Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Zihao Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Mengke Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Yixin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Susu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Xuwu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China.
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| |
Collapse
|
2
|
Zhang H, Mu Y, Zhang H, Yu C. Maintenance of stem cell activity in plant development and stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1302046. [PMID: 38155857 PMCID: PMC10754534 DOI: 10.3389/fpls.2023.1302046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023]
Abstract
Stem cells residing in plant apical meristems play an important role during postembryonic development. These stem cells are the wellspring from which tissues and organs of the plant emerge. The shoot apical meristem (SAM) governs the aboveground portions of a plant, while the root apical meristem (RAM) orchestrates the subterranean root system. In their sessile existence, plants are inextricably bound to their environment and must adapt to various abiotic stresses, including osmotic stress, drought, temperature fluctuations, salinity, ultraviolet radiation, and exposure to heavy metal ions. These environmental challenges exert profound effects on stem cells, potentially causing severe DNA damage and disrupting the equilibrium of reactive oxygen species (ROS) and Ca2+ signaling in these vital cells, jeopardizing their integrity and survival. In response to these challenges, plants have evolved mechanisms to ensure the preservation, restoration, and adaptation of the meristematic stem cell niche. This enduring response allows plants to thrive in their habitats over extended periods. Here, we presented a comprehensive overview of the cellular and molecular intricacies surrounding the initiation and maintenance of the meristematic stem cell niche. We also delved into the mechanisms employed by stem cells to withstand and respond to abiotic stressors.
Collapse
Affiliation(s)
- Huankai Zhang
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Yangwei Mu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hui Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Caiyu Yu
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| |
Collapse
|
3
|
Partap M, Warghat AR, Kumar S. Cambial meristematic cell culture: a sustainable technology toward in vitro specialized metabolites production. Crit Rev Biotechnol 2022:1-19. [PMID: 35658789 DOI: 10.1080/07388551.2022.2055995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cambial meristematic cells (CMCs) culture has received a fair share of scientific and industrial attention among the trending topics of plant cell culture, especially their potential toward secondary metabolites production. However, the conventional plant cell culture is often not commercially feasible because of difficulties associated with culture dedifferentiated cells. Several reports have been published to culture CMCs and bypass the dedifferentiation process in plant cell culture. Numerous mitochondria, multiple vacuoles, genetic stability, self-renewal, higher biomass, and stable metabolites accumulation are the characteristics features of CMCs compared with dedifferentiated cells (DDCs) culture. The CMCs culture has a broader application to produce large-scale natural compounds for: pharmaceuticals, food, and cosmetic industries. Cutting-edge progress in plant cellular and molecular biology has allowed unprecedented insights into cambial stem cell culture and its fundamental processes. Therefore, regarding sustainability and natural compound production, cambial cell culture ranks among the most vital biotechnological interventions for industrial and economic perspectives. This review highlights the recent advances in plant stem cell culture and understands the cambial cells induction and culture mechanisms that affect the growth and natural compounds production.
Collapse
Affiliation(s)
- Mahinder Partap
- Biotechnology Division, CSIR - Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ashish R Warghat
- Biotechnology Division, CSIR - Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR - Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
4
|
Bayat F, Afshar A, Baghban N. Algal Cells-Derived Extracellular Vesicles: A Review With Special Emphasis on Their Antimicrobial Effects. Front Microbiol 2022; 12:785716. [PMID: 35003018 PMCID: PMC8733718 DOI: 10.3389/fmicb.2021.785716] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) originated from different cells of approximately all kinds of organisms, recently got more attention because of their potential in the treatment of diseases and reconstructive medicine. To date, lots of studies have been performed on mammalian-derived vesicles, but little attention has been paid to algae and marine cells as valuable sources of EVs. Proving the promising role of EVs in medicine requires sufficient resources to produce qualified microvesicles. Algae, same as its other sister groups, such as plants, have stem cells and stem cell niches. Previous studies showed the EVs in plants and marine cells. So, this study was set out to talk about algal extracellular vesicles. EVs play a major role in cell-to-cell communication to convey molecules, such as RNA/DNA, metabolites, proteins, and lipids within. The components of EVs depends on the origin of the primitive cells or tissues and the isolation method. Sufficient resources are needed to produce high-quality, stable, and compatible EVs as a drug or drug delivery system. Plant stem cells have great potential as a new controllable resource for the production of EVs. The EVs secreted from stem cells can easily be extracted from the cell culture medium and evaluated for medicinal uses. In this review, the aim is to introduce algae stem cells as well as EVs derived from algal cells. In the following, the production of the EVs¸ the properties of EVs extracted from these sources and their antimicrobial effects will be discussed.
Collapse
Affiliation(s)
- Fereshteh Bayat
- Department of Plant Genetics and Production Engineering, College of Agriculture and Natural Resources, Persian Gulf University, Bushehr, Iran
| | - Alireza Afshar
- The Persian Gulf Biomedical Sciences Research Institute, The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Neda Baghban
- The Persian Gulf Biomedical Sciences Research Institute, The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| |
Collapse
|
5
|
Chen K, Guo T, Li XM, Yang YB, Dong NQ, Shi CL, Ye WW, Shan JX, Lin HX. NAL8 encodes a prohibitin that contributes to leaf and spikelet development by regulating mitochondria and chloroplasts stability in rice. BMC PLANT BIOLOGY 2019; 19:395. [PMID: 31510917 PMCID: PMC6737680 DOI: 10.1186/s12870-019-2007-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/30/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Leaf morphology and spikelet number are two important traits associated with grain yield. To understand how genes coordinating with sink and sources of cereal crops is important for grain yield improvement guidance. Although many researches focus on leaf morphology or grain number in rice, the regulating molecular mechanisms are still unclear. RESULTS In this study, we identified a prohibitin complex 2α subunit, NAL8, that contributes to multiple developmental process and is required for normal leaf width and spikelet number at the reproductive stage in rice. These results were consistent with the ubiquitous expression pattern of NAL8 gene. We used genetic complementation, CRISPR/Cas9 gene editing system, RNAi gene silenced system and overexpressing system to generate transgenic plants for confirming the fuctions of NAL8. Mutation of NAL8 causes a reduction in the number of plastoglobules and shrunken thylakoids in chloroplasts, resulting in reduced cell division. In addition, the auxin levels in nal8 mutants are higher than in TQ, while the cytokinin levels are lower than in TQ. Moreover, RNA-sequencing and proteomics analysis shows that NAL8 is involved in multiple hormone signaling pathways as well as photosynthesis in chloroplasts and respiration in mitochondria. CONCLUSIONS Our findings provide new insights into the way that NAL8 functions as a molecular chaperone in regulating plant leaf morphology and spikelet number through its effects on mitochondria and chloroplasts associated with cell division.
Collapse
Affiliation(s)
- Ke Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Xin-Min Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Chuan-Lin Shi
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|