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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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Zeng J, Geng X, Zhao Z, Zhou W. Tipping the balance: The dynamics of stem cell maintenance and stress responses in plant meristems. CURRENT OPINION IN PLANT BIOLOGY 2024; 78:102510. [PMID: 38266375 DOI: 10.1016/j.pbi.2024.102510] [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: 07/06/2023] [Revised: 11/24/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024]
Abstract
Plant meristems contain pools of dividing stem cells that produce new organs for plant growth and development. Environmental factors, including biotic and abiotic stresses and nutrient availability, affect meristem activity and thus the architecture of roots and shoots; understanding how meristems react to changing environmental conditions will shed light on how plants optimize nutrient acquisition and acclimate to different environmental conditions. This review highlights recent exciting advances in this field, mainly in Arabidopsis. We discuss the signaling pathways, genetic regulators, and molecular mechanisms involved in the response of plant meristems to environmental and nutrient cues, and compare the similarities and differences of stress responses between the shoot and root apical meristems.
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Affiliation(s)
- Jian Zeng
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Xin Geng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhong Zhao
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Wenkun Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Qiao L, Lin J, Suzaki T, Liang P. Staying hungry: a roadmap to harnessing central regulators of symbiotic nitrogen fixation under fluctuating nitrogen availability. ABIOTECH 2024; 5:107-113. [PMID: 38576431 PMCID: PMC10987428 DOI: 10.1007/s42994-023-00123-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/27/2023] [Indexed: 04/06/2024]
Abstract
Legumes have evolved specific inventions to enhance nitrogen (N) acquisition by establishing symbiotic interactions with N-fixing rhizobial bacteria. Because symbiotic N fixation is energetically costly, legumes have developed sophisticated mechanisms to ensure carbon-nitrogen balance, in a variable environment, both locally and at the whole plant level, by monitoring nodule number, nodule development, and nodular nitrogenase activity, as well as controlling nodule senescence. Studies of the autoregulation of nodulation and regulation of nodulation by nodule inception (NIN) and NIN-LIKE PROTEINs (NLPs) have provided great insights into the genetic mechanisms underlying the nitrate-induced regulation of root nodulation for adapting to N availability in the rhizosphere. However, many aspects of N-induced pleiotropic regulation remain to be fully explained, such as N-triggered senescence in mature nodules. Wang et al. determined that this process is governed by a transcriptional network regulated by NAC-type transcription factors. Characterization and dissection of these soybean nitrogen-associated NAPs (SNAPs) transcription factor-mastered networks have yielded a roadmap for exploring how legumes rewire nodule functions across a range of N levels, laying the foundation for enhancing the growth of N-deprived crops in agricultural settings.
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Affiliation(s)
- Lijin Qiao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
- MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Jieshun Lin
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Takuya Suzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Pengbo Liang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
- MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, China Agricultural University, Beijing, China
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Zhang YC, Zhuang LH, Zhou JJ, Song SW, Li J, Huang HZ, Chi BJ, Zhong YH, Liu JW, Zheng HL, Zhu XY. Combined metabolome and transcriptome analysis reveals a critical role of lignin biosynthesis and lignification in stem-like pneumatophore development of the mangrove Avicennia marina. PLANTA 2023; 259:12. [PMID: 38057597 DOI: 10.1007/s00425-023-04291-0] [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: 11/14/2023] [Indexed: 12/08/2023]
Abstract
MAIN CONCLUSION Transcriptional and metabolic regulation of lignin biosynthesis and lignification plays crucial roles in Avicennia marina pneumatophore development, facilitating its adaptation to coastal habitats. Avicennia marina is a pioneer mangrove species in coastal wetland. To cope with the periodic intertidal flooding and hypoxia environment, this species has developed a complex and extensive root system, with its most unique feature being a pneumatophore with a distinct above- and below-ground morphology and vascular structure. However, the characteristics of pneumatophore lignification remain unknown. Studies comparing the anatomy among above-ground pneumatophore, below-ground pneumatophore, and feeding root have suggested that vascular structure development in the pneumatophore is more like the development of a stem than of a root. Metabolome and transcriptome analysis illustrated that the accumulation of syringyl (S) and guaiacyl (G) units in the pneumatophore plays a critical role in lignification of the stem-like structure. Fourteen differentially accumulated metabolites (DAMs) and 10 differentially expressed genes involved in the lignin biosynthesis pathway were targeted. To identify genes significantly associated with lignification, we analyzed the correlation between 14 genes and 8 metabolites and further built a co-expression network between 10 transcription factors (TFs), including 5 for each of MYB and NAC, and 23 enzyme-coding genes involved in lignin biosynthesis. 4-Coumarate-CoA ligase, shikimate/quinate hydroxycinnamoyl transferase, cinnamyl alcohol dehydrogenase, caffeic acid 3-O-methyltransferase, phenylalanine ammonia-lyase, and peroxidase were identified to be strongly correlated with these TFs. Finally, we examined 9 key candidate genes through quantitative real-time PCR to validate the reliability of transcriptome data. Together, our metabolome and transcriptome findings reveal that lignin biosynthesis and lignification regulate pneumatophore development in the mangrove species A. marina and facilitate its adaptation to coastal habitats.
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Affiliation(s)
- Yu-Chen Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China
| | - Li-Han Zhuang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China
| | - Jia-Jie Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China
| | - Shi-Wei Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China
| | - Jing Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China
| | - He-Zi Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China
| | - Bing-Jie Chi
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China
| | - You-Hui Zhong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China
| | - Jing-Wen Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China.
| | - Xue-Yi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361105, Fujian, China.
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Wang T, Chen X, Ju C, Wang C. Calcium signaling in plant mineral nutrition: From uptake to transport. PLANT COMMUNICATIONS 2023; 4:100678. [PMID: 37635354 PMCID: PMC10721523 DOI: 10.1016/j.xplc.2023.100678] [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: 04/16/2023] [Revised: 05/26/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
Plant mineral nutrition is essential for crop yields and human health. However, the uneven distribution of mineral elements over time and space leads to a lack or excess of available mineral elements in plants. Among the essential nutrients, calcium (Ca2+) stands out as a prominent second messenger that plays crucial roles in response to extracellular stimuli in all eukaryotes. Distinct Ca2+ signatures with unique parameters are induced by different stresses and deciphered by various Ca2+ sensors. Recent research on the participation of Ca2+ signaling in regulation of mineral elements has made great progress. In this review, we focus on the impact of Ca2+ signaling on plant mineral uptake and detoxification. Specifically, we emphasize the significance of Ca2+ signaling for regulation of plant mineral nutrition and delve into key points and novel avenues for future investigations, aiming to offer new insights into plant ion homeostasis.
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Affiliation(s)
- Tian Wang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Xuanyi Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Chuanfeng Ju
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China.
| | - Cun Wang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China.
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