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Rutowicz K, Lüthi J, de Groot R, Holtackers R, Yakimovich Y, Pazmiño DM, Gandrillon O, Pelkmans L, Baroux C. Multiscale chromatin dynamics and high entropy in plant iPSC ancestors. J Cell Sci 2024; 137:jcs261703. [PMID: 38738286 PMCID: PMC11234377 DOI: 10.1242/jcs.261703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Plant protoplasts provide starting material for of inducing pluripotent cell masses that are competent for tissue regeneration in vitro, analogous to animal induced pluripotent stem cells (iPSCs). Dedifferentiation is associated with large-scale chromatin reorganisation and massive transcriptome reprogramming, characterised by stochastic gene expression. How this cellular variability reflects on chromatin organisation in individual cells and what factors influence chromatin transitions during culturing are largely unknown. Here, we used high-throughput imaging and a custom supervised image analysis protocol extracting over 100 chromatin features of cultured protoplasts. The analysis revealed rapid, multiscale dynamics of chromatin patterns with a trajectory that strongly depended on nutrient availability. Decreased abundance in H1 (linker histones) is hallmark of chromatin transitions. We measured a high heterogeneity of chromatin patterns indicating intrinsic entropy as a hallmark of the initial cultures. We further measured an entropy decline over time, and an antagonistic influence by external and intrinsic factors, such as phytohormones and epigenetic modifiers, respectively. Collectively, our study benchmarks an approach to understand the variability and evolution of chromatin patterns underlying plant cell reprogramming in vitro.
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Affiliation(s)
- Kinga Rutowicz
- Plant Developmental Genetics, Institute of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Joel Lüthi
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Reinoud de Groot
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - René Holtackers
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Yauhen Yakimovich
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Diana M. Pazmiño
- Plant Developmental Genetics, Institute of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Olivier Gandrillon
- Laboratory of Biology and Modeling of the Cell, University of Lyon, ENS de Lyon,69342 Lyon, France
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Célia Baroux
- Plant Developmental Genetics, Institute of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
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2
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Wójcikowska B, Chwiałkowska K, Nowak K, Citerne S, Morończyk J, Wójcik AM, Kiwior-Wesołowska A, Francikowski J, Kwaśniewski M, Gaj MD. Transcriptomic profiling reveals histone acetylation-regulated genes involved in somatic embryogenesis in Arabidopsis thaliana. BMC Genomics 2024; 25:788. [PMID: 39148037 PMCID: PMC11325840 DOI: 10.1186/s12864-024-10623-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed. RESULTS To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors - TFs) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction. CONCLUSION The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants.
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Affiliation(s)
- Barbara Wójcikowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Katarzyna Nowak
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Sylvie Citerne
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Joanna Morończyk
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Anna Maria Wójcik
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Agnieszka Kiwior-Wesołowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Jacek Francikowski
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Mirosław Kwaśniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Małgorzata Danuta Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
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Ben-Amar A, Allel D, Bouamama-Gzara B. Osmotic priming-induced cryotolerance uncovers rejuvenation of grapevine cell cultures: morphogenetic changes and gene expression pattern highlighting enhanced embryogenic potential. PROTOPLASMA 2024:10.1007/s00709-024-01968-5. [PMID: 38980351 DOI: 10.1007/s00709-024-01968-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/25/2024] [Indexed: 07/10/2024]
Abstract
Cryopreservation is a reliable technique for the long-term storage and preservation of embryogenic cells, maintaining their viability without loss of their embryogenic capacity. However, the large-scale conservation of grapevine embryogenic lines in cryobanks remains limited. A significant challenge is understanding somatic cell rejuvenation. Here, we investigate the encapsulation/dehydration and encapsulation/vitrification for cryopreserving embryogenic material. Cell rejuvenation and enhanced embryogenic competence were observed after cryopreservation, as evidenced through structural cellular changes observed by histology and electron scanning microscopy. Results showed that cryopreserved samples of 110-Richter, Riesling, and Tempranillo using encapsulation/dehydration had better survival rates, averaging 81%, 62%, and 48%, respectively, while encapsulation/vitrification yielded lower survival rates, averaging 58%, 42%, and 32%, respectively. Cryopreservation also improved post-thaw recovery and regeneration efficiency assessed through regrowth of proembryogenic masses and somatic embryo conversion reaching 54-72% against 11-17% in control samples. Cryopreservation triggered changes in gene expression patterns and exhibited considerable increase at genotype-specific basis of 1.5- to 4.5-fold in SERK1, BBM, and WOX associated to embryogenic competence as well as in ChitIV and LEA involved in stress response. Membrane stability index, hydrogen peroxide, and proline contents were used as indicators of oxidative stress uncovering a key role of an osmotic trans-priming effect leading to cryotolerance. Our finding highlighted that cryopreservation enhances embryogenic capacity in senescent callus and probably acts as a screening process allowing safe maintenance of proembryogenic cells and promoting their recovery. This study provides a high throughput innovation to set up cryolines for cell rejuvenation of grapevine and other important plant species.
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Affiliation(s)
- Anis Ben-Amar
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia.
| | - Dorsaf Allel
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia
| | - Badra Bouamama-Gzara
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia
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4
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Rhaman MS, Ali M, Ye W, Li B. Opportunities and Challenges in Advancing Plant Research with Single-cell Omics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae026. [PMID: 38996445 DOI: 10.1093/gpbjnl/qzae026] [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: 04/12/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 07/14/2024]
Abstract
Plants possess diverse cell types and intricate regulatory mechanisms to adapt to the ever-changing environment of nature. Various strategies have been employed to study cell types and their developmental progressions, including single-cell sequencing methods which provide high-dimensional catalogs to address biological concerns. In recent years, single-cell sequencing technologies in transcriptomics, epigenomics, proteomics, metabolomics, and spatial transcriptomics have been increasingly used in plant science to reveal intricate biological relationships at the single-cell level. However, the application of single-cell technologies to plants is more limited due to the challenges posed by cell structure. This review outlines the advancements in single-cell omics technologies, their implications in plant systems, future research applications, and the challenges of single-cell omics in plant systems.
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Affiliation(s)
- Mohammad Saidur Rhaman
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Muhammad Ali
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Wenxiu Ye
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
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5
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Zhang B, Zhang H, Xia Y. Harnessing spatial transcriptomics for advancing plant regeneration research. TRENDS IN PLANT SCIENCE 2024; 29:718-720. [PMID: 38418271 DOI: 10.1016/j.tplants.2024.02.004] [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: 12/11/2023] [Revised: 02/03/2024] [Accepted: 02/19/2024] [Indexed: 03/01/2024]
Abstract
Song et al. utilized spatial transcriptomics to study the molecular characteristics of various cells - such as shoot primordia and chlorenchyma cells - in tomato callus during shoot regeneration. This research enhances our knowledge of shoot regeneration and demonstrates the potential of spatial transcriptomics in advancing plant biology.
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Affiliation(s)
- Bingxu Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Hailei Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China; State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China.
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6
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Chen C, Hu Y, Ikeuchi M, Jiao Y, Prasad K, Su YH, Xiao J, Xu L, Yang W, Zhao Z, Zhou W, Zhou Y, Gao J, Wang JW. Plant regeneration in the new era: from molecular mechanisms to biotechnology applications. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1338-1367. [PMID: 38833085 DOI: 10.1007/s11427-024-2581-2] [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: 01/31/2024] [Accepted: 03/26/2024] [Indexed: 06/06/2024]
Abstract
Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design.
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Affiliation(s)
- Chunli Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences (CAS), China National Botanical Garden, Beijing, 100093, China.
| | - Momoko Ikeuchi
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan.
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| | - Kalika Prasad
- Indian Institute of Science Education and Research, Pune, 411008, India.
- , Thiruvananthapuram, 695551, India.
| | - Ying Hua Su
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- Sino-German Joint Research Center on Agricultural Biology, Shandong Agricultural University, Tai'an, 271018, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology (IGDB), CAS, Beijing, 100101, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), IGDB, CAS, Beijing, 100101, China.
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
- CEPAMS, SIPPE, CAS, Shanghai, 200032, China.
| | - Zhong Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale, CEMPS, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Wenkun Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Yun Zhou
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, 47907, USA.
| | - Jian Gao
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Key Laboratory of Plant Carbon Capture, CAS, Shanghai, 200032, China.
- New Cornerstone Science Laboratory, Shanghai, 200032, China.
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7
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Lee HS, Han JE, Bae EK, Jie EY, Kim SW, Kwon HJ, Lee HS, Yeon SH, Murthy HN, Park SY. Response surface methodology mediated optimization of phytosulfokine and plant growth regulators for enhanced protoplast division, callus induction, and somatic embryogenesis in Angelica Gigas Nakai. BMC PLANT BIOLOGY 2024; 24:527. [PMID: 38858674 PMCID: PMC11165744 DOI: 10.1186/s12870-024-05243-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Angelica Gigas (Purple parsnip) is an important medicinal plant that is cultivated and utilized in Korea, Japan, and China. It contains bioactive substances especially coumarins with anti-inflammatory, anti-platelet aggregation, anti-cancer, anti-diabetic, antimicrobial, anti-obesity, anti-oxidant, immunomodulatory, and neuroprotective properties. This medicinal crop can be genetically improved, and the metabolites can be obtained by embryonic stem cells. In this context, we established the protoplast-to-plant regeneration methodology in Angelica gigas. RESULTS In the present investigation, we isolated the protoplast from the embryogenic callus by applying methods that we have developed earlier and established protoplast cultures using Murashige and Skoog (MS) liquid medium and by embedding the protoplast in thin alginate layer (TAL) methods. We supplemented the culture medium with growth regulators namely 2,4-dichlorophenoxyaceticacid (2,4-D, 0, 0.75, 1.5 mg L- 1), kinetin (KN, 0, 0.5, and 1.0 mg L- 1) and phytosulfokine (PSK, 0, 50, 100 nM) to induce protoplast division, microcolony formation, and embryogenic callus regeneration. We applied central composite design (CCD) and response surface methodology (RSM) for the optimization of 2,4-D, KN, and PSK levels during protoplast division, micro-callus formation, and induction of embryogenic callus stages. The results revealed that 0.04 mg L- 1 2,4-D + 0.5 mg L- 1 KN + 2 nM PSK, 0.5 mg L- 1 2,4-D + 0.9 mg L- 1 KN and 90 nM PSK, and 1.5 mg L- 1 2,4-D and 1 mg L- 1 KN were optimum for protoplast division, micro-callus formation and induction embryogenic callus. MS basal semi-solid medium without growth regulators was good for the development of embryos and plant regeneration. CONCLUSIONS This study demonstrated successful protoplast culture, protoplast division, micro-callus formation, induction embryogenic callus, somatic embryogenesis, and plant regeneration in A. gigas. The methodologies developed here are quite useful for the genetic improvement of this important medicinal plant.
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Affiliation(s)
- Han-Sol Lee
- Department of Horticultural Science, Division of Animal, Horticultural and Food Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jong-Eun Han
- Department of Horticultural Science, Division of Animal, Horticultural and Food Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Eun-Kyung Bae
- Department of Forest Bioresources, National Institute of Forest Science, 39 Onjeong-ro, Suwon, 16631, Republic of Korea
| | - Eun Yee Jie
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea.
| | - Hyuk Joon Kwon
- Food Science R&D Center, Kolmar BNH Co., Seocho-gu, Seoul, 30003, Republic of Korea
| | - Hak Sung Lee
- Food Science R&D Center, Kolmar BNH Co., Seocho-gu, Seoul, 30003, Republic of Korea
| | - Soo-Ho Yeon
- Food Science R&D Center, Kolmar BNH Co., Seocho-gu, Seoul, 30003, Republic of Korea
| | - Hosakatte Niranjana Murthy
- Department of Horticultural Science, Division of Animal, Horticultural and Food Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
- Department of Botany, Karnatak University, Dharwad, 580003, India
- Department of Biotechnology, KLE Technological University, Hubballi, 580039, India
| | - So-Young Park
- Department of Horticultural Science, Division of Animal, Horticultural and Food Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Guo H, Zhang L, Guo H, Cui X, Fan Y, Li T, Qi X, Yan T, Chen A, Shi F, Zeng F. Single-cell transcriptome atlas reveals somatic cell embryogenic differentiation features during regeneration. PLANT PHYSIOLOGY 2024; 195:1414-1431. [PMID: 38401160 DOI: 10.1093/plphys/kiae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/15/2023] [Accepted: 01/16/2024] [Indexed: 02/26/2024]
Abstract
Understanding somatic cell totipotency remains a challenge facing scientific inquiry today. Plants display remarkable cell totipotency expression, illustrated by single-cell differentiation during somatic embryogenesis (SE) for plant regeneration. Determining cell identity and exploring gene regulation in such complex heterogeneous somatic cell differentiation have been major challenges. Here, we performed high-throughput single-cell sequencing assays to define the precise cellular landscape and revealed the modulation mode of marker genes during embryogenic differentiation in cotton (Gossypium hirsutum L.) as the crop for biotechnology application. We demonstrated that nonembryogenic calli (NEC) and primary embryogenic calli (PEC) tissues were composed of heterogeneous cells that could be partitioned into four broad populations with six distinct cell clusters. Enriched cell clusters and cell states were identified in NEC and PEC samples, respectively. Moreover, a broad repertoire of new cluster-specific genes and associated expression modules were identified. The energy metabolism, signal transduction, environmental adaptation, membrane transport pathways, and a series of transcription factors were preferentially enriched in cell embryogenic totipotency expression. Notably, the SE-ASSOCIATED LIPID TRANSFER PROTEIN (SELTP) gene dose-dependently marked cell types with distinct embryogenic states and exhibited a parabolic curve pattern along the somatic cell embryogenic differentiation trajectory, suggesting that SELTP could serve as a favorable quantitative cellular marker for detecting embryogenic expression at the single-cell level. In addition, RNA velocity and Scissor analysis confirmed the pseudo-temporal model and validated the accuracy of the scRNA-seq data, respectively. This work provides valuable marker-genes resources and defines precise cellular taxonomy and trajectory atlases for somatic cell embryogenic differentiation in plant regeneration.
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Affiliation(s)
- Huihui Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Li Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Haixia Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Xiwang Cui
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Yupeng Fan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Tongtong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Xiushan Qi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Tongdi Yan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Aiyun Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Fengjuan Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Fanchang Zeng
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
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North BJ, Ohnstad AE, Ragusa MJ, Shoemaker CJ. The LC3-interacting region of NBR1 is a protein interaction hub enabling optimal flux. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593318. [PMID: 38766171 PMCID: PMC11100792 DOI: 10.1101/2024.05.09.593318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
During autophagy, potentially toxic cargo is enveloped by a newly formed autophagosome and trafficked to the lysosome for degradation. Ubiquitinated protein aggregates, a key target for autophagy, are identified by multiple autophagy receptors. NBR1 is an archetypal autophagy receptor and an excellent model for deciphering the role of the multivalent, heterotypic interactions made by cargo-bound receptors. Using NBR1 as a model, we find that three critical binding partners - ATG8-family proteins, FIP200, and TAX1BP1 - each bind to a short linear interaction motif (SLiM) within NBR1. Mutational peptide arrays indicate that these binding events are mediated by distinct overlapping determinants, rather than a single, convergent, SLiM. AlphaFold modeling underlines the need for conformational flexibility within the NBR1 SLiM, as distinct conformations mediate each binding event. To test the extent to which overlapping SLiMs exist beyond NBR1, we performed peptide binding arrays on >100 established LC3-interacting regions (LIRs), revealing that FIP200 and/or TAX1BP1 binding to LIRs is a common phenomenon and suggesting LIRs as protein interaction hotspots. Comparative analysis of phosphomimetic peptides highlights that while FIP200 and Atg8-family binding are generally augmented by phosphorylation, TAX1BP1 binding is nonresponsive, suggesting differential regulation of these binding events. In vivo studies confirm that LIR-mediated interactions with TAX1BP1 enhance NBR1 activity, increasing autophagosomal delivery by leveraging an additional LIR from TAX1BP1. In sum, these results reveal a one-to-many binding modality in NBR1, providing key insights into the cooperative mechanisms among autophagy receptors. Furthermore, these findings underscore the pervasive role of multifunctional SLiMs in autophagy, offering substantial avenues for further exploration into their regulatory functions.
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Affiliation(s)
- Brian J North
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Amelia E Ohnstad
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | | | - Christopher J Shoemaker
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
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10
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Guo H, Guo H, Zhang L, Tian X, Wu J, Fan Y, Li T, Gou Z, Sun Y, Gao F, Wang J, Shan G, Zeng F. Organelle Ca 2+/CAM1-SELTP confers somatic cell embryogenic competence acquisition and transformation in plant regeneration. THE NEW PHYTOLOGIST 2024; 242:1172-1188. [PMID: 38501463 DOI: 10.1111/nph.19679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/20/2024] [Indexed: 03/20/2024]
Abstract
Somatic cell totipotency in plant regeneration represents the forefront of the compelling scientific puzzles and one of the most challenging problems in biology. How somatic embryogenic competence is achieved in regeneration remains elusive. Here, we discover uncharacterized organelle-based embryogenic differentiation processes of intracellular acquisition and intercellular transformation, and demonstrate the underlying regulatory system of somatic embryogenesis-associated lipid transfer protein (SELTP) and its interactor calmodulin1 (CAM1) in cotton as the pioneer crop for biotechnology application. The synergistic CAM1 and SELTP exhibit consistent dynamical amyloplast-plasmodesmata (PD) localization patterns but show opposite functional effects. CAM1 inhibits the effect of SELTP to regulate embryogenic differentiation for plant regeneration. It is noteworthy that callus grafting assay reflects intercellular trafficking of CAM1 through PD for embryogenic transformation. This work originally provides insight into the mechanisms responsible for embryogenic competence acquisition and transformation mediated by the Ca2+/CAM1-SELTP regulatory pathway, suggesting a principle for plant regeneration and cell/genetic engineering.
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Affiliation(s)
- Huihui Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Haixia Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Li Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Xindi Tian
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Jianfei Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Yupeng Fan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Tongtong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Zhongyuan Gou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Yuxiao Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Fan Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Jianjun Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Guangyao Shan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Fanchang Zeng
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
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11
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Li J, Zhang Q, Wang Z, Liu Q. The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions. PLANT PHYSIOLOGY 2024; 194:2022-2038. [PMID: 38290051 PMCID: PMC10980418 DOI: 10.1093/plphys/kiae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.
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Affiliation(s)
- Jiawen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zejia Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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12
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Yan Y, Luo H, Qin Y, Yan T, Jia J, Hou Y, Liu Z, Zhai J, Long Y, Deng X, Cao X. Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5. Proc Natl Acad Sci U S A 2024; 121:e2317408121. [PMID: 38285953 PMCID: PMC10861865 DOI: 10.1073/pnas.2317408121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/29/2023] [Indexed: 01/31/2024] Open
Abstract
Light plays a central role in plant growth and development, providing an energy source and governing various aspects of plant morphology. Previous study showed that many polyadenylated full-length RNA molecules within the nucleus contain unspliced introns (post-transcriptionally spliced introns, PTS introns), which may play a role in rapidly responding to changes in environmental signals. However, the mechanism underlying post-transcriptional regulation during initial light exposure of young, etiolated seedlings remains elusive. In this study, we used FLEP-seq2, a Nanopore-based sequencing technique, to analyze nuclear RNAs in Arabidopsis (Arabidopsis thaliana) seedlings under different light conditions and found numerous light-responsive PTS introns. We also used single-nucleus RNA sequencing (snRNA-seq) to profile transcripts in single nucleus and investigate the distribution of light-responsive PTS introns across distinct cell types. We established that light-induced PTS introns are predominant in mesophyll cells during seedling de-etiolation following exposure of etiolated seedlings to light. We further demonstrated the involvement of the splicing-related factor A. thaliana PROTEIN ARGININE METHYLTRANSFERASE 5 (AtPRMT5), working in concert with the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a critical repressor of light signaling pathways. We showed that these two proteins orchestrate light-induced PTS events in mesophyll cells and facilitate chloroplast development, photosynthesis, and morphogenesis in response to ever-changing light conditions. These findings provide crucial insights into the intricate mechanisms underlying plant acclimation to light at the cell-type level.
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Affiliation(s)
- Yan Yan
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Haofei Luo
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Yuwei Qin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Tingting Yan
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou571100, China
| | - Jinbu Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Yifeng Hou
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Zhijian Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Yanping Long
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Xian Deng
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Xiaofeng Cao
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
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13
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Kean-Galeno T, Lopez-Arredondo D, Herrera-Estrella L. The Shoot Apical Meristem: An Evolutionary Molding of Higher Plants. Int J Mol Sci 2024; 25:1519. [PMID: 38338798 PMCID: PMC10855264 DOI: 10.3390/ijms25031519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/27/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and other meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understanding of SAM morphology and regulation is based on studies conducted mainly on some angiosperms, including economically important crops such as maize (Zea mays) and rice (Oryza sativa), and the model species Arabidopsis (Arabidopsis thaliana). However, studies in other plant species from the gymnosperms are scant, making difficult comparative analyses that help us understand SAM regulation in diverse plant species. This limitation prevents deciphering the mechanisms by which evolution gave rise to the multiple plant structures within the plant kingdom and determines the conserved mechanisms involved in SAM maintenance and operation. This review aims to integrate and analyze the current knowledge of SAM evolution by combining the morphological and molecular information recently reported from the plant kingdom.
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Affiliation(s)
- Tania Kean-Galeno
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
| | - Damar Lopez-Arredondo
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
- Unidad de Genómica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36821, Mexico
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14
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Shao J, Peng B, Zhang Y, Yan X, Yao X, Hu X, Li L, Fu X, Zheng H, Tang K. A high-efficient protoplast transient system for screening gene editing elements in Salvia miltiorrhiza. PLANT CELL REPORTS 2024; 43:45. [PMID: 38261110 DOI: 10.1007/s00299-023-03134-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]
Abstract
KEY MESSAGE A high-efficiency protoplast transient system was devised to screen genome editing elements in Salvia miltiorrhiza. Medicinal plants with high-value pharmaceutical ingredients have attracted research attention due to their beneficial effects on human health. Cell wall-free protoplasts of plants can be used to evaluate the efficiency of genome editing mutagenesis. The capabilities of gene editing in medicinal plants remain to be fully explored owing to their complex genetic background and shortfall of suitable transformation. Here, we took the Salvia miltiorrhiza as a representative example for developing a method to screen favorable gene editing elements with high editing efficiency in medical plants by a PEG-mediated protoplast transformation. Results indicated that using the endogenous SmU6.1 of S. miltiorrhiza to drive sgRNA and the plant codon-optimized Cas9 driven by the promoter SlEF1α can enhance the efficiency of editing. In summary, we uncover an efficacious transient method for screening editing elements and shed new light on increasing gene editing efficiency in medicinal plants.
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Affiliation(s)
- Jin Shao
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bowen Peng
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yaojie Zhang
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Yan
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinghao Yao
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinyi Hu
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ling Li
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueqing Fu
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Han Zheng
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Kexuan Tang
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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15
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Vu TV, Nguyen NT, Kim J, Hong JC, Kim J. Prime editing: Mechanism insight and recent applications in plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:19-36. [PMID: 37794706 PMCID: PMC10754014 DOI: 10.1111/pbi.14188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Prime editing (PE) technology utilizes an extended prime editing guide RNA (pegRNA) to direct a fusion peptide consisting of nCas9 (H840) and reverse transcriptase (RT) to a specific location in the genome. This enables the installation of base changes at the targeted site using the extended portion of the pegRNA through RT activity. The resulting product of the RT reaction forms a 3' flap, which can be incorporated into the genomic site through a series of biochemical steps involving DNA repair and synthesis pathways. PE has demonstrated its effectiveness in achieving almost all forms of precise gene editing, such as base conversions (all types), DNA sequence insertions and deletions, chromosomal translocation and inversion and long DNA sequence insertion at safe harbour sites within the genome. In plant science, PE could serve as a groundbreaking tool for precise gene editing, allowing the creation of desired alleles to improve crop varieties. Nevertheless, its application has encountered limitations due to efficiency constraints, particularly in dicotyledonous plants. In this review, we discuss the step-by-step mechanism of PE, shedding light on the critical aspects of each step while suggesting possible solutions to enhance its efficiency. Additionally, we present an overview of recent advancements and future perspectives in PE research specifically focused on plants, examining the key technical considerations of its applications.
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Affiliation(s)
- Tien V. Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Ngan Thi Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
- Nulla Bio Inc.JinjuKorea
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16
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Feng Y, Zhao Y, Ma Y, Liu D, Shi H. Single-cell transcriptome analyses reveal cellular and molecular responses to low nitrogen in burley tobacco leaves. PHYSIOLOGIA PLANTARUM 2023; 175:e14118. [PMID: 38148214 DOI: 10.1111/ppl.14118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/28/2023]
Abstract
Tobacco (Nicotiana tabacum) is cultivated and consumed worldwide. It requires great amounts of nitrogen (N) to achieve the best yield and quality. With a view to sustainable and environmentally friendly agriculture, developing new genotypes with high productivity under low N conditions is an important approach. It is unclear how genes in tobacco are expressed at the cellular level and the precise mechanisms by which cells respond to environmental stress, especially in the case of low N. Here, we characterized the transcriptomes in tobacco leaves grown in normal and low-N conditions by performing scRNA-seq. We identified 10 cell types with 17 transcriptionally distinct cell clusters with the assistance of marker genes and constructed the first single-cell atlas of tobacco leaves. Distinct gene expression patterns of cell clusters were observed under low-N conditions, and the mesophyll cells were the most important responsive cell type and displayed heterogene responses among its three subtypes. Pseudo-time trajectory analysis revealed low-N stress decelerates the differentiation towards mesophyll cells. In combination with scRNA-seq, WGCNA, and bulk RNA-seq results, we found that genes involved in porphyrin metabolism, nitrogen metabolism, carbon fixation, photosynthesis, and photosynthesis-antenna pathway play an essential role in response to low N. Moreover, we identified COL16, GATA24, MYB73, and GLK1 as key TFs in the regulation of N-responsive genes. Collectively, our findings are the first observation of the cellular and molecular responses of tobacco leaves under low N stress and lay the cornerstone for future tobacco scRNA-seq investigations.
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Affiliation(s)
- Yuqing Feng
- College of Tobacco, Henan Agricultural University, Zhengzhou, Henan, P.R.China
| | - Yuanyuan Zhao
- College of Tobacco, Henan Agricultural University, Zhengzhou, Henan, P.R.China
| | - Yanjun Ma
- Technology Center, Shanghai Tobacco Group Beijing Cigarette Factory Co., Ltd, Beijing, China
| | - Deshui Liu
- Technology Center, Shanghai Tobacco Group Beijing Cigarette Factory Co., Ltd, Beijing, China
| | - Hongzhi Shi
- College of Tobacco, Henan Agricultural University, Zhengzhou, Henan, P.R.China
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17
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Zhu X, Xu Z, Wang G, Cong Y, Yu L, Jia R, Qin Y, Zhang G, Li B, Yuan D, Tu L, Yang X, Lindsey K, Zhang X, Jin S. Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem. Genome Biol 2023; 24:194. [PMID: 37626404 PMCID: PMC10463415 DOI: 10.1186/s13059-023-03032-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Somatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely unclear. Recent advances in single-cell technologies enable us to explore the mechanism of plant regeneration at single-cell resolution. RESULTS We generate a high-resolution single-cell transcriptomic landscape of hypocotyl tissue from the highly regenerable cotton genotype Jin668 and the recalcitrant TM-1. We identify nine putative cell clusters and 23 cluster-specific marker genes for both cultivars. We find that the primary vascular cell is the major cell type that undergoes cell fate transition in response to external stimulation. Further developmental trajectory and gene regulatory network analysis of these cell clusters reveals that a total of 41 hormone response-related genes, including LAX2, LAX1, and LOX3, exhibit different expression patterns in the primary xylem and cambium region of Jin668 and TM-1. We also identify novel genes, including CSEF, PIS1, AFB2, ATHB2, PLC2, and PLT3, that are involved in regeneration. We demonstrate that LAX2, LAX1 and LOX3 play important roles in callus proliferation and plant regeneration by CRISPR/Cas9 editing and overexpression assay. CONCLUSIONS This study provides novel insights on the role of the regulatory network in cell fate transition and reprogramming during plant regeneration driven by somatic embryogenesis.
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Affiliation(s)
- Xiangqian Zhu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhongping Xu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Guanying Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yulong Cong
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lu Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ruoyu Jia
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yuan Qin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Guangyu Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bo Li
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Wulumuqi, 830000, Xinjiang, China
| | - Daojun Yuan
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lili Tu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiyan Yang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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18
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Fehér A. A Common Molecular Signature Indicates the Pre-Meristematic State of Plant Calli. Int J Mol Sci 2023; 24:13122. [PMID: 37685925 PMCID: PMC10488067 DOI: 10.3390/ijms241713122] [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: 07/29/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
In response to different degrees of mechanical injury, certain plant cells re-enter the division cycle to provide cells for tissue replenishment, tissue rejoining, de novo organ formation, and/or wound healing. The intermediate tissue formed by the dividing cells is called a callus. Callus formation can also be induced artificially in vitro by wounding and/or hormone (auxin and cytokinin) treatments. The callus tissue can be maintained in culture, providing starting material for de novo organ or embryo regeneration and thus serving as the basis for many plant biotechnology applications. Due to the biotechnological importance of callus cultures and the scientific interest in the developmental flexibility of somatic plant cells, the initial molecular steps of callus formation have been studied in detail. It was revealed that callus initiation can follow various ways, depending on the organ from which it develops and the inducer, but they converge on a seemingly identical tissue. It is not known, however, if callus is indeed a special tissue with a defined gene expression signature, whether it is a malformed meristem, or a mass of so-called "undifferentiated" cells, as is mostly believed. In this paper, I review the various mechanisms of plant regeneration that may converge on callus initiation. I discuss the role of plant hormones in the detour of callus formation from normal development. Finally, I compare various Arabidopsis gene expression datasets obtained a few days, two weeks, or several years after callus induction and identify 21 genes, including genes of key transcription factors controlling cell division and differentiation in meristematic regions, which were upregulated in all investigated callus samples. I summarize the information available on all 21 genes that point to the pre-meristematic nature of callus tissues underlying their wide regeneration potential.
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Affiliation(s)
- Attila Fehér
- Institute of Plant Biology, Biological Research Centre, 62 Temesvári Körút, 6726 Szeged, Hungary; or
- Department of Plant Biology, University of Szeged, 52 Közép Fasor, 6726 Szeged, Hungary
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19
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Morinaka H, Sakamoto Y, Iwase A, Sugimoto K. How do plants reprogramme the fate of differentiated cells? CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102377. [PMID: 37167921 DOI: 10.1016/j.pbi.2023.102377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 05/13/2023]
Abstract
Being able to change cell fate after differentiation highlights the remarkable developmental plasticity of plant cells. Recent studies show that phytohormones, such as auxin and cytokinin, promote cell cycle reactivation, a critical first step to reprogramme mitotically inactive, differentiated cells into organogenic stem cells. Accumulating evidence suggests that wounding provides an additional cue to convert the identity of differentiated cells by promoting the loss of existing cell fate and/or acquisition of new cell fate. Differentiated cells can also alter cell fate without undergoing cell division and in this case, wounding and phytohormones induce master regulators that can directly assign new cell fate.
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Affiliation(s)
- Hatsune Morinaka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
| | - Yuki Sakamoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan; Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
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20
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Liao RY, Wang JW. Analysis of meristems and plant regeneration at single-cell resolution. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102378. [PMID: 37172363 DOI: 10.1016/j.pbi.2023.102378] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/23/2023] [Accepted: 04/12/2023] [Indexed: 05/14/2023]
Abstract
Rapid development of high-throughput single-cell RNA sequencing (scRNA-seq) technologies offers exciting opportunities to reveal new and rare cell types, previously hidden cell states, and continuous developmental trajectories. In this review, we first illustrate the ways in which scRNA-seq enables researchers to distinguish between distinct plant cell populations, delineate cell cycle continuums, and infer continuous differentiation trajectories of diverse cell types in shoots, roots, and floral and vascular meristems with unprecedented resolution. We then highlight the emerging power of scRNA-seq to dissect cell heterogeneity in regenerating tissues and uncover the cellular basis of cell reprogramming and stem cell commitment during plant regeneration. We conclude by discussing related outstanding questions in the field.
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Affiliation(s)
- Ren-Yu Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China; University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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21
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Liu X, Bie XM, Lin X, Li M, Wang H, Zhang X, Yang Y, Zhang C, Zhang XS, Xiao J. Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation. NATURE PLANTS 2023; 9:908-925. [PMID: 37142750 DOI: 10.1038/s41477-023-01406-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/29/2023] [Indexed: 05/06/2023]
Abstract
Genetic transformation is important for gene functional study and crop improvement. However, it is less effective in wheat. Here we employed a multi-omic analysis strategy to uncover the transcriptional regulatory network (TRN) responsible for wheat regeneration. RNA-seq, ATAC-seq and CUT&Tag techniques were utilized to profile the transcriptional and chromatin dynamics during early regeneration from the scutellum of immature embryos in the wheat variety Fielder. Our results demonstrate that the sequential expression of genes mediating cell fate transition during regeneration is induced by auxin, in coordination with changes in chromatin accessibility, H3K27me3 and H3K4me3 status. The built-up TRN driving wheat regeneration was found to be dominated by 446 key transcription factors (TFs). Further comparisons between wheat and Arabidopsis revealed distinct patterns of DNA binding with one finger (DOF) TFs in the two species. Experimental validations highlighted TaDOF5.6 (TraesCS6A02G274000) and TaDOF3.4 (TraesCS2B02G592600) as potential enhancers of transformation efficiency in different wheat varieties.
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Affiliation(s)
- Xuemei Liu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiao Min Bie
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Menglu Li
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Hongzhe Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyu Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Nanjing Agricultural University, Nanjing, China
| | - Chunyan Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xian Sheng Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing, China.
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22
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Morinaka H, Coleman D, Sugimoto K, Iwase A. Molecular Mechanisms of Plant Regeneration from Differentiated Cells: Approaches from Historical Tissue Culture Systems. PLANT & CELL PHYSIOLOGY 2023; 64:297-304. [PMID: 36546730 PMCID: PMC10016324 DOI: 10.1093/pcp/pcac172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/23/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Plants can exert remarkable capacity for cell reprogramming even from differentiated cells. This ability allows plants to regenerate tissues/organs and even individuals in nature and in vitro. In recent decades, Arabidopsis research has uncovered molecular mechanisms of plant regeneration; however, our understanding of how plant cells retain both differentiated status and developmental plasticity is still obscure. In this review, we first provide a brief outlook of the representative modes of plant regeneration and key factors revealed by Arabidopsis research. We then re-examine historical tissue culture systems that enable us to investigate the molecular details of cell reprogramming in differentiated cells and discuss the different approaches, specifically highlighting our recent progress in shoot regeneration from the epidermal cell of Torenia fournieri.
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Affiliation(s)
- Hatsune Morinaka
- *Corresponding authors: Hatsune Morinaka, E-mail, ; Akira Iwase, E-mail,
| | - Duncan Coleman
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Keiko Sugimoto
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Akira Iwase
- *Corresponding authors: Hatsune Morinaka, E-mail, ; Akira Iwase, E-mail,
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23
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Wang D, Hu X, Ye H, Wang Y, Yang Q, Liang X, Wang Z, Zhou Y, Wen M, Yuan X, Zheng X, Ye W, Guo B, Yusuyin M, Russinova E, Zhou Y, Wang K. Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton. Genome Biol 2023; 24:49. [PMID: 36918913 PMCID: PMC10012527 DOI: 10.1186/s13059-023-02886-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/26/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The epidermis of cotton ovule produces fibers, the most important natural cellulose source for the global textile industry. However, the molecular mechanism of fiber cell growth is still poorly understood. RESULTS Here, we develop an optimized protoplasting method, and integrate single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) to systematically characterize the cells of the outer integument of ovules from wild type and fuzzless/lintless (fl) cotton (Gossypium hirsutum). By jointly analyzing the scRNA-seq data from wildtype and fl, we identify five cell populations including the fiber cell type and construct the development trajectory for fiber lineage cells. Interestingly, by time-course diurnal transcriptomic analysis, we demonstrate that the primary growth of fiber cells is a highly regulated circadian rhythmic process. Moreover, we identify a small peptide GhRALF1 that circadian rhythmically controls fiber growth possibly through oscillating auxin signaling and proton pump activity in the plasma membrane. Combining with scATAC-seq, we further identify two cardinal cis-regulatory elements (CREs, TCP motif, and TCP-like motif) which are bound by the trans factors GhTCP14s to modulate the circadian rhythmic metabolism of mitochondria and protein translation through regulating approximately one third of genes that are highly expressed in fiber cells. CONCLUSIONS We uncover a fiber-specific circadian clock-controlled gene expression program in regulating fiber growth. This study unprecedentedly reveals a new route to improve fiber traits by engineering the circadian clock of fiber cells.
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Affiliation(s)
- Dehe Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiao Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Hanzhe Ye
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Yue Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Qian Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaodong Liang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Zilin Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Yifan Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Miaomiao Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, China.,TaiKang Center for Life and Medical Sciences, RNA Institute, Remin Hospital, Wuhan University, Wuhan, China
| | - Xueyan Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaomin Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wen Ye
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, School of Medicine, Wuhan University, Wuhan, China
| | - Boyu Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Mayila Yusuyin
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yu Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China. .,Institute for Advanced Studies, Wuhan University, Wuhan, China. .,TaiKang Center for Life and Medical Sciences, RNA Institute, Remin Hospital, Wuhan University, Wuhan, China. .,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, School of Medicine, Wuhan University, Wuhan, China.
| | - Kun Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China. .,Institute for Advanced Studies, Wuhan University, Wuhan, China.
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24
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Liu X, Zhu K, Xiao J. Recent advances in understanding of the epigenetic regulation of plant regeneration. ABIOTECH 2023; 4:31-46. [PMID: 37220541 PMCID: PMC10199984 DOI: 10.1007/s42994-022-00093-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/27/2022] [Indexed: 05/22/2023]
Abstract
Ever since the concept of "plant cell totipotency" was first proposed in the early twentieth century, plant regeneration has been a major focus of study. Regeneration-mediated organogenesis and genetic transformation are important topics in both basic research and modern agriculture. Recent studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant regeneration. The hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA methylation. Here, we summarize how various aspects of epigenetic regulation, including histone modifications and variants, chromatin accessibility dynamics, DNA methylation, and microRNAs, modulate plant regeneration. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in boosting crop breeding, especially if coupled with emerging single-cell omics technologies.
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Affiliation(s)
- Xuemei Liu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Kehui Zhu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
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25
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Evaluation of CRISPR/Cas9 Constructs in Wheat Cell Suspension Cultures. Int J Mol Sci 2023; 24:ijms24032162. [PMID: 36768486 PMCID: PMC9916915 DOI: 10.3390/ijms24032162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Despite intensive optimization efforts, developing an efficient sequence-specific CRISPR/Cas-mediated genome editing method remains a challenge, especially in polyploid cereal species such as wheat. Validating the efficacy of nuclease constructs prior to using them in planta is, thus, a major step of every editing experiment. Several construct evaluation strategies were proposed, with PEG-mediated plasmid transfection of seedling-derived protoplasts becoming the most popular. However, the usefulness of this approach is affected by associated construct copy number bias and chromatin relaxation, both influencing the outcome. Therefore, to achieve a reliable evaluation of CRISPR/Cas9 constructs, we proposed a system based on an Agrobacterium-mediated transformation of established wheat cell suspension cultures. This system was used for the evaluation of a CRISPR/Cas9 construct designed to target the ABA 8'-hydroxylase 1 gene. The efficiency of editing was verified by cost-effective means of Sanger sequencing and bioinformatic analysis. We discuss advantages and potential future developments of this method in contrast to other in vitro approaches.
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26
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Ren S, Wang Y. Protoplast Isolation for Plant Single-Cell RNA-seq. Methods Mol Biol 2023; 2686:301-305. [PMID: 37540365 DOI: 10.1007/978-1-0716-3299-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The growth and development of plants depends on diversified gene expression in different cell types. Compared to traditional bulk RNA sequencing, droplet-based single-cell RNA sequencing (scRNA-seq) allows for transcriptome profiling of individual cells within heterogeneous tissues. scRNA-seq provides a high-resolution atlas of cellular characterization and vastly improves our understandings of the interactions between individual cells and the microenvironment. However, the difficulty in protoplast isolation has limited the application of single-cell sequencing technology in plant research. Here we describe a high-efficiency protoplast isolation protocol for scRNA-seq.
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Affiliation(s)
- Shulin Ren
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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27
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Müller-Xing R, Xing Q. The plant stem-cell niche and pluripotency: 15 years of an epigenetic perspective. FRONTIERS IN PLANT SCIENCE 2022; 13:1018559. [PMID: 36388540 PMCID: PMC9659954 DOI: 10.3389/fpls.2022.1018559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Pluripotent stem-cells are slowly dividing cells giving rise to daughter cells that can either differentiate to new tissues and organs, or remain stem-cells. In plants, stem-cells are located in specific niches of the shoot and root apical meristems (SAMs and RAMs). After ablation of stem-cell niches, pluripotent meristematic cells can establish new stem-cells, whereas the removal of the whole meristem destructs the regeneration process. In tissue cultures, after detached plant organs are transferred to rooting or callus induction medium (G5 or CIM), vasculature-associated pluripotent cells (VPCs) immediately start proliferation to form adventitious roots or callus, respectively, while other cell types of the organ explants basically play no part in the process. Hence, in contrast to the widely-held assumption that all plant cells have the ability to reproduce a complete organism, only few cell types are pluripotent in practice, raising the question how pluripotent stem-cells differ from differentiated cells. It is now clear that, in addition to gene regulatory networks of pluripotency factors and phytohormone signaling, epigenetics play a crucial role in initiation, maintenance and determination of plant stem-cells. Although, more and more epigenetic regulators have been shown to control plant stem-cell fate, only a few studies demonstrate how they are recruited and how they change the chromatin structure and transcriptional regulation of pluripotency factors. Here, we highlight recent breakthroughs but also revisited classical studies of epigenetic regulation and chromatin dynamics of plant stem-cells and their pluripotent precursor-cells, and point out open questions and future directions.
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28
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Van den Broeck L, Schwartz MF, Krishnamoorthy S, Tahir MA, Spurney RJ, Madison I, Melvin C, Gobble M, Nguyen T, Peters R, Hunt A, Muhammad A, Li B, Stuiver M, Horn T, Sozzani R. Establishing a reproducible approach to study cellular functions of plant cells with 3D bioprinting. SCIENCE ADVANCES 2022; 8:eabp9906. [PMID: 36240264 PMCID: PMC9565790 DOI: 10.1126/sciadv.abp9906] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Capturing cell-to-cell signals in a three-dimensional (3D) environment is key to studying cellular functions. A major challenge in the current culturing methods is the lack of accurately capturing multicellular 3D environments. In this study, we established a framework for 3D bioprinting plant cells to study cell viability, cell division, and cell identity. We established long-term cell viability for bioprinted Arabidopsis and soybean cells. To analyze the generated large image datasets, we developed a high-throughput image analysis pipeline. Furthermore, we showed the cell cycle reentry of bioprinted cells for which the timing coincides with the induction of core cell cycle genes and regeneration-related genes, ultimately leading to microcallus formation. Last, the identity of bioprinted Arabidopsis root cells expressing endodermal markers was maintained for longer periods. The framework established here paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle reentry toward tissue regeneration.
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Affiliation(s)
- Lisa Van den Broeck
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Michael F. Schwartz
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Srikumar Krishnamoorthy
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Maimouna Abderamane Tahir
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
- Mechanical and Aerospace Engineering Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Ryan J. Spurney
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
- Electrical and Computer Engineering Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Imani Madison
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Charles Melvin
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Mariah Gobble
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Thomas Nguyen
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Rachel Peters
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Aitch Hunt
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Atiyya Muhammad
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Baochun Li
- Innovation Center of BASF, Morrisville, NC 27560, USA
| | - Maarten Stuiver
- BASF Innovation Center, Technologiepark 101, 9052 Zwijnaarde, Belgium
| | - Timothy Horn
- Mechanical and Aerospace Engineering Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695, USA
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29
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Embryogenic Stem Cell Identity after Protoplast Isolation from Daucus carota and Recovery of Regeneration Ability through Protoplast Culture. Int J Mol Sci 2022; 23:ijms231911556. [PMID: 36232857 PMCID: PMC9570137 DOI: 10.3390/ijms231911556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2022] Open
Abstract
Protoplasts are single cells isolated from tissues or organs and are considered a suitable system for cell studies in plants. Embryogenic cells are totipotent stem cells, but their regeneration ability decreases or becomes lost altogether with extension of the culture period. In this study, we isolated and cultured EC-derived protoplasts (EC-pts) from carrots and compared them with non-EC-derived protoplasts (NEC-pts) with respect to their totipotency. The protoplast isolation conditions were optimized, and the EC-pts and NEC-pts were characterized by their cell size and types. Both types of protoplasts were then embedded using the alginate layer (TAL) method, and the resulting EC-pt-TALs and NEC-pt-TALs were cultured for further regeneration. The expression of the EC-specific genes SERK1, WUS, BBM, LEC1, and DRN was analyzed to confirm whether EC identity was maintained after protoplast isolation. The protoplast isolation efficiency for EC-pts was 2.4-fold higher than for NEC-pts (3.5 × 106 protoplasts·g−1 FW). In the EC-pt group, protoplasts < 20 µm accounted for 58% of the total protoplasts, whereas in the NEC-pt group, small protoplasts accounted for only 26%. In protoplast culture, the number of protoplasts that divided was 2.6-fold higher for EC-pts than for NEC-pts (7.7 × 104 protoplasts·g−1 FW), with a high number of plants regenerated for EC-pt-TALs, whereas no plants were induced by NEC-pt-TAL. Five times more plants were regenerated from EC-pts than from ECs. Regarding the expression of EC-specific genes, WUS and SERK1 expression increased 12-fold, and LEC1 and BBM expression increased 3.6−6.4-fold in isolated protoplasts compared with ECs prior to protoplast isolation (control). These results reveal that the protoplast isolation process did not affect the embryogenic cell identity; rather, it increased the plant regeneration rate, confirming that EC-derived protoplast culture may be an efficient system for increasing the regeneration ability of old EC cultures through the elimination of old and inactivate cells. EC-derived protoplasts may also represent an efficient single-cell system for application in new breeding technologies such as genome editing.
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30
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Transcriptome Analysis of Sugarcane Young Leaves and Protoplasts after Enzymatic Digestion. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081210. [PMID: 36013389 PMCID: PMC9410293 DOI: 10.3390/life12081210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 02/01/2023]
Abstract
Sugarcane somatic cell hybridization can break through the barrier of genetic incompatibility between distantly related species in traditional breeding. However, the molecular mechanisms of sugarcane protoplast regeneration and the conditions for protoplast preparation remain largely unknown. In this study, young sugarcane (ROC22) leaves were enzymatically digested, and the viability of protoplasts reached more than 90% after enzymatic digestion (Enzymatic combination: 2% cellulase + 0.5% pectinase + 0.1% dissociative enzyme + 0.3% hemicellulase, pH = 5.8). Transcriptome sequencing was performed on young sugarcane leaves and protoplasts after enzymatic digestion to analyze the differences in gene expression in somatic cells before and after enzymatic digestion. A total of 117,411 unigenes and 43,460 differentially expressed genes were obtained, of which 21,123 were up-regulated and 22,337 down-regulated. The GO terms for the 43,460 differentially expressed genes (DEGs) were classified into three main categories: biological process, cellular component and molecular function, which related to developmental process, growth, cell proliferation, transcription regulator activity, signal transducer activity, antioxidant activity, oxidative stress, kinase activity, cell cycle, cell differentiation, plant hormone signal transduction, and so on. After enzymatic digestion of young sugarcane leaves, the expressions of GAUT, CESA, PSK, CyclinB, CyclinA, CyclinD3 and cdc2 genes associated with plant regeneration were significantly down-regulated to 65%, 47%, 2%, 18.60%, 21.32%, 52% and 45% of young leaves, respectively. After enzymatic digestion, Aux/IAA expression was up-regulated compared with young leaves, and Aux/IAA expression was 3.53 times higher than that of young leaves. Compared with young leaves, these key genes were significantly changed after enzymatic digestion. These results indicate that the process of somatic enzymatic digestion process may affect the regeneration of heterozygous cells to a certain extent.
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31
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Rather GA, Ayzenshtat D, Teper-Bamnolker P, Kumar M, Forotan Z, Eshel D, Bocobza S. Advances in protoplast transfection promote efficient CRISPR/Cas9-mediated genome editing in tetraploid potato. PLANTA 2022; 256:14. [PMID: 35713718 DOI: 10.1007/s00425-022-03933-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
An efficient method of DNA-free gene-editing in potato protoplasts was developed using linearized DNA fragments, UBIQUITIN10 promoters of several plant species, kanamycin selection, and transient overexpression of the BABYBOOM transcription factor. Plant protoplasts represent a reliable experimental system for the genetic manipulation of desired traits using gene editing. Nevertheless, the selection and regeneration of mutated protoplasts are challenging and subsequent recovery of successfully edited plants is a significant bottleneck in advanced plant breeding technologies. In an effort to alleviate the obstacles related to protoplasts' transgene expression and protoplasts' regeneration, a new method was developed. In so doing, it was shown that linearized DNA could efficiently transfect potato protoplasts and that UBIQUITIN10 promoters from various plants could direct transgene expression in an effective manner. Also, the inhibitory concentration of kanamycin was standardized for transfected protoplasts, and the NEOMYCIN PHOSPHOTRANSFERASE2 (NPT2) gene could be used as a potent selection marker for the enrichment of transfected protoplasts. Furthermore, transient expression of the BABYBOOM (BBM) transcription factor promoted the regeneration of protoplast-derived calli. Together, these methods significantly increased the selection for protoplasts that displayed high transgene expression, and thereby significantly increased the rate of gene editing events in protoplast-derived calli to 95%. The method developed in this study facilitated gene-editing in tetraploid potato plants and opened the way to sophisticated genetic manipulation in polyploid organisms.
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Affiliation(s)
- Gulzar A Rather
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Dana Ayzenshtat
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Paula Teper-Bamnolker
- Department of Postharvest Science, The Institute of Postharvest and Food Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Manoj Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Zohar Forotan
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Dani Eshel
- Department of Postharvest Science, The Institute of Postharvest and Food Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Samuel Bocobza
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel.
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Bae SH, Noh YS, Seo PJ. REGENOMICS: A web-based application for plant REGENeration-associated transcriptOMICS analyses. Comput Struct Biotechnol J 2022; 20:3234-3247. [PMID: 35832616 PMCID: PMC9249971 DOI: 10.1016/j.csbj.2022.06.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 01/09/2023] Open
Abstract
In plants, differentiated somatic cells exhibit an exceptional ability to regenerate new tissues, organs, or whole plants. Recent studies have unveiled core genetic components and pathways underlying cellular reprogramming and de novo tissue regeneration in plants. Although high-throughput analyses have led to key discoveries in plant regeneration, a comprehensive organization of large-scale data is needed to further enhance our understanding of plant regeneration. Here, we collected all currently available transcriptome datasets related to wounding responses, callus formation, de novo organogenesis, somatic embryogenesis, and protoplast regeneration to construct REGENOMICS, a web-based application for plant REGENeration-associated transcriptOMICS analyses. REGENOMICS supports single- and multi-query analyses of plant regeneration-related gene-expression dynamics, co-expression networks, gene-regulatory networks, and single-cell expression profiles. Furthermore, it enables user-friendly transcriptome-level analysis of REGENOMICS-deposited and user-submitted RNA-seq datasets. Overall, we demonstrate that REGENOMICS can serve as a key hub of plant regeneration transcriptome analysis and greatly enhance our understanding on gene-expression networks, new molecular interactions, and the crosstalk between genetic pathways underlying each mode of plant regeneration. The REGENOMICS web-based application is available at http://plantregeneration.snu.ac.kr.
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Affiliation(s)
- Soon Hyung Bae
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Yoo-Sun Noh
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, South Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, South Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, South Korea
- Corresponding author at: Department of Chemistry, Seoul National University, Seoul 08826, South Korea.
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Mo Y, Jiao Y. Advances and applications of single-cell omics technologies in plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1551-1563. [PMID: 35426954 DOI: 10.1111/tpj.15772] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Single-cell sequencing approaches reveal the intracellular dynamics of individual cells and answer biological questions with high-dimensional catalogs of millions of cells, including genomics, transcriptomics, chromatin accessibility, epigenomics, and proteomics data across species. These emerging yet thriving technologies have been fully embraced by the field of plant biology, with a constantly expanding portfolio of applications. Here, we introduce the current technical advances used for single-cell omics, especially single-cell genome and transcriptome sequencing. Firstly, we overview methods for protoplast and nucleus isolation and genome and transcriptome amplification. Subsequently, we use well-executed benchmarking studies to highlight advances made through the application of single-cell omics techniques. Looking forward, we offer a glimpse of additional hurdles and future opportunities that will introduce broad adoption of single-cell sequencing with revolutionary perspectives in plant biology.
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Affiliation(s)
- Yajin Mo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Dawson J, Pandey S, Yu Q, Schaub P, Wüst F, Moradi AB, Dovzhenko O, Palme K, Welsch R. Determination of protoplast growth properties using quantitative single-cell tracking analysis. PLANT METHODS 2022; 18:64. [PMID: 35585602 PMCID: PMC9118701 DOI: 10.1186/s13007-022-00895-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Although quantitative single-cell analysis is frequently applied in animal systems, e.g. to identify novel drugs, similar applications on plant single cells are largely missing. We have exploited the applicability of high-throughput microscopic image analysis on plant single cells using tobacco leaf protoplasts, cell-wall free single cells isolated by lytic digestion. Protoplasts regenerate their cell wall within several days after isolation and have the potential to expand and proliferate, generating microcalli and finally whole plants after the application of suitable regeneration conditions. RESULTS High-throughput automated microscopy coupled with the development of image processing pipelines allowed to quantify various developmental properties of thousands of protoplasts during the initial days following cultivation by immobilization in multi-well-plates. The focus on early protoplast responses allowed to study cell expansion prior to the initiation of proliferation and without the effects of shape-compromising cell walls. We compared growth parameters of wild-type tobacco cells with cells expressing the antiapoptotic protein Bcl2-associated athanogene 4 from Arabidopsis (AtBAG4). CONCLUSIONS AtBAG4-expressing protoplasts showed a higher proportion of cells responding with positive area increases than the wild type and showed increased growth rates as well as increased proliferation rates upon continued cultivation. These features are associated with reported observations on a BAG4-mediated increased resilience to various stress responses and improved cellular survival rates following transformation approaches. Moreover, our single-cell expansion results suggest a BAG4-mediated, cell-independent increase of potassium channel abundance which was hitherto reported for guard cells only. The possibility to explain plant phenotypes with single-cell properties, extracted with the single-cell processing and analysis pipeline developed, allows to envision novel biotechnological screening strategies able to determine improved plant properties via single-cell analysis.
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Affiliation(s)
- Jonathan Dawson
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- Institute of General Electrical Engineering, University of Rostock, Albert-Einstein-Str. 2, 18059, Rostock, Germany
- Augusta University, 1201 Goss Ln, Augusta, GA, 30912, USA
| | - Saurabh Pandey
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Qiuju Yu
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- ScreenSYS GmbH, Engesserstr. 4, 79108, Freiburg, Germany
| | - Patrick Schaub
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- ScreenSYS GmbH, Engesserstr. 4, 79108, Freiburg, Germany
| | - Florian Wüst
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- ScreenSYS GmbH, Engesserstr. 4, 79108, Freiburg, Germany
| | - Amir Bahram Moradi
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Oleksandr Dovzhenko
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- ScreenSYS GmbH, Engesserstr. 4, 79108, Freiburg, Germany
| | - Klaus Palme
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- ScreenSYS GmbH, Engesserstr. 4, 79108, Freiburg, Germany
- BIOSS Center for Biological Signaling Studies, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Ralf Welsch
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.
- ScreenSYS GmbH, Engesserstr. 4, 79108, Freiburg, Germany.
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Hansberg W. A critical analysis on the conception of "Pre-existent gene expression programs" for cell differentiation and development. Differentiation 2022; 125:1-8. [DOI: 10.1016/j.diff.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 11/15/2022]
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Swift J, Greenham K, Ecker JR, Coruzzi GM, McClung CR. The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:764-778. [PMID: 34797944 PMCID: PMC9215356 DOI: 10.1111/tpj.15589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 05/26/2023]
Abstract
As sessile organisms, plants are finely tuned to respond dynamically to developmental, circadian and environmental cues. Genome-wide studies investigating these types of cues have uncovered the intrinsically different ways they can impact gene expression over time. Recent advances in single-cell sequencing and time-based bioinformatic algorithms are now beginning to reveal the dynamics of these time-based responses within individual cells and plant tissues. Here, we review what these techniques have revealed about the spatiotemporal nature of gene regulation, paying particular attention to the three distinct ways in which plant tissues are time sensitive. (i) First, we discuss how studying plant cell identity can reveal developmental trajectories hidden in pseudotime. (ii) Next, we present evidence that indicates that plant cell types keep their own local time through tissue-specific regulation of the circadian clock. (iii) Finally, we review what determines the speed of environmental signaling responses, and how they can be contingent on developmental and circadian time. By these means, this review sheds light on how these different scales of time-based responses can act with tissue and cell-type specificity to elicit changes in whole plant systems.
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Affiliation(s)
- Joseph Swift
- Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Kathleen Greenham
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Gloria M. Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, NY, USA
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Ishikawa M, Hasebe M. Molecular mechanisms of reprogramming of differentiated cells into stem cells in the moss Physcomitrium patens. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102123. [PMID: 34735974 DOI: 10.1016/j.pbi.2021.102123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/14/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Plant and animal stem cells can self-renew and give rise to differentiated cells to form tissues or organs. Unlike differentiated cells in animals, those in land plants can be readily reprogrammed into stem cells, reflecting the plasticity of plant cell identity. The moss Physcomitrium patens (synonym: Physcomitrella patens) is highly regenerable, and its leaf cells can be reprogrammed into stem cells in response to wounding or by transient DNA damage without wounding. Wounding and DNA damage induce STEM CELL-INDUCING FACTOR 1, an APETALA2/ETHYLENE RESPONSE FACTOR. Here, we summarize the genetic networks that regulate cellular reprogramming in P. patens and the roles of STEMIN1 and discuss the generality and divergence of the molecular mechanisms underlying cellular reprogramming in land plants and animals.
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Affiliation(s)
- Masaki Ishikawa
- National Institute for Basic Biology, Okazaki, 444-8585, Japan; School of Life Science, The Graduate University for Advanced Studies, Okazaki, 444-8585, Japan.
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, 444-8585, Japan; School of Life Science, The Graduate University for Advanced Studies, Okazaki, 444-8585, Japan.
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Yin Y, Wang C, Xiao D, Liang Y, Wang Y. Advances and Perspectives of Transgenic Technology and Biotechnological Application in Forest Trees. FRONTIERS IN PLANT SCIENCE 2021; 12:786328. [PMID: 34917116 PMCID: PMC8669725 DOI: 10.3389/fpls.2021.786328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/25/2021] [Indexed: 06/14/2023]
Abstract
Transgenic technology is increasingly used in forest-tree breeding to overcome the disadvantages of traditional breeding methods, such as a long breeding cycle, complex cultivation environment, and complicated procedures. By introducing exogenous DNA, genes tightly related or contributed to ideal traits-including insect, disease, and herbicide resistance-were transferred into diverse forest trees, and genetically modified (GM) trees including poplars were cultivated. It is beneficial to develop new varieties of GM trees of high quality and promote the genetic improvement of forests. However, the low transformation efficiency has hampered the cultivation of GM trees and the identification of the molecular genetic mechanism in forest trees compared to annual herbaceous plants such as Oryza sativa. In this study, we reviewed advances in transgenic technology of forest trees, including the principles, advantages and disadvantages of diverse genetic transformation methods, and their application for trait improvement. The review provides insight into the establishment and improvement of genetic transformation systems for forest tree species. Challenges and perspectives pertaining to the genetic transformation of forest trees are also discussed.
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Affiliation(s)
- Yiyi Yin
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Chun Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Dandan Xiao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Yanting Liang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Yanwei Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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Gonzalez JH, Taylor JS, Reed KM, Wright RC, Bargmann BOR. Temporal Control of Morphogenic Factor Expression Determines Efficacy in Enhancing Regeneration. PLANTS (BASEL, SWITZERLAND) 2021; 10:2271. [PMID: 34834634 PMCID: PMC8617614 DOI: 10.3390/plants10112271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Regeneration of fertile plants from tissue culture is a critical bottleneck in the application of new plant breeding technologies. Ectopic overexpression of morphogenic factors is a promising workaround for this hurdle. METHODS Conditional overexpression of WUS and ARF5Δ was used to study the effect of timing the overexpression of these morphogenic factors during shoot regeneration from root explants in Arabidopsis. In addition, their effect on auxin-signaling activation was examined by visualization and cytometric quantification of the DR5:GFP auxin-signaling reporter in roots and protoplasts, respectively. RESULTS The induced expression of both WUS and ARF5Δ led to an activation of auxin signaling in roots. Activation of auxin signaling by WUS and ARF5Δ was further quantified by transient transformation of protoplasts. Ectopic overexpression of both WUS and ARF5Δ enhanced regeneration efficiency, but only during the shoot-induction stage of regeneration and not during the callus-induction stage. CONCLUSIONS The overexpression of WUS and ARF5Δ both lead to activation of auxin signaling. Expression during the shoot-induction stage is critical for the enhancement of shoot regeneration by WUS and ARF5Δ.
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Affiliation(s)
- Juan H Gonzalez
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
| | - Joseph S Taylor
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
| | - Kelsey M Reed
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
| | - Bastiaan O R Bargmann
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
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Post-Embryonic Lateral Organ Development and Adaxial-Abaxial Polarity Are Regulated by the Combined Effect of ENHANCER OF SHOOT REGENERATION 1 and WUSCHEL in Arabidopsis Shoots. Int J Mol Sci 2021; 22:ijms221910621. [PMID: 34638958 PMCID: PMC8508843 DOI: 10.3390/ijms221910621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/19/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
The development of above-ground lateral organs is initiated at the peripheral zone of the shoot apical meristem (SAM). The coordination of cell fate determination and the maintenance of stem cells are achieved through a complex regulatory network comprised of transcription factors. Two AP2/ERF transcription factor family genes, ESR1/DRN and ESR2/DRNL/SOB/BOL, regulate cotyledon and flower formation and de novo organogenesis in tissue culture. However, their roles in post-embryonic lateral organ development remain elusive. In this study, we analyzed the genetic interactions among SAM-related genes, WUS and STM, two ESR genes, and one of the HD-ZIP III members, REV, whose protein product interacts with ESR1 in planta. We found that esr1 mutations substantially enhanced the wus and stm phenotypes, which bear a striking resemblance to those of the wus rev and stm rev double mutants, respectively. Aberrant adaxial–abaxial polarity is observed in wus esr1 at relatively low penetrance. On the contrary, the esr2 mutation partially suppressed stm phenotypes in the later vegetative phase. Such complex genetic interactions appear to be attributed to the distinct expression pattern of two ESR genes because the ESR1 promoter-driving ESR2 is capable of rescuing phenotypes caused by the esr1 mutation. Our results pose the unique genetic relevance of ESR1 and the SAM-related gene interactions in the development of rosette leaves.
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