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Alazem M, Burch-Smith TM. Roles of ROS and redox in regulating cell-to-cell communication: Spotlight on viral modulation of redox for local spread. PLANT, CELL & ENVIRONMENT 2024; 47:2830-2841. [PMID: 38168864 DOI: 10.1111/pce.14805] [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: 11/10/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
Reactive oxygen species (ROS) are important signalling molecules that influence many aspects of plant biology. One way in which ROS influence plant growth and development is by modifying intercellular trafficking through plasmodesmata (PD). Viruses have evolved to use PD for their local cell-to-cell spread between plant cells, so it is therefore not surprising that they have found ways to modulate ROS and redox signalling to optimise PD function for their benefit. This review examines how intracellular signalling via ROS and redox pathways regulate intercellular trafficking via PD during development and stress. The relationship between viruses and ROS-redox systems, and the strategies viruses employ to control PD function by interfering with ROS-redox in plants is also discussed.
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Affiliation(s)
- Mazen Alazem
- Donald Danforth Plant Science Center, Saint Louis, Missouri, USA
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2
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Lou H, Wang F, Zhang J, Wei G, Wei J, Hu H, Li Y, Wang K, Wang Z, Huang Y, Wu J, Pei D, Huang J, Zhang Q. JrGA20ox1-transformed rootstocks deliver drought response signals to wild-type scions in grafted walnut. HORTICULTURE RESEARCH 2024; 11:uhae143. [PMID: 38988618 PMCID: PMC11233861 DOI: 10.1093/hr/uhae143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 05/13/2024] [Indexed: 07/12/2024]
Abstract
Targeted regulation using transgrafting technology has become a trend. However, the mechanisms of transgene-derived signal communication between rootstocks and scions remain unclear in woody plants. Here, we grafted wild-type (WT) walnut (Juglans regia L.) on WT (WT/WT), JrGA20ox1 (encodes a gibberellin 20-oxidase)-overexpressing (WT/OE), and JrGA20ox1-RNAi transformation (WT/RNAi) walnut in vitro. We aimed to elucidate the mechanisms of JrGA20ox1-derived signal communication under PEG-simulated drought stress between rootstocks and scions in walnut. We demonstrated that JrGA20ox1-OE and JrGA20ox1-RNAi rootstocks could transport active gibberellins (GAs) and JrGA20ox1-RNAi vector-produced sRNAs to WT scions under PEG-simulated drought stress, respectively. The movement of sRNAs further led to a successive decline in JrGA20ox1 expression and active GA content. Meanwhile, unknown mobile signals may move between rootstocks and scions. These mobile signals reduced the expression of a series of GA-responsive and GA-non-responsive genes, and induced ROS production in guard cells and an increase in ABA content, which may contribute to the drought tolerance of WT/RNAi, while the opposite occurred in WT/OE. The findings suggest that JrGA20ox1-derived rootstock-to-scion movement of signals is involved in drought tolerance of scions. Our research will provide a feasible approach for studying signal communication in woody plants.
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Affiliation(s)
- Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Fengmin Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Jiaqi Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Guangli Wei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Jingjing Wei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Hengkang Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Ketao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Youjun Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jianqin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Qixiang Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
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3
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Burch-Smith TM. The varied forms and functions of plasmodesmata. THE NEW PHYTOLOGIST 2024; 243:5-6. [PMID: 38708440 DOI: 10.1111/nph.19794] [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] [Indexed: 05/07/2024]
Abstract
This article is a Commentary on Tee & Faulkner (2024), 243: 32–47.
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4
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Fonseca A, Riveras E, Moyano TC, Alvarez JM, Rosa S, Gutiérrez RA. Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38950037 DOI: 10.1111/pce.15018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 05/23/2024] [Accepted: 06/14/2024] [Indexed: 07/03/2024]
Abstract
Nitrate is a nutrient and signal that regulates gene expression. The nitrate response has been extensively characterized at the organism, organ, and cell-type-specific levels, but intracellular mRNA dynamics remain unexplored. To characterize nuclear and cytoplasmic transcriptome dynamics in response to nitrate, we performed a time-course expression analysis after nitrate treatment in isolated nuclei, cytoplasm, and whole roots. We identified 402 differentially localized transcripts (DLTs) in response to nitrate treatment. Induced DLT genes showed rapid and transient recruitment of the RNA polymerase II, together with an increase in the mRNA turnover rates. DLTs code for genes involved in metabolic processes, localization, and response to stimulus indicating DLTs include genes with relevant functions for the nitrate response that have not been previously identified. Using single-molecule RNA FISH, we observed early nuclear accumulation of the NITRATE REDUCTASE 1 (NIA1) transcripts in their transcription sites. We found that transcription of NIA1, a gene showing delayed cytoplasmic accumulation, is rapidly and transiently activated; however, its transcripts become unstable when they reach the cytoplasm. Our study reveals the dynamic localization of mRNAs between the nucleus and cytoplasm as an emerging feature in the temporal control of gene expression in response to nitrate treatment in Arabidopsis roots.
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Affiliation(s)
- Alejandro Fonseca
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Eleodoro Riveras
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tomás C Moyano
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - José M Alvarez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Rodrigo A Gutiérrez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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5
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Fang L, Li M, Zhang J, Jia C, Qiang Y, He X, Liu T, Zhou Q, Luo D, Han Y, Li Z, Liu W, Yang Y, Liu J, Liu Z. Chromosome-level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant. Mol Ecol Resour 2024; 24:e13966. [PMID: 38695851 DOI: 10.1111/1755-0998.13966] [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: 02/22/2023] [Revised: 07/11/2023] [Accepted: 04/15/2024] [Indexed: 06/04/2024]
Abstract
Parasitic plants have a heterotrophic lifestyle, in which they withdraw all or part of their nutrients from their host through the haustorium. Despite the release of many draft genomes of parasitic plants, the genome evolution related to the parasitism feature of facultative parasites remains largely unknown. In this study, we present a high-quality chromosomal-level genome assembly for the facultative parasite Pedicularis kansuensis (Orobanchaceae), which invades both legume and grass host species in degraded grasslands on the Qinghai-Tibet Plateau. This species has the largest genome size compared with other parasitic species, and expansions of long terminal repeat retrotransposons accounting for 62.37% of the assembly greatly contributed to the genome size expansion of this species. A total of 42,782 genes were annotated, and the patterns of gene loss in P. kansuensis differed from other parasitic species. We also found many mobile mRNAs between P. kansuensis and one of its host species, but these mobile mRNAs could not compensate for the functional losses of missing genes in P. kansuensis. In addition, we identified nine horizontal gene transfer (HGT) events from rosids and monocots, as well as one single-gene duplication events from HGT genes, which differ distinctly from that of other parasitic species. Furthermore, we found evidence for HGT through transferring genomic fragments from phylogenetically remote host species. Taken together, these findings provide genomic insights into the evolution of facultative parasites and broaden our understanding of the diversified genome evolution in parasitic plants and the molecular mechanisms of plant parasitism.
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Affiliation(s)
- Longfa Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Mingyu Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jia Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Chenglin Jia
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuqing Qiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaojuan He
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Tao Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Qiang Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Dong Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuling Han
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhen Li
- National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Wenxian Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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6
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Tee EE, Faulkner C. Plasmodesmata and intercellular molecular traffic control. THE NEW PHYTOLOGIST 2024; 243:32-47. [PMID: 38494438 DOI: 10.1111/nph.19666] [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: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 03/19/2024]
Abstract
Plasmodesmata are plasma membrane-lined connections that join plant cells to their neighbours, establishing an intercellular cytoplasmic continuum through which molecules can travel between cells, tissues, and organs. As plasmodesmata connect almost all cells in plants, their molecular traffic carries information and resources across a range of scales, but dynamic control of plasmodesmal aperture can change the possible domains of molecular exchange under different conditions. Plasmodesmal aperture is controlled by specialised signalling cascades accommodated in spatially discrete membrane and cell wall domains. Thus, the composition of plasmodesmata defines their capacity for molecular trafficking. Further, their shape and density can likewise define trafficking capacity, with the cell walls between different cell types hosting different numbers and forms of plasmodesmata to drive molecular flux in physiologically important directions. The molecular traffic that travels through plasmodesmata ranges from small metabolites through to proteins, and possibly even larger mRNAs. Smaller molecules are transmitted between cells via passive mechanisms but how larger molecules are efficiently trafficked through plasmodesmata remains a key question in plasmodesmal biology. How plasmodesmata are formed, the shape they take, what they are made of, and what passes through them regulate molecular traffic through plants, underpinning a wide range of plant physiology.
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Affiliation(s)
- Estee E Tee
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Christine Faulkner
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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7
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Li X, Uslu VV, Chen Y, Han X, Berr A, Zhang W, Dong Y. Specific chromatin states and m6A modifications are associated with mRNA mobility in planta. HORTICULTURE RESEARCH 2024; 11:uhae101. [PMID: 38863994 PMCID: PMC11165156 DOI: 10.1093/hr/uhae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 06/13/2024]
Affiliation(s)
- Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Veli Vural Uslu
- RLP AgroScience GmbH, Neustadt an der Weinstraße 67435, Germany
- MAPS, Center for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Ying Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Xiao Han
- College of Biology Science and Engineering, Fuzhou University, Fuzhou, China
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Yihan Dong
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
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8
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Liu MJ, Fang JC, Ma Y, Chong GL, Huang CK, Takeuchi A, Takayanagi N, Ohtani M. Frontiers in plant RNA research in ICAR2023: from lab to innovative agriculture. PLANT MOLECULAR BIOLOGY 2024; 114:45. [PMID: 38630407 DOI: 10.1007/s11103-024-01436-x] [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: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 04/19/2024]
Abstract
The recent growth in global warming, soil contamination, and climate instability have widely disturbed ecosystems, and will have a significant negative impact on the growth of plants that produce grains, fruits and woody biomass. To conquer this difficult situation, we need to understand the molecular bias of plant environmental responses and promote development of new technologies for sustainable maintenance of crop production. Accumulated molecular biological data have highlighted the importance of RNA-based mechanisms for plant stress responses. Here, we report the most advanced plant RNA research presented in the 33rd International Conference on Arabidopsis Research (ICAR2023), held as a hybrid event on June 5-9, 2023 in Chiba, Japan, and focused on "Arabidopsis for Sustainable Development Goals". Six workshops/concurrent sessions in ICAR2023 targeted plant RNA biology, and many RNA-related topics could be found in other sessions. In this meeting report, we focus on the workshops/concurrent sessions targeting RNA biology, to share what is happening now at the forefront of plant RNA research.
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Affiliation(s)
- Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica (AS-BCST), Tainan, Taiwan.
| | - Jhen-Cheng Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica (AS-BCST), Tainan, Taiwan
| | - Ya Ma
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 227-8562, Japan
| | - Geeng Loo Chong
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Chun-Kai Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Ami Takeuchi
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 227-8562, Japan
| | - Natsu Takayanagi
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 227-8562, Japan
| | - Misato Ohtani
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 227-8562, Japan.
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan.
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.
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9
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Chen J, Ham BK, Kochian LV, Lucas WJ. A cucumber protein, Phloem Phosphate Stress-Repressed 1, rapidly degrades in response to a phosphate stress condition. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2176-2190. [PMID: 38113277 DOI: 10.1093/jxb/erad504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
Under depleted external phosphate (Pi), many plant species adapt to this stress by initiating downstream signaling cascades. In plants, the vascular system delivers nutrients and signaling agents to control physiological and developmental processes. Currently, limited information is available regarding the direct role of phloem-borne long-distance signals in plant growth and development under Pi stress conditions. Here, we report on the identification and characterization of a cucumber protein, Cucumis sativus Phloem Phosphate Stress-Repressed 1 (CsPPSR1), whose level in the phloem translocation stream rapidly responds to imposed Pi-limiting conditions. CsPPSR1 degradation is mediated by the 26S proteasome; under Pi-sufficient conditions, CsPPSR1 is stabilized by its phosphorylation within the sieve tube system through the action of CsPPSR1 kinase. Further, we discovered that CsPPSR1 kinase was susceptible to Pi starvation-induced degradation in the sieve tube system. Our findings offer insight into a molecular mechanism underlying the response of phloem-borne proteins to Pi-limited stress conditions.
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Affiliation(s)
- Jieyu Chen
- Department of Plant Biology, University of California, Davis, CA, USA
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Byung-Kook Ham
- Department of Plant Biology, University of California, Davis, CA, USA
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Plant Sciences & Soil Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - William J Lucas
- Department of Plant Biology, University of California, Davis, CA, USA
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10
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Castañón-Suárez CA, Arrizubieta M, Castelán-Muñoz N, Sánchez-Rodríguez DB, Caballero-Cordero C, Zluhan-Martínez E, Patiño-Olvera SC, Arciniega-González J, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. The MADS-box genes SOC1 and AGL24 antagonize XAL2 functions in Arabidopsis thaliana root development. FRONTIERS IN PLANT SCIENCE 2024; 15:1331269. [PMID: 38576790 PMCID: PMC10994003 DOI: 10.3389/fpls.2024.1331269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/06/2024] [Indexed: 04/06/2024]
Abstract
MADS-domain transcription factors play pivotal roles in numerous developmental processes in Arabidopsis thaliana. While their involvement in flowering transition and floral development has been extensively examined, their functions in root development remain relatively unexplored. Here, we explored the function and genetic interaction of three MADS-box genes (XAL2, SOC1 and AGL24) in primary root development. By analyzing loss-of-function and overexpression lines, we found that SOC1 and AGL24, both critical components in flowering transition, redundantly act as repressors of primary root growth as the loss of function of either SOC1 or AGL24 partially recovers the primary root growth, meristem cell number, cell production rate, and the length of fully elongated cells of the short-root mutant xal2-2. Furthermore, we observed that the simultaneous overexpression of AGL24 and SOC1 leads to short-root phenotypes, affecting meristem cell number and fully elongated cell size, whereas SOC1 overexpression is sufficient to affect columella stem cell differentiation. Additionally, qPCR analyses revealed that these genes exhibit distinct modes of transcriptional regulation in roots compared to what has been previously reported for aerial tissues. We identified 100 differentially expressed genes in xal2-2 roots by RNA-seq. Moreover, our findings revealed that the expression of certain genes involved in cell differentiation, as well as stress responses, which are either upregulated or downregulated in the xal2-2 mutant, reverted to WT levels in the absence of SOC1 or AGL24.
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Affiliation(s)
- Claudio A. Castañón-Suárez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Maite Arrizubieta
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Natalia Castelán-Muñoz
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Postgrado en Recursos Genéticos y Productividad-Fisiología Vegetal, Colegio de Postgraduados, Texcoco, Estado de México, Mexico
| | - Diana Belén Sánchez-Rodríguez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Carolina Caballero-Cordero
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sandra C. Patiño-Olvera
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - J.Arturo Arciniega-González
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Li W, Chu C, Li H, Zhang H, Sun H, Wang S, Wang Z, Li Y, Foster TM, López-Girona E, Yu J, Li Y, Ma Y, Zhang K, Han Y, Zhou B, Fan X, Xiong Y, Deng CH, Wang Y, Xu X, Han Z. Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing. Nat Genet 2024; 56:505-516. [PMID: 38347217 DOI: 10.1038/s41588-024-01657-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/08/2024] [Indexed: 03/16/2024]
Abstract
Dwarfing rootstocks have transformed the production of cultivated apples; however, the genetic basis of rootstock-induced dwarfing remains largely unclear. We have assembled chromosome-level, near-gapless and haplotype-resolved genomes for the popular dwarfing rootstock 'M9', the semi-vigorous rootstock 'MM106' and 'Fuji', one of the most commonly grown apple cultivars. The apple orthologue of auxin response factor 3 (MdARF3) is in the Dw1 region of 'M9', the major locus for rootstock-induced dwarfing. Comparing 'M9' and 'MM106' genomes revealed a 9,723-bp allele-specific long terminal repeat retrotransposon/gypsy insertion, DwTE, located upstream of MdARF3. DwTE is cosegregated with the dwarfing trait in two segregating populations, suggesting its prospective utility in future dwarfing rootstock breeding. In addition, our pipeline discovered mobile mRNAs that may contribute to the development of dwarfed scion architecture. Our research provides valuable genomic resources and applicable methodology, which have the potential to accelerate breeding dwarfing rootstocks for apple and other perennial woody fruit trees.
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Affiliation(s)
- Wei Li
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Hui Li
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Hengtao Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Haochen Sun
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Shiyao Wang
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Zijun Wang
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Yuqi Li
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Toshi M Foster
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Motueka, New Zealand
| | - Elena López-Girona
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Jiaxin Yu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, USA
| | - Yue Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yongming Han
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Bowen Zhou
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Xingqiang Fan
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Yao Xiong
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Auckland, New Zealand.
| | - Yi Wang
- Institute for Horticultural Plants, China Agricultural University, Beijing, China.
| | - Xuefeng Xu
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Zhenhai Han
- Institute for Horticultural Plants, China Agricultural University, Beijing, China.
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12
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Tolnai Z, Sharma H, Soós V. D27-like carotenoid isomerases: at the crossroads of strigolactone and abscisic acid biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1148-1158. [PMID: 38006582 DOI: 10.1093/jxb/erad475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/24/2023] [Indexed: 11/27/2023]
Abstract
Strigolactones and abscisic acid (ABA) are apocarotenoid-derived plant hormones. Their biosynthesis starts with the conversion of trans-carotenes into cis forms, which serve as direct precursors. Iron-containing DWARF27 isomerases were shown to catalyse or contribute to the trans/cis conversions of these precursor molecules. D27 converts trans-β-carotene into 9-cis-β-carotene, which is the first committed step in strigolactone biosynthesis. Recent studies found that its paralogue, D27-LIKE1, also catalyses this conversion. A crucial step in ABA biosynthesis is the oxidative cleavage of 9-cis-violaxanthin and/or 9-cis-neoxanthin, which are formed from their trans isomers by unknown isomerases. Several lines of evidence point out that D27-like proteins directly or indirectly contribute to 9-cis-violaxanthin conversion, and eventually ABA biosynthesis. Apparently, the diversity of D27-like enzymatic activity is essential for the optimization of cis/trans ratios, and hence act to maintain apocarotenoid precursor pools. In this review, we discuss the functional divergence and redundancy of D27 paralogues and their potential direct contribution to ABA precursor biosynthesis. We provide updates on their gene expression regulation and alleged Fe-S cluster binding feature. Finally, we conclude that the functional divergence of these paralogues is not fully understood and we provide an outlook on potential directions in research.
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Affiliation(s)
- Zoltán Tolnai
- Agricultural Institute, Centre for Agricultural Research, ELKH, 2462 Martonvásár, Brunszvik u. 2, Hungary
| | - Himani Sharma
- Agricultural Institute, Centre for Agricultural Research, ELKH, 2462 Martonvásár, Brunszvik u. 2, Hungary
| | - Vilmos Soós
- Agricultural Institute, Centre for Agricultural Research, ELKH, 2462 Martonvásár, Brunszvik u. 2, Hungary
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13
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Rosa-Téllez S, Alcántara-Enguídanos A, Martínez-Seidel F, Casatejada-Anchel R, Saeheng S, Bailes CL, Erban A, Barbosa-Medeiros D, Alepúz P, Matus JT, Kopka J, Muñoz-Bertomeu J, Krueger S, Roje S, Fernie AR, Ros R. The serine-glycine-one-carbon metabolic network orchestrates changes in nitrogen and sulfur metabolism and shapes plant development. THE PLANT CELL 2024; 36:404-426. [PMID: 37804096 PMCID: PMC10827325 DOI: 10.1093/plcell/koad256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
L-serine (Ser) and L-glycine (Gly) are critically important for the overall functioning of primary metabolism. We investigated the interaction of the phosphorylated pathway of Ser biosynthesis (PPSB) with the photorespiration-associated glycolate pathway of Ser biosynthesis (GPSB) using Arabidopsis thaliana PPSB-deficient lines, GPSB-deficient mutants, and crosses of PPSB with GPSB mutants. PPSB-deficient lines mainly showed retarded primary root growth. Mutation of the photorespiratory enzyme Ser-hydroxymethyltransferase 1 (SHMT1) in a PPSB-deficient background resumed primary root growth and induced a change in the plant metabolic pattern between roots and shoots. Grafting experiments demonstrated that metabolic changes in shoots were responsible for the changes in double mutant development. PPSB disruption led to a reduction in nitrogen (N) and sulfur (S) contents in shoots and a general transcriptional response to nutrient deficiency. Disruption of SHMT1 boosted the Gly flux out of the photorespiratory cycle, which increased the levels of the one-carbon (1C) metabolite 5,10-methylene-tetrahydrofolate and S-adenosylmethionine. Furthermore, disrupting SHMT1 reverted the transcriptional response to N and S deprivation and increased N and S contents in shoots of PPSB-deficient lines. Our work provides genetic evidence of the biological relevance of the Ser-Gly-1C metabolic network in N and S metabolism and in interorgan metabolic homeostasis.
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Affiliation(s)
- Sara Rosa-Téllez
- Institut de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Spain
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46100 Burjassot, Spain
| | - Andrea Alcántara-Enguídanos
- Institut de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Spain
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46100 Burjassot, Spain
| | | | - Ruben Casatejada-Anchel
- Institut de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Spain
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46100 Burjassot, Spain
| | - Sompop Saeheng
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Clayton L Bailes
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | | | - Paula Alepúz
- Institut de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Spain
- Departament de Bioquímica y Biologia Molecular, Facultat de Biologia, Universitat de València, 46100 Burjassot, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology, I²SysBio, Universitat de València—CSIC, 46908 Paterna, Spain
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Jesús Muñoz-Bertomeu
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46100 Burjassot, Spain
| | - Stephan Krueger
- Institute for Plant Sciences, University of Cologne, Zülpicherstraße 47b, 50674 Cologne, Germany
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Roc Ros
- Institut de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Spain
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46100 Burjassot, Spain
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14
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Huang NC, Tien HC, Yu TS. Arabidopsis leaf-expressed AGAMOUS-LIKE 24 mRNA systemically specifies floral meristem differentiation. THE NEW PHYTOLOGIST 2024; 241:504-515. [PMID: 37766487 DOI: 10.1111/nph.19293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
Abstract
Plants can record external stimuli in mobile mRNAs and systemically deliver them to distal tissues to adjust development. Despite the identification of thousands of mobile mRNAs, the functional relevance of mobile mRNAs remains limited. Many mobile mRNAs are synthesized in the source cells that perceive environmental stimuli, but specifically exert their functions upon transportation to the recipient cells. However, the translation of mobile mRNA-encoded protein in the source cells could locally activate downstream target genes. How plants avoid ectopic functions of mobile mRNAs in the source cells to achieve tissue specificity remains to be elucidated. Here, we show that Arabidopsis AGAMOUS-LIKE 24 (AGL24) is a mobile mRNA whose movement is necessary and sufficient to specify floral organ identity. Although AGL24 mRNA is expressed in vegetative tissues, AGL24 protein exclusively accumulates in the shoot apex. In leaves, AGL24 proteins are degraded to avoid ectopically activating its downstream target genes. Our results reveal how selective protein degradation in source cells provides a strategy to limit the local effects associated with proteins encoded by mobile mRNAs, which ensures that mobile mRNAs specifically trigger systemic responses only in recipient tissues.
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Affiliation(s)
- Nien-Chen Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Huan-Chi Tien
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
| | - Tien-Shin Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
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15
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Zhou H, Shi H, Yang Y, Feng X, Chen X, Xiao F, Lin H, Guo Y. Insights into plant salt stress signaling and tolerance. J Genet Genomics 2024; 51:16-34. [PMID: 37647984 DOI: 10.1016/j.jgg.2023.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Soil salinization is an essential environmental stressor, threatening agricultural yield and ecological security worldwide. Saline soils accumulate excessive soluble salts which are detrimental to most plants by limiting plant growth and productivity. It is of great necessity for plants to efficiently deal with the adverse effects caused by salt stress for survival and successful reproduction. Multiple determinants of salt tolerance have been identified in plants, and the cellular and physiological mechanisms of plant salt response and adaption have been intensely characterized. Plants respond to salt stress signals and rapidly initiate signaling pathways to re-establish cellular homeostasis with adjusted growth and cellular metabolism. This review summarizes the advances in salt stress perception, signaling, and response in plants. A better understanding of plant salt resistance will contribute to improving crop performance under saline conditions using multiple engineering approaches. The rhizosphere microbiome-mediated plant salt tolerance as well as chemical priming for enhanced plant salt resistance are also discussed in this review.
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Affiliation(s)
- Huapeng Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Haifan Shi
- College of Grassland Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yongqing Yang
- State Key Laboratory of Plant Environmental Resilience, China Agricultural University, Beijing 100193, China
| | - Xixian Feng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xi Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Fei Xiao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang 830046, China
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, China Agricultural University, Beijing 100193, China.
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16
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Hani S, Mercier C, David P, Desnos T, Escudier JM, Bertrand E, Nussaume L. smFISH for Plants. Methods Mol Biol 2024; 2784:87-100. [PMID: 38502480 DOI: 10.1007/978-1-0716-3766-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Single-molecule fluorescence in situ hybridization (smFISH) is a powerful method for the visualization and quantification of individual RNA molecules within intact cells. With its ability to probe gene expression at the single cell and single-molecule level, the technique offers valuable insights into cellular processes and cell-to-cell heterogeneity. Although widely used in the animal field, its use in plants has been limited. Here, we present an experimental smFISH workflow that allows researchers to overcome hybridization and imaging challenges in plants, including sample preparation, probe hybridization, and signal detection. Overall, this protocol holds great promise for unraveling the intricacies of gene expression regulation and RNA dynamics at the single-molecule level in whole plants.
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Affiliation(s)
- Sahar Hani
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, Saint-Paul lez Durance, France
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Caroline Mercier
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, Saint-Paul lez Durance, France
- Biochimie et Physiologie Moléculaire des Plantes, Univesité de Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Pascale David
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, Saint-Paul lez Durance, France
| | - Thierry Desnos
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, Saint-Paul lez Durance, France
| | - Jean-Marc Escudier
- Laboratoire Synthèse et Physico-Chimie de Molécules d'intérêt Biologique, Université Paul Sabatier, CNRS, Toulouse, France
| | - Edouard Bertrand
- Institut de Génétique Humaine, CNRS, UMR9002, Montpellier, France
| | - Laurent Nussaume
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, Saint-Paul lez Durance, France.
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17
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Luo KR, Huang NC, Chang YH, Jan YW, Yu TS. Arabidopsis cyclophilins direct intracellular transport of mobile mRNA via organelle hitchhiking. NATURE PLANTS 2024; 10:161-171. [PMID: 38177664 DOI: 10.1038/s41477-023-01597-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/24/2023] [Indexed: 01/06/2024]
Abstract
Plants convert external cues into mobile mRNAs to synchronize meristematic differentiation with environmental dynamics. These mRNAs are selectively transported to intercellular pores, plasmodesmata (PD), for cell-to-cell movement. However, how plants recognize and deliver mobile mRNAs to PD remains unknown. Here we show that mobile mRNAs hitchhike on organelle trafficking to transport towards PD. Perturbed cytoskeleton organization or organelle trafficking severely disrupts the subcellular distribution of mobile mRNAs. Arabidopsis rotamase cyclophilins (ROCs), which are organelle-localized RNA-binding proteins, specifically bind mobile mRNAs on the surface of organelles to direct intracellular transport. Arabidopsis roc mutants exhibit phenotype alterations and disruptions in the transport of mobile mRNAs. These findings suggest that ROCs play a crucial role in facilitating the systemic delivery of mobile mRNAs. Our results highlight that an RNA-binding protein-mediated hitchhiking system is specifically recruited to orient plant mobile mRNAs for intercellular transport.
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Affiliation(s)
- Kai-Ren Luo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Nien-Chen Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Hsin Chang
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Yu-Wen Jan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Tien-Shin Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
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18
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Kitagawa M, Tran TM, Jackson D. Traveling with purpose: cell-to-cell transport of plant mRNAs. Trends Cell Biol 2024; 34:48-57. [PMID: 37380581 DOI: 10.1016/j.tcb.2023.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/19/2023] [Accepted: 05/29/2023] [Indexed: 06/30/2023]
Abstract
Messenger RNAs (mRNAs) in multicellular organisms can act as signals transported cell-to-cell and over long distances. In plants, mRNAs traffic cell-to-cell via plasmodesmata (PDs) and over long distances via the phloem vascular system to control diverse biological processes - such as cell fate and tissue patterning - in destination organs. Research on long-distance transport of mRNAs in plants has made remarkable progress, including the cataloguing of many mobile mRNAs, characterization of mRNA features important for transport, identification of mRNA-binding proteins involved in their transport, and understanding of the physiological roles of mRNA transport. However, information on short-range mRNA cell-to-cell transport is still limited. This review discusses the regulatory mechanisms and physiological functions of mRNA transport at the cellular and whole plant levels.
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Affiliation(s)
- Munenori Kitagawa
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Thu M Tran
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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19
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Tamizhselvan P, Madhavan S, Constan-Aguilar C, Elrefaay ER, Liu J, Pěnčík A, Novák O, Cairó A, Hrtyan M, Geisler M, Tognetti VB. Chloroplast Auxin Efflux Mediated by ABCB28 and ABCB29 Fine-Tunes Salt and Drought Stress Responses in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2023; 13:7. [PMID: 38202315 PMCID: PMC10780339 DOI: 10.3390/plants13010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/26/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024]
Abstract
Photosynthesis is among the first processes negatively affected by environmental cues and its performance directly determines plant cell fitness and ultimately crop yield. Primarily sites of photosynthesis, chloroplasts are unique sites also for the biosynthesis of precursors of the growth regulator auxin and for sensing environmental stress, but their role in intracellular auxin homeostasis, vital for plant growth and survival in changing environments, remains poorly understood. Here, we identified two ATP-binding cassette (ABC) subfamily B transporters, ABCB28 and ABCB29, which export auxin across the chloroplast envelope to the cytosol in a concerted action in vivo. Moreover, we provide evidence for an auxin biosynthesis pathway in Arabidopsis thaliana chloroplasts. The overexpression of ABCB28 and ABCB29 influenced stomatal regulation and resulted in significantly improved water use efficiency and survival rates during salt and drought stresses. Our results suggest that chloroplast auxin production and transport contribute to stomata regulation for conserving water upon salt stress. ABCB28 and ABCB29 integrate photosynthesis and auxin signals and as such hold great potential to improve the adaptation potential of crops to environmental cues.
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Affiliation(s)
- Prashanth Tamizhselvan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Sharmila Madhavan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Christian Constan-Aguilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Eman Ryad Elrefaay
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Jie Liu
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland; (J.L.); (M.G.)
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences, & Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (A.P.); (O.N.)
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences, & Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (A.P.); (O.N.)
| | - Albert Cairó
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Mónika Hrtyan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Markus Geisler
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland; (J.L.); (M.G.)
| | - Vanesa Beatriz Tognetti
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
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20
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Xu J, He J, Hu B, Hou N, Guo J, Wang C, Li X, Li Z, Zhai J, Zhang T, Ma C, Ma F, Guan Q. Global hypermethylation of the N6-methyladenosine RNA modification associated with apple heterografting. PLANT PHYSIOLOGY 2023; 193:2513-2537. [PMID: 37648253 PMCID: PMC10663141 DOI: 10.1093/plphys/kiad470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/20/2023] [Indexed: 09/01/2023]
Abstract
Grafting can facilitate better scion performance and is widely used in plants. Numerous studies have studied the involvement of mRNAs, small RNAs, and epigenetic regulations in the grafting process. However, it remains unclear whether the mRNA N6-methyladenosine (m6A) modification participates in the apple (Malus x domestica Borkh.) grafting process. Here, we decoded the landscape of m6A modification profiles in 'Golden delicious' (a cultivar, Gd) and Malus prunifolia 'Fupingqiuzi' (a unique rootstock with resistance to environmental stresses, Mp), as well as their heterografted and self-grafted plants. Interestingly, global hypermethylation of m6A occurred in both heterografted scion and rootstock compared with their self-grafting controls. Gene Ontology (GO) term enrichment analysis showed that grafting-induced differentially m6A-modified genes were mainly involved in RNA processing, epigenetic regulation, stress response, and development. Differentially m6A-modified genes harboring expression alterations were mainly involved in various stress responses and fatty acid metabolism. Furthermore, grafting-induced mobile mRNAs with m6A and gene expression alterations mainly participated in ABA synthesis and transport (e.g. carotenoid cleavage dioxygenase 1 [CCD1] and ATP-binding cassette G22 [ABCG22]) and abiotic and biotic stress responses, which might contribute to the better performance of heterografted plants. Additionally, the DNA methylome analysis also demonstrated the DNA methylation alterations during grafting. Downregulated expression of m6A methyltransferase gene MdMTA (ortholog of METTL3) in apples induced the global m6A hypomethylation and distinctly activated the expression level of DNA demethylase gene MdROS1 (REPRESSOR OF SILENCING 1) showing the possible association between m6A and 5mC methylation in apples. Our results reveal the m6A modification profiles in the apple grafting process and enhance our understanding of the m6A regulatory mechanism in plant biological processes.
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Affiliation(s)
- Jidi Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Bichun Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Caixia Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jingjing Zhai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ting Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
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21
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Hibbert LE, Qian Y, Smith HK, Milner S, Katz E, Kliebenstein DJ, Taylor G. Making watercress ( Nasturtium officinale) cropping sustainable: genomic insights into enhanced phosphorus use efficiency in an aquatic crop. FRONTIERS IN PLANT SCIENCE 2023; 14:1279823. [PMID: 38023842 PMCID: PMC10662076 DOI: 10.3389/fpls.2023.1279823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023]
Abstract
Watercress (Nasturtium officinale) is a nutrient-dense salad crop with high antioxidant capacity and glucosinolate concentration and with the potential to contribute to nutrient security as a locally grown outdoor aquatic crop in northern temperate climates. However, phosphate-based fertilizers used to support plant growth contribute to the eutrophication of aquatic habitats, often pristine chalk streams, downstream of farms, increasing pressure to minimize fertilizer use and develop a more phosphorus-use efficient (PUE) crop. Here, we grew genetically distinct watercress lines selected from a bi-parental mapping population on a commercial watercress farm either without additional phosphorus (P-) or under a commercial phosphate-based fertilizer regime (P+), to decipher effects on morphology, nutritional profile, and the transcriptome. Watercress plants sustained shoot yield in P- conditions, through enhanced root biomass, but with shorter stems and smaller leaves. Glucosinolate concentration was not affected by P- conditions, but both antioxidant capacity and the concentration of sugars and starch in shoot tissue were enhanced. We identified two watercress breeding lines, with contrasting strategies for enhanced PUE: line 60, with highly plastic root systems and increased root growth in P-, and line 102, maintaining high yield irrespective of P supply, but less plastic. RNA-seq analysis revealed a suite of genes involved in cell membrane remodeling, root development, suberization, and phosphate transport as potential future breeding targets for enhanced PUE. We identified watercress gene targets for enhanced PUE for future biotechnological and breeding approaches enabling less fertilizer inputs and reduced environmental damage from watercress cultivation.
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Affiliation(s)
- Lauren E. Hibbert
- Department of Plant Sciences, University of California Davis, Davis, CA, United States
- School of Biological Sciences, University of Southampton, Hampshire, United Kingdom
| | - Yufei Qian
- Department of Plant Sciences, University of California Davis, Davis, CA, United States
| | | | | | - Ella Katz
- Department of Plant Sciences, University of California Davis, Davis, CA, United States
| | | | - Gail Taylor
- Department of Plant Sciences, University of California Davis, Davis, CA, United States
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22
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Zaman QU, Raza A, Gill RA, Hussain MA, Wang HF, Varshney RK. New possibilities for trait improvement via mobile CRISPR-RNA. Trends Biotechnol 2023; 41:1335-1338. [PMID: 37258389 DOI: 10.1016/j.tibtech.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/17/2023] [Accepted: 05/08/2023] [Indexed: 06/02/2023]
Abstract
CRISPR/Cas9 gene technology is transported as RNA from transgenic roots to distal parts of unmodified grafted scion, where it is translated into proteins to induce heritable mutagenesis at desired loci. This technique has the potential to produce transgene-free and genetically stable plants in difficult-to-propagate and near-extinct species.
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Affiliation(s)
- Qamar U Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Ali Raza
- College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Muhammad Azhar Hussain
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Hua Feng Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia.
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23
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Kondhare KR, Patil NS, Siddappa S, Banerjee AK, Hannapel DJ. Tandem Expression of a Mobile RNA and Its RNA-Binding Protein(s) Enhances Tuber Productivity in Potato. Int J Mol Sci 2023; 24:15754. [PMID: 37958738 PMCID: PMC10647900 DOI: 10.3390/ijms242115754] [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: 08/30/2023] [Revised: 10/07/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
A significant number of discoveries in past two decades have established the importance of long-distance signaling in controlling plant growth, development, and biotic and abiotic stress responses. Numerous mobile signals, such as mRNAs, proteins, including RNA-binding proteins, small RNAs, sugars, and phytohormones, are shown to regulate various agronomic traits such as flowering, fruit, seed development, and tuberization. Potato is a classic model tuber crop, and several mobile signals are known to govern tuber development. However, it is unknown if these mobile signals have any synergistic effects on potato crop improvement. Here, we employed a simple innovative strategy to test the cumulative effects of a key mobile RNA, StBEL5, and its RNA-binding proteins, StPTB1, and -6 on tuber productivity of two potato cultivars, Solanum tuberosum cv. Désirée and subspecies andigena, using a multi-gene stacking approach. In this approach, the coding sequences of StBEL5 and StPTB1/6 are driven by their respective native promoters to efficiently achieve targeted expression in phloem for monitoring tuber productivity. We demonstrate that this strategy resulted in earliness for tuberization and enhanced tuber productivity by 2-4 folds under growth chamber, greenhouse, and field conditions. This multi-gene stacking approach could be adopted to other crops, whose agronomic traits are governed by mobile macromolecules, expanding the possibilities to develop crops with improved traits and enhanced yields.
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Affiliation(s)
- Kirtikumar R. Kondhare
- Biology Division, Indian Institute of Science Education and Research (IISER), Homi Bhabha Road, Pune 411008, Maharashtra, India; (K.R.K.); (N.S.P.)
| | - Nikita S. Patil
- Biology Division, Indian Institute of Science Education and Research (IISER), Homi Bhabha Road, Pune 411008, Maharashtra, India; (K.R.K.); (N.S.P.)
| | - Sundaresha Siddappa
- Crop Improvement Division, Central Potato Research Institute (CPRI), Shimla 171001, Himachal Pradesh, India
| | - Anjan K. Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Homi Bhabha Road, Pune 411008, Maharashtra, India; (K.R.K.); (N.S.P.)
| | - David J. Hannapel
- Plant Biology Major, 253 Horticulture Hall, Iowa State University (ISU), Ames, IA 50011, USA
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24
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Olukayode T, Chen J, Zhao Y, Quan C, Kochian LV, Ham BK. Phloem-Mobile MYB44 Negatively Regulates Expression of PHOSPHATE TRANSPORTER 1 in Arabidopsis Roots. PLANTS (BASEL, SWITZERLAND) 2023; 12:3617. [PMID: 37896080 PMCID: PMC10610484 DOI: 10.3390/plants12203617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023]
Abstract
Phosphorus (P) is an essential plant macronutrient; however, its availability is often limited in soils. Plants have evolved complex mechanisms for efficient phosphate (Pi) absorption, which are responsive to changes in external and internal Pi concentration, and orchestrated through local and systemic responses. To explore these systemic Pi responses, here we identified AtMYB44 as a phloem-mobile mRNA, an Arabidopsis homolog of Cucumis sativus MYB44, that is responsive to the Pi-starvation stress. qRT-PCR assays revealed that AtMYB44 was up-regulated and expressed in both shoot and root in response to Pi-starvation stress. The atmyb44 mutant displayed higher shoot and root biomass compared to wild-type plants, under Pi-starvation conditions. Interestingly, the expression of PHOSPHATE TRANSPORTER1;2 (PHT1;2) and PHT1;4 was enhanced in atmyb44 in response to a Pi-starvation treatment. A split-root assay showed that AtMYB44 expression was systemically regulated under Pi-starvation conditions, and in atmyb44, systemic controls on PHT1;2 and PHT1;4 expression were moderately disrupted. Heterografting assays confirmed graft transmission of AtMYB44 transcripts, and PHT1;2 and PHT1;4 expression was decreased in heterografted atmyb44 rootstocks. Taken together, our findings support the hypothesis that mobile AtMYB44 mRNA serves as a long-distance Pi response signal, which negatively regulates Pi transport and utilization in Arabidopsis.
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Affiliation(s)
- Toluwase Olukayode
- Global Institute for Food Security (GIFS), University of Saskatchewan, 421 Downey Rd, Saskatoon, SK S7N 4L8, Canada; (T.O.); (J.C.); (Y.Z.); (C.Q.); (L.V.K.)
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
| | - Jieyu Chen
- Global Institute for Food Security (GIFS), University of Saskatchewan, 421 Downey Rd, Saskatoon, SK S7N 4L8, Canada; (T.O.); (J.C.); (Y.Z.); (C.Q.); (L.V.K.)
| | - Yang Zhao
- Global Institute for Food Security (GIFS), University of Saskatchewan, 421 Downey Rd, Saskatoon, SK S7N 4L8, Canada; (T.O.); (J.C.); (Y.Z.); (C.Q.); (L.V.K.)
| | - Chuanhezi Quan
- Global Institute for Food Security (GIFS), University of Saskatchewan, 421 Downey Rd, Saskatoon, SK S7N 4L8, Canada; (T.O.); (J.C.); (Y.Z.); (C.Q.); (L.V.K.)
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
| | - Leon V. Kochian
- Global Institute for Food Security (GIFS), University of Saskatchewan, 421 Downey Rd, Saskatoon, SK S7N 4L8, Canada; (T.O.); (J.C.); (Y.Z.); (C.Q.); (L.V.K.)
- Department of Plant Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Byung-Kook Ham
- Global Institute for Food Security (GIFS), University of Saskatchewan, 421 Downey Rd, Saskatoon, SK S7N 4L8, Canada; (T.O.); (J.C.); (Y.Z.); (C.Q.); (L.V.K.)
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
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25
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Chiang CP, Li JL, Chiou TJ. Dose-dependent long-distance movement of microRNA399 duplex regulates phosphate homeostasis in Arabidopsis. THE NEW PHYTOLOGIST 2023; 240:802-814. [PMID: 37547977 DOI: 10.1111/nph.19182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/13/2023] [Indexed: 08/08/2023]
Abstract
MicroRNA399 (miR399), a phosphate (Pi) starvation-induced long-distance signal, is first produced in shoots and moves to roots to suppress PHO2 encoding a ubiquitin conjugase, leading to enhanced Pi uptake and root-to-shoot translocation. However, the molecular mechanism underlying miR399 long-distance movement remains elusive. Hypocotyl grafting with various Arabidopsis mutants or transgenic lines expressing artificial miR399f was employed. The movement of miR399 across graft junction and the rootstock PHO2 transcript and scion Pi levels were analyzed to elucidate the potential factors involved. Our results showed that miR399f precursors are cell-autonomous and mature miR399f movement is independent of its biogenesis, sequence context, and length (21 or 22 nucleotides). Expressing viral silencing suppressor P19 in the root stele or blocking unloading in the root phloem pore pericycle (PPP) antagonized its silencing effect, suggesting that the miR399f/miR399f* duplex is a mobile entity unloaded through PPP. Notably, the scion miR399f level positively correlates with its amount translocated to rootstocks, implying dose-dependent movement. This study uncovers the molecular basis underlying the miR399-mediated long-distance silencing in coordinating shoot Pi demand with Pi acquisition and translocation activities in the roots.
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Affiliation(s)
- Chih-Pin Chiang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Jia-Ling Li
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
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26
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Ma D, Fukuda H, Sotta N, Fujiwara T. Arabidopsis thaliana RPL13aC affects root system architecture through shoot potassium accumulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:497-509. [PMID: 37433637 DOI: 10.1111/tpj.16386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/13/2023]
Abstract
Plant root system architecture shows complex patterns adapting to different nutritional conditions. In Arabidopsis thaliana, root slanting is a behaviour that is observed when plants are grown on a solid agar plate vertically. However, the regulatory mechanisms of root slanting in response to nutrient conditions are not fully understood. In this study, we found that mutants of A. thaliana ribosome protein RPL13aC, which is expressed in root tips and leaves, exhibit a decreased root-slanting phenotype. Ionomic analysis revealed that rpl13ac mutants have a reduced K content in shoots but not in roots. Because K+ availability has been suggested to affect root coiling, we hypothesized that the decreased root slanting of rpl13ac mutants is caused by the decrease in K content in their shoots. Decapitating shoots or limiting K supply dramatically decreased root slanting in wild-type (WT) plants. We found that the expression of HIGH-AFFINITY K+ TRANSPORTER 5 (HAK5) significantly decreased in the roots of rpl13ac mutants. Mutants of hak5 showed decreased shoot K contents and decreased root slanting, supporting that the decreased shoot K+ accumulation results in less root slanting. K+ replenishment to the shoots of rpl13ac, hak5 mutants and K-starved WT plants recovered their root slanting significantly. These results indicate that plants adjust root slanting in response to K+ accumulation in shoots. Further analysis showed that rpl13ac mutants have abnormal thigmotropic responses, which may be responsible for their defects in root slanting. Altogether, these results revealed K+ -dependent mechanisms that affect root system architecture.
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Affiliation(s)
- Dichao Ma
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hirofumi Fukuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Naoyuki Sotta
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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27
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He J, Xu Z, Azhar MT, Zhang Z, Li P, Gong J, Jiang X, Fan S, Ge Q, Yuan Y, Shang H. Comparative transcriptional and co-expression network analysis of two upland cotton accessions with extreme phenotypic differences reveals molecular mechanisms of fiber development. FRONTIERS IN PLANT SCIENCE 2023; 14:1189490. [PMID: 37719229 PMCID: PMC10502173 DOI: 10.3389/fpls.2023.1189490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 07/26/2023] [Indexed: 09/19/2023]
Abstract
Introduction Upland cotton (Gossypium hirsutum) is the main source of natural fiber in the global textile industry, and thus its fiber quality and yield are important parameters. In this study, comparative transcriptomics was used to analyze differentially expressed genes (DEGs) due to its ability to effectively screen candidate genes during the developmental stages of cotton fiber. However, research using this method is limited, particularly on fiber development. The aim of this study was to uncover the molecular mechanisms underlying the whole period of fiber development and the differences in transcriptional levels. Methods Comparative transcriptomes are used to analyze transcriptome data and to screen for differentially expressed genes. STEM and WGCNA were used to screen for key genes involved in fiber development. qRT-PCR was performed to verify gene expression of selected DEGs and hub genes. Results Two accessions of upland cotton with extreme phenotypic differences, namely EZ60 and ZR014121, were used to carry out RNA sequencing (RNA-seq) on fiber samples from different fiber development stages. The results identified 704, 376, 141, 269, 761, and 586 genes that were upregulated, and 1,052, 476, 355, 259, 702, and 847 genes that were downregulated at 0, 5, 10, 15, 20, and 25 days post anthesis, respectively. Similar expression patterns of DEGs were monitored using short time-series expression miner (STEM) analysis, and associated pathways of DEGs within profiles were investigated. In addition, weighted gene co-expression network analysis (WGCNA) identified five key modules in fiber development and screened 20 hub genes involved in the development of fibers. Discussion Through the annotation of the genes, it was found that the excessive expression of resistance-related genes in the early fiber development stages affects the fiber yield, whereas the sustained expression of cell elongation-related genes is critical for long fibers. This study provides new information that can be used to improve fibers in newly developed upland cotton genotypes.
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Affiliation(s)
- Jiasen He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou Henan, China
| | - Zhongyang Xu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou Henan, China
| | - Muhammad Tehseen Azhar
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou Henan, China
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Zhen Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Pengtao Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang Institute of Technology, Anyang, China
| | - Juwu Gong
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiao Jiang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Senmiao Fan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Youlu Yuan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haihong Shang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou Henan, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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28
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Mann CWG, Sawyer A, Gardiner DM, Mitter N, Carroll BJ, Eamens AL. RNA-Based Control of Fungal Pathogens in Plants. Int J Mol Sci 2023; 24:12391. [PMID: 37569766 PMCID: PMC10418863 DOI: 10.3390/ijms241512391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20-40% due to pests and pathogens. There is a growing call for more ecologically sustainable pathogen control measures. RNA-based biopesticides offer an eco-friendly alternative to the use of conventional fungicides for crop protection. The genetic modification (GM) of crops remains controversial in many countries, though expression of transgenes inducing pathogen-specific RNA interference (RNAi) has been proven effective against many agronomically important fungal pathogens. The topical application of pathogen-specific RNAi-inducing sprays is a more responsive, GM-free approach to conventional RNAi transgene-based crop protection. The specific targeting of essential pathogen genes, the development of RNAi-nanoparticle carrier spray formulations, and the possible structural modifications to the RNA molecules themselves are crucial to the success of this novel technology. Here, we outline the current understanding of gene silencing pathways in plants and fungi and summarize the pioneering and recent work exploring RNA-based biopesticides for crop protection against fungal pathogens, with a focus on spray-induced gene silencing (SIGS). Further, we discuss factors that could affect the success of RNA-based control strategies, including RNA uptake, stability, amplification, and movement within and between the plant host and pathogen, as well as the cost and design of RNA pesticides.
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Affiliation(s)
- Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
| | - Anne Sawyer
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Donald M. Gardiner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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29
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Xoconostle-Morán BB, Xoconostle-Cázares B, Vargas-Hernández BY, Núñez-Muñoz LA, Calderón-Pérez B, Ruiz-Medrano R. Long-Distance Movement of Solanum tuberosum Translationally Controlled Tumor Protein ( StTCTP) mRNA. PLANTS (BASEL, SWITZERLAND) 2023; 12:2839. [PMID: 37570993 PMCID: PMC10420919 DOI: 10.3390/plants12152839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Long-distance signaling molecules in plants, including different RNA species, play a crucial role in the development and environmental responses. Among these mobile signals, the Translationally Controlled Tumor Protein (TCTP) mRNA is one of the most abundant. TCTP regulates cell-cycle progression and programmed cell death and is involved in responses to abiotic and biotic stress as well as plant regeneration, among other functions. Considering that the ability to induce plant regeneration is linked to a possible role of TCTP in vegetative propagation and asexual reproduction, we analyzed TCTP overexpression in a solanaceous plant model that can reproduce asexually by regeneration from stolons and tubers. Therefore, in this study, the effect of transient expression of Solanum tuberosum TCTP (StTCTP) on tuber development and vegetative propagation was described. StTCTP mRNA was shown to be transported long-distance. Additionally, transient overexpression of StTCTP resulted in sprouts with a greater diameter compared to control plants. Furthermore, the early stages of tuberization were induced compared to control plants, in which only mature tubers were observed. These results suggest a role of TCTP in vegetative propagation and asexual reproduction.
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Affiliation(s)
| | | | | | | | | | - Roberto Ruiz-Medrano
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Avenida Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Ciudad de México 07360, Mexico; (B.B.X.-M.); (B.X.-C.); (B.Y.V.-H.); (L.A.N.-M.); (B.C.-P.)
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30
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Bakirbas A, Castro-Rodriguez R, Walker EL. The Small RNA Component of Arabidopsis thaliana Phloem Sap and Its Response to Iron Deficiency. PLANTS (BASEL, SWITZERLAND) 2023; 12:2782. [PMID: 37570935 PMCID: PMC10421156 DOI: 10.3390/plants12152782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 08/13/2023]
Abstract
In order to discover sRNA that might function during iron deficiency stress, RNA was prepared from phloem exudates of Arabidopsis thaliana, and used for RNA-seq. Bioanalyzer results indicate that abundant RNA from phloem is small in size-less than 200 nt. Moreover, typical rRNA bands were not observed. Sequencing of eight independent phloem RNA samples indicated that tRNA-derived fragments, specifically 5' tRFs and 5' tRNA halves, are highly abundant in phloem sap, comprising about 46% of all reads. In addition, a set of miRNAs that are present in phloem sap was defined, and several miRNAs and sRNAs were identified that are differentially expressed during iron deficiency.
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Affiliation(s)
- Ahmet Bakirbas
- Biology Department and Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA;
| | | | - Elsbeth L. Walker
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
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31
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Hao L, Wang S, Zhang Y, Xu C, Yu Y, Xiang L, Huang W, Tian B, Li T, Wang S. Long-distance transport of the pear HMGR1 mRNA via the phloem is associated with enhanced salt tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 332:111705. [PMID: 37059127 DOI: 10.1016/j.plantsci.2023.111705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/03/2023] [Accepted: 04/08/2023] [Indexed: 05/27/2023]
Abstract
Grafting is the main asexual propagation method for horticultural crops and can enhance their resistance to biotic or abiotic stress. Many mRNAs can be transported over long distances through the graft union, however, the function of mobile mRNAs remains poorly understood. Here, we exploited lists of candidate mobile mRNAs harboring potential 5-methylcytosine (m5C) modification in pear (Pyrus betulaefolia). dCAPS RT-PCR and RT-PCR were employed to demonstrate the mobility of the 3-hydroxy-3-methylglutaryl-coenzyme A reductase1 (PbHMGR1) mRNA in grafted plants of both pear and tobacco (Nicotiana tabacum). Overexpressing PbHMGR1 in tobacco plants enhanced salt tolerance during seed germination. In addition, both histochemical staining and GUS expression analysis showed that PbHMGR1 could directly respond to salt stress. Furthermore, it was found that the relative abundance of PbHMGR1 increased in heterografted scion, which avoided serious damage under salt stress. Collectively, these findings established that PbHMGR1 mRNA could act as a salt-responsive signal and move through the graft union to enhance salt tolerance of scion, which might be used as a new plant breeding technique to improve resistance of scion through a stress-tolerant rootstock.
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Affiliation(s)
- Li Hao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China; College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Shengyuan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yi Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chaoran Xu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yunfei Yu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Ling Xiang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Wenting Huang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China; College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Baihui Tian
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China.
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China.
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32
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Kirschner GK. Local call or long-distance call: studying cell-to-cell transport by Arabidopsis callus grafting. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:299-300. [PMID: 37449309 DOI: 10.1111/tpj.16358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
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33
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Palos K, Yu L, Railey CE, Nelson Dittrich AC, Nelson ADL. Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs. THE PLANT CELL 2023; 35:1762-1786. [PMID: 36738093 PMCID: PMC10226578 DOI: 10.1093/plcell/koad027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 05/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pregenomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.
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Affiliation(s)
- Kyle Palos
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Li’ang Yu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Caylyn E Railey
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Graduate Field, Cornell University, Ithaca, NY 14853, USA
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Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: How RNA structure informs function. THE PLANT CELL 2023; 35:1671-1707. [PMID: 36747354 DOI: 10.1093/plcell/koad026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 05/30/2023]
Abstract
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.
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Affiliation(s)
- Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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35
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Mateos JL, Staiger D. Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association. THE PLANT CELL 2023; 35:1708-1726. [PMID: 36461946 PMCID: PMC10226577 DOI: 10.1093/plcell/koac345] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 05/30/2023]
Abstract
RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.
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Affiliation(s)
- Julieta L Mateos
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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36
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Kiryushkin AS, Ilina EL, Guseva ED, Pawlowski K, Demchenko KN. Lateral Root Initiation in Cucumber ( Cucumis sativus): What Does the Expression Pattern of Rapid Alkalinization Factor 34 ( RALF34) Tell Us? Int J Mol Sci 2023; 24:ijms24098440. [PMID: 37176146 PMCID: PMC10179419 DOI: 10.3390/ijms24098440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
In Arabidopsis, the small signaling peptide (peptide hormone) RALF34 is involved in the gene regulatory network of lateral root initiation. In this study, we aimed to understand the nature of the signals induced by RALF34 in the non-model plant cucumber (Cucumis sativus), where lateral root primordia are induced in the apical meristem of the parental root. The RALF family members of cucumber were identified using phylogenetic analysis. The sequence of events involved in the initiation and development of lateral root primordia in cucumber was examined in detail. To elucidate the role of the small signaling peptide CsRALF34 and its receptor CsTHESEUS1 in the initial stages of lateral root formation in the parental root meristem in cucumber, we studied the expression patterns of both genes, as well as the localization and transport of the CsRALF34 peptide. CsRALF34 is expressed in all plant organs. CsRALF34 seems to differ from AtRALF34 in that its expression is not regulated by auxin. The expression of AtRALF34, as well as CsRALF34, is regulated in part by ethylene. CsTHESEUS1 is expressed constitutively in cucumber root tissues. Our data suggest that CsRALF34 acts in a non-cell-autonomous manner and is not involved in lateral root initiation in cucumber.
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Affiliation(s)
- Alexey S Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Elena L Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Elizaveta D Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
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37
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Lu H, Wang F, Wang Y, Lin R, Wang Z, Mao C. Molecular mechanisms and genetic improvement of low-phosphorus tolerance in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1104-1119. [PMID: 36208118 DOI: 10.1111/pce.14457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/01/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Phosphorus (P) is a macronutrient required for plant growth and reproduction. Orthophosphate (Pi), the preferred P form for plant uptake, is easily fixed in the soil, making it unavailable to plants. Limited phosphate rock resources, low phosphate fertilizer use efficiency and high demands for green agriculture production make it important to clarify the molecular mechanisms underlying plant responses to P deficiency and to improve plant phosphate efficiency in crops. Over the past 20 years, tremendous progress has been made in understanding the regulatory mechanisms of the plant P starvation response. Here, we systematically review current research on the mechanisms of Pi acquisition, transport and distribution from the rhizosphere to the shoot; Pi redistribution and reuse during reproductive growth; and the molecular mechanisms of arbuscular mycorrhizal symbiosis in rice (Oryza sativa L.) under Pi deficiency. Furthermore, we discuss several strategies for boosting P utilization efficiency and yield in rice.
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Affiliation(s)
- Hong Lu
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yan Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Rongbin Lin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chuanzao Mao
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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38
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Niccolò T, Anderson AW, Emidio A. Apomixis: oh, what a tangled web we have! PLANTA 2023; 257:92. [PMID: 37000270 PMCID: PMC10066125 DOI: 10.1007/s00425-023-04124-0] [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: 09/24/2022] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Apomixis is a complex evolutionary trait with many possible origins. Here we discuss various clues and causes, ultimately proposing a model harmonizing the three working hypotheses on the topic. Asexual reproduction through seeds, i.e., apomixis, is the holy grail of plant biology. Its implementation in modern breeding could be a game-changer for agriculture. It has the potential to generate clonal crops and maintain valuable complex genotypes and their associated heterotic traits without inbreeding depression. The genetic basis and origins of apomixis are still unclear. There are three central hypothesis for the development of apomixis that could be: i) a deviation from the sexual developmental program caused by an asynchronous development, ii) environmentally triggered through epigenetic regulations (a polyphenism of sex), iii) relying on one or more genes/alleles. Because of the ever-increasing complexity of the topic, the path toward a detailed understanding of the mechanisms underlying apomixis remains unclear. Here, we discuss the most recent advances in the evolution perspective of this multifaceted trait. We incorporated our understanding of the effect of endogenous effectors, such as small RNAs, epigenetic regulation, hormonal pathways, protein turnover, and cell wall modification in response to an upside stress. This can be either endogenous (hybridization or polyploidization) or exogenous environmental stress, mainly due to oxidative stress and the corresponding ROS (Reacting Oxygen Species) effectors. Finally, we graphically represented this tangled web.
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Affiliation(s)
- Terzaroli Niccolò
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
| | - Aaron W Anderson
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Fulbright Scholar From Department of Plant Sciences, University of California, Davis, USA
| | - Albertini Emidio
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Consorzio Interuniversitario per le Biotecnologie (CIB), Trieste, Italy
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39
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Jeynes-Cupper K, Catoni M. Long distance signalling and epigenetic changes in crop grafting. FRONTIERS IN PLANT SCIENCE 2023; 14:1121704. [PMID: 37021313 PMCID: PMC10067726 DOI: 10.3389/fpls.2023.1121704] [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: 12/12/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Humans have used grafting for more than 4000 years to improve plant production, through physically joining two different plants, which can continue to grow as a single organism. Today, grafting is becoming increasingly more popular as a technique to increase the production of herbaceous horticultural crops, where rootstocks can introduce traits such as resistance to several pathogens and/or improving the plant vigour. Research in model plants have documented how long-distance signalling mechanisms across the graft junction, together with epigenetic regulation, can produce molecular and phenotypic changes in grafted plants. Yet, most of the studied examples rely on proof-of-concept experiments or on limited specific cases. This review explores the link between research findings in model plants and crop species. We analyse studies investigating the movement of signalling molecules across the graft junction and their implications on epigenetic regulation. The improvement of genomics analyses and the increased availability of genetic resources has allowed to collect more information on potential benefits of grafting in horticultural crop models. Ultimately, further research into this topic will enhance our ability to use the grafting technique to exploit genetic and epigenetic variation in crops, as an alternative to traditional breeding.
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Affiliation(s)
| | - Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, Italy
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40
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Yang L, Zhou Y, Wang S, Xu Y, Ostendorp S, Tomkins M, Kehr J, Morris RJ, Kragler F. Noncell-autonomous HSC70.1 chaperone displays homeostatic feedback regulation by binding its own mRNA. THE NEW PHYTOLOGIST 2023; 237:2404-2421. [PMID: 36564968 DOI: 10.1111/nph.18703] [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: 11/04/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
The HSC70/HSP70 family of heat shock proteins are evolutionarily conserved chaperones involved in protein folding, protein transport, and RNA binding. Arabidopsis HSC70 chaperones are thought to act as housekeeping chaperones and as such are involved in many growth-related pathways. Whether Arabidopsis HSC70 binds RNA and whether this interaction is functional has remained an open question. We provide evidence that the HSC70.1 chaperone binds its own mRNA via its C-terminal short variable region (SVR) and inhibits its own translation. The SVR encoding mRNA region is necessary for HSC70.1 transcript mobility to distant tissues and that HSC70.1 transcript and not protein mobility is required to rescue root growth and flowering time of hsc70 mutants. We propose that this negative protein-transcript feedback loop may establish an on-demand chaperone pool that allows for a rapid response to stress. In summary, our data suggest that the Arabidopsis HSC70.1 chaperone can form a complex with its own transcript to regulate its translation and that both protein and transcript can act in a noncell-autonomous manner, potentially maintaining chaperone homeostasis between tissues.
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Affiliation(s)
- Lei Yang
- Max-Planck-Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Golm, Germany
| | - Yuan Zhou
- Max-Planck-Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Golm, Germany
| | - Shuangfeng Wang
- Max-Planck-Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Golm, Germany
| | - Ying Xu
- Max-Planck-Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Golm, Germany
| | - Steffen Ostendorp
- Institute for Plant Science and Microbiology, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Melissa Tomkins
- Computational and Systems Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Julia Kehr
- Institute for Plant Science and Microbiology, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Richard J Morris
- Computational and Systems Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Friedrich Kragler
- Max-Planck-Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Golm, Germany
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Dervisi I, Petropoulos O, Agalou A, Podia V, Papandreou N, Iconomidou VA, Haralampidis K, Roussis A. The SAH7 Homologue of the Allergen Ole e 1 Interacts with the Putative Stress Sensor SBP1 (Selenium-Binding Protein 1) in Arabidopsis thaliana. Int J Mol Sci 2023; 24:3580. [PMID: 36834990 PMCID: PMC9962204 DOI: 10.3390/ijms24043580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
In this study, we focused on a member of the Ole e 1 domain-containing family, AtSAH7, in Arabidopsis thaliana. Our lab reports for the first time on this protein, AtSAH7, that was found to interact with Selenium-binding protein 1 (AtSBP1). We studied by GUS assisted promoter deletion analysis the expression pattern of AtSAH7 and determined that the sequence 1420 bp upstream of the transcription start can act as a minimal promoter inducing expression in vasculature tissues. Moreover, mRNA levels of AtSAH7 were acutely increased under selenite treatment in response to oxidative stress. We confirmed the aforementioned interaction in vivo, in silico and in planta. Following a bimolecular fluorescent complementation approach, we determined that the subcellular localization of the AtSAH7 and the AtSAH7/AtSBP1 interaction occur in the ER. Our results indicate the participation of AtSAH7 in a biochemical network regulated by selenite, possibly associated with responses to ROS production.
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Affiliation(s)
- Irene Dervisi
- Department of Botany, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Orfeas Petropoulos
- Department of Botany, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Adamantia Agalou
- Laboratory of Toxicological Control of Pesticides, Scientific Directorate of Pesticides’ Control & Phytopharmacy, Benaki Phytopathological Institute (BPI), 8 Stefanou Delta Street, Kifissia, 14561 Athens, Greece
| | - Varvara Podia
- Department of Botany, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Nikolaos Papandreou
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Vassiliki A. Iconomidou
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Kosmas Haralampidis
- Department of Botany, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Andreas Roussis
- Department of Botany, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
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42
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Alcantud R, Weiss J, Terry MI, Bernabé N, Verdú-Navarro F, Fernández-Breis JT, Egea-Cortines M. Flower transcriptional response to long term hot and cold environments in Antirrhinum majus. FRONTIERS IN PLANT SCIENCE 2023; 14:1120183. [PMID: 36778675 PMCID: PMC9911551 DOI: 10.3389/fpls.2023.1120183] [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: 12/09/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Short term experiments have identified heat shock and cold response elements in many biological systems. However, the effect of long-term low or high temperatures is not well documented. To address this gap, we grew Antirrhinum majus plants from two-weeks old until maturity under control (normal) (22/16°C), cold (15/5°C), and hot (30/23°C) conditions for a period of two years. Flower size, petal anthocyanin content and pollen viability obtained higher values in cold conditions, decreasing in middle and high temperatures. Leaf chlorophyll content was higher in cold conditions and stable in control and hot temperatures, while pedicel length increased under hot conditions. The control conditions were optimal for scent emission and seed production. Scent complexity was low in cold temperatures. The transcriptomic analysis of mature flowers, followed by gene enrichment analysis and CNET plot visualization, showed two groups of genes. One group comprised genes controlling the affected traits, and a second group appeared as long-term adaptation to non-optimal temperatures. These included hypoxia, unsaturated fatty acid metabolism, ribosomal proteins, carboxylic acid, sugar and organic ion transport, or protein folding. We found a differential expression of floral organ identity functions, supporting the flower size data. Pollinator-related traits such as scent and color followed opposite trends, indicating an equilibrium for rendering the organs for pollination attractive under changing climate conditions. Prolonged heat or cold cause structural adaptations in protein synthesis and folding, membrane composition, and transport. Thus, adaptations to cope with non-optimal temperatures occur in basic cellular processes.
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Affiliation(s)
- Raquel Alcantud
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Julia Weiss
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Marta I. Terry
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Nuria Bernabé
- Department of Informatics and Systems, Campus de Espinardo, Universidad de Murcia, Instituto Murciano de Investigaciones Biomédicas (IMIB)-Arrixaca, Murcia, Spain
| | - Fuensanta Verdú-Navarro
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, Cartagena, Spain
- R&D Department, Bionet Engineering, Av/Azul, Parque Tecnológico Fuente Álamo, Murcia, Spain
| | - Jesualdo Tomás Fernández-Breis
- Department of Informatics and Systems, Campus de Espinardo, Universidad de Murcia, Instituto Murciano de Investigaciones Biomédicas (IMIB)-Arrixaca, Murcia, Spain
| | - Marcos Egea-Cortines
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, Cartagena, Spain
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Li JH, Muhammad Aslam M, Gao YY, Dai L, Hao GF, Wei Z, Chen MX, Dini-Andreote F. Microbiome-mediated signal transduction within the plant holobiont. Trends Microbiol 2023; 31:616-628. [PMID: 36702670 DOI: 10.1016/j.tim.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Microorganisms colonizing the plant rhizosphere and phyllosphere play crucial roles in plant growth and health. Recent studies provide new insights into long-distance communication from plant roots to shoots in association with their commensal microbiome. In brief, these recent advances suggest that specific plant-associated microbial taxa can contribute to systemic plant responses associated with the enhancement of plant health and performance in face of a variety of biotic and abiotic stresses. However, most of the mechanisms associated with microbiome-mediated signal transduction in plants remain poorly understood. In this review, we provide an overview of long-distance signaling mechanisms within plants mediated by the commensal plant-associated microbiomes. We advocate the view of plants and microbes as a holobiont and explore key molecules and mechanisms associated with plant-microbe interactions and changes in plant physiology activated by signal transduction.
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Affiliation(s)
- Jian-Hong Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Mehtab Muhammad Aslam
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yang-Yang Gao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Mo-Xian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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Ye K, Teng T, Yang T, Zhao D, Zhao Y. Transcriptome analysis reveals the effect of grafting on gossypol biosynthesis and gland formation in cotton. BMC PLANT BIOLOGY 2023; 23:37. [PMID: 36642721 PMCID: PMC9841644 DOI: 10.1186/s12870-022-04010-z] [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: 03/15/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Gossypol is a unique secondary metabolite and sesquiterpene in cotton, which is mainly synthesized in the root system of cotton and exhibits many biological activities. Previous research found that grafting affected the density of pigment glands and the gossypol content in cotton. RESULTS This study performed a transcriptome analysis on cotton rootstocks and scions of four grafting methods. The gene expression of mutual grafting and self-grafting was compared to explore the potential genes involved in gossypol biosynthesis. A total of six differentially expressed enzymes were found in the main pathway of gossypol synthesis-sesquiterpene and triterpene biosynthesis (map00909): lupeol synthase (LUP1, EC:5.4.99.41), beta-amyrin synthase (LUP2, EC:5.4.99.39), squalene monooxygenase (SQLE, EC:1.14.14.17), squalene synthase (FDFT1, EC:2.5.1.21), (-)-germacrene D synthase (GERD, EC:4.2.3.75), ( +)-delta-cadinene synthase (CADS, EC:4.2.3.13). By comparing the results of the gossypol content and the density of the pigment gland, we speculated that these six enzymes might affect the biosynthesis of gossypol. It was verified by qRT-PCR analysis that grafting could influence gene expression of scion and stock. After suppressing the expression of the LUP1, FDFT1, and CAD genes by VIGS technology, the gossypol content in plants was significantly down-regulated. CONCLUSIONS These results indicate the potential molecular mechanism of gossypol synthesis during the grafting process and provide a theoretical foundation for further research on gossypol biosynthesis.
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Affiliation(s)
- Kun Ye
- College of Tea Sciences, College of Life Sciences, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
| | - Teng Teng
- College of Tea Sciences, College of Life Sciences, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
| | - Teng Yang
- College of Tea Sciences, College of Life Sciences, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
| | - Degang Zhao
- College of Tea Sciences, College of Life Sciences, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
- Plant Conservation Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Yichen Zhao
- College of Tea Sciences, College of Life Sciences, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
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Yang L, Machin F, Wang S, Saplaoura E, Kragler F. Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks. Nat Biotechnol 2023:10.1038/s41587-022-01585-8. [PMID: 36593415 DOI: 10.1038/s41587-022-01585-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 10/20/2022] [Indexed: 01/03/2023]
Abstract
Generation of stable gene-edited plant lines using clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) requires a lengthy process of outcrossing to eliminate CRISPR-Cas9-associated sequences and produce transgene-free lines. We have addressed this issue by designing fusions of Cas9 and guide RNA transcripts to tRNA-like sequence motifs that move RNAs from transgenic rootstocks to grafted wild-type shoots (scions) and achieve heritable gene editing, as demonstrated in wild-type Arabidopsis thaliana and Brassica rapa. The graft-mobile gene editing system enables the production of transgene-free offspring in one generation without the need for transgene elimination, culture recovery and selection, or use of viral editing vectors. We anticipate that using graft-mobile editing systems for transgene-free plant production may be applied to a wide range of breeding programs and crop plants.
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Affiliation(s)
- Lei Yang
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Frank Machin
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Shuangfeng Wang
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
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Scion-to-Rootstock Mobile Transcription Factor CmHY5 Positively Modulates the Nitrate Uptake Capacity of Melon Scion Grafted on Squash Rootstock. Int J Mol Sci 2022; 24:ijms24010162. [PMID: 36613606 PMCID: PMC9820822 DOI: 10.3390/ijms24010162] [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: 11/28/2022] [Revised: 12/18/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
It is generally recognized that the root uptake capacity of grafted plants strongly depends on the rootstocks' well-developed root system. However, we found that grafted plants showed different nitrate uptake capacities when different varieties of oriental melon scion were grafted onto the same squash rootstock, suggesting that the scion regulated the nitrate uptake capacity of the rootstock root. In this study, we estimated the nitrate uptake capacity of grafted plants with the different oriental melon varieties' seedlings grafted onto the same squash rootstocks. The results indicated a significant difference in the nitrate uptake rate and activity of two heterologous grafting plants. We also showed a significant difference in CmoNRT2.1 expression in the roots of two grafting combinations and verified the positive regulation of nitrate uptake by CmoNRT2.1 expression. In addition, the two varieties of oriental melon scion had highly significant differences in CmHY5 expression, which was transported to the rootstock and positively induced CmoHY5-1 and CmoHY5-2 expression in the rootstock roots. Meanwhile, CmHY5 could positively regulate CmoNRT2.1 expression in the rootstock roots. Furthermore, CmoHY5-1 and CmoHY5-2 also positively regulated CmoNRT2.1 expression, respectively, and CmoHY5-1 dominated the positive regulation of CmoNRT2.1, while CmHY5 could interact with CmoHY5-1 and CmoHY5-2, respectively, to jointly regulate CmoNRT2.1 expression. The oriental melon scion regulated the nitrate uptake capacity of the melon/squash grafting plant roots, and the higher expression of CmHY5 in the oriental melon scion leaves, the more substantial the nitrate uptake capacity of squash rootstock roots.
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Tomkins M, Hoerbst F, Gupta S, Apelt F, Kehr J, Kragler F, Morris RJ. Exact Bayesian inference for the detection of graft-mobile transcripts from sequencing data. J R Soc Interface 2022; 19:20220644. [PMID: 36514890 PMCID: PMC9748499 DOI: 10.1098/rsif.2022.0644] [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] [Indexed: 12/15/2022] Open
Abstract
The long-distance transport of messenger RNAs (mRNAs) has been shown to be important for several developmental processes in plants. A popular method for identifying travelling mRNAs is to perform RNA-Seq on grafted plants. This approach depends on the ability to correctly assign sequenced mRNAs to the genetic background from which they originated. The assignment is often based on the identification of single-nucleotide polymorphisms (SNPs) between otherwise identical sequences. A major challenge is therefore to distinguish SNPs from sequencing errors. Here, we show how Bayes factors can be computed analytically using RNA-Seq data over all the SNPs in an mRNA. We used simulations to evaluate the performance of the proposed framework and demonstrate how Bayes factors accurately identify graft-mobile transcripts. The comparison with other detection methods using simulated data shows how not taking the variability in read depth, error rates and multiple SNPs per transcript into account can lead to incorrect classification. Our results suggest experimental design criteria for successful graft-mobile mRNA detection and show the pitfalls of filtering for sequencing errors or focusing on single SNPs within an mRNA.
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Affiliation(s)
- Melissa Tomkins
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR47UH, UK
| | - Franziska Hoerbst
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR47UH, UK
| | - Saurabh Gupta
- Max Planck Institute of Molecular Plant Physiology, Max Planck Institute, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Federico Apelt
- Max Planck Institute of Molecular Plant Physiology, Max Planck Institute, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Julia Kehr
- Institute of Plant Science and Microbiology, Universität Hamburg, Ohnhorststrasse 18, Hamburg 22609, Germany
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, Max Planck Institute, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Richard J. Morris
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR47UH, UK
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Gulyás Z, Moncsek B, Hamow KÁ, Stráner P, Tolnai Z, Badics E, Incze N, Darkó É, Nagy V, Perczel A, Kovács L, Soós V. D27-LIKE1 isomerase has a preference towards trans/cis and cis/cis conversions of carotenoids in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1377-1395. [PMID: 36308414 DOI: 10.1111/tpj.16017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Carotenoids contribute to a variety of physiological processes in plants, functioning also as biosynthesis precursors of ABA and strigolactones (SLs). SL biosynthesis starts with the enzymatic conversion of all-trans-β-carotene to 9-cis-β-carotene by the DWARF27 (D27) isomerase. In Arabidopsis, D27 has two closely related paralogs, D27-LIKE1 and D27-LIKE2, which were predicted to be β-carotene-isomerases. In the present study, we characterised D27-LIKE1 and identified some key aspects of its physiological and enzymatic functions in Arabidopsis. d27-like1-1 mutant does not display any strigolactone-deficient traits and exhibits a substantially higher 9-cis-violaxanthin content, which is accompanied by a slightly higher ABA level. In vitro feeding assays with recombinant D27-LIKE1 revealed that the protein exhibits affinity to all β-carotene isoforms but with an exclusive preference towards trans/cis conversions and the interconversion between 9-cis, 13-cis and 15-cis-β-carotene forms, and accepts zeaxanthin and violaxanthin as substrates. Finally, we present evidence showing that D27-LIKE1 mRNA is phloem mobile and D27-LIKE1 is an ancient isomerase with a long evolutionary history. In summary, we demonstrate that D27-LIKE1 is a carotenoid isomerase with multi-substrate specificity and has a characteristic preference towards the catalysation of cis/cis interconversion of carotenoids. Therefore, D27-LIKE1 is a potential regulator of carotenoid cis pools and, eventually, SL and ABA biosynthesis pathways.
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Affiliation(s)
- Zsolt Gulyás
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Blanka Moncsek
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter s. 1/A, Budapest, 1117, Hungary
| | - Kamirán Áron Hamow
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Pál Stráner
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter s. 1/A, Budapest, 1117, Hungary
| | - Zoltán Tolnai
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Eszter Badics
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter s. 1/A, Budapest, 1117, Hungary
| | - Norbert Incze
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter s. 1/A, Budapest, 1117, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Valéria Nagy
- Biological Research Centre, ELKH, 6726, Szeged, Temesvári krt. 62, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter s. 1/A, Budapest, 1117, Hungary
| | - László Kovács
- Biological Research Centre, ELKH, 6726, Szeged, Temesvári krt. 62, Hungary
| | - Vilmos Soós
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
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Genome-Wide Identification and Analysis of DOF Gene Family in Eugenia uniflora L. (Myrtaceae). Genes (Basel) 2022; 13:genes13122235. [PMID: 36553502 PMCID: PMC9778057 DOI: 10.3390/genes13122235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022] Open
Abstract
Eugenia uniflora is a Brazilian native plant species with great ecological and economic importance. It is distributed throughout the Atlantic forest, where two distinct populations show local adaptation to the contrasting conditions of restinga and riparian forest. Among various TFs described in plants, the DOF TF family has been reported to affect flowering and vascular development, making them promising candidates for characterization in E. uniflora. In this study, 28 DOF genes were identified by a genome-wide analysis, of which 20 were grouped into 11 MCOGs by Bayesian phylogeny, suggesting a shared functionallity between members. Based on RNA-seq experiments, we have detected eight drought responsive genes, and SNPs identification revealed population unique polymorphisms, implying a role in local adapatation mechanisms. Finally, analysis of conserved motifs through MEME revealed 15 different protein motifs, and a promoter region analysis returned 40 enriched TF binding motifs, both reporting novel biological functions circa the DOF gene family. In general, the DOF family is found to be conserved both in sequence and expression. Furthermore, this study contributes to both DOF literature and the genetic exploration of native species, elucidating their genetic potential and bringing to light new research topics, paving the way to future studies.
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Khan A, Korban SS. Breeding and genetics of disease resistance in temperate fruit trees: challenges and new opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3961-3985. [PMID: 35441862 DOI: 10.1007/s00122-022-04093-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Climate change, large monocultures of disease-susceptible cultivars, overuse of pesticides, and the emergence of new pathogens or pathogenic strains causing economic losses are all major threats to our environment, health, food, and nutritional supply. Temperate tree fruit crops belonging to the Rosaceae family are the most economically important and widely grown fruit crops. These long-lived crops are under attack from many different pathogens, incurring major economic losses. Multiple chemical sprays to control various diseases annually is a common practice, resulting in significant input costs, as well as environmental and health concerns. Breeding for disease resistance has been undertaken primarily in pome fruit crops (apples and pears) for a few fungal and bacterial diseases, and to a lesser extent in some stone fruit crops. These breeding efforts have taken multiple decades due to the biological constraints and complex genetics of these tree fruit crops. Over the past couple of decades, major advances have been made in genetic and physical mapping, genomics, biotechnology, genome sequencing, and phenomics, along with accumulation of large germplasm collections in repositories. These valuable resources offer opportunities to make significant advances in greatly reducing the time needed to either develop new cultivars or modify existing economic cultivars for enhanced resistance to multiple diseases. This review will cover current knowledge, challenges, and opportunities in breeding for disease resistance in temperate tree fruit crops.
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Affiliation(s)
- Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA.
| | - Schuyler S Korban
- Department of Natural Sciences and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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