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Bian X, Li X, Qu C, Zhang M, Li D, Wang Y, Jiang J, Liu G. Transcriptome sequencing-based analysis of primary vein development in Betula pendula 'Dalecarlica'. Gene 2024; 933:148948. [PMID: 39277147 DOI: 10.1016/j.gene.2024.148948] [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: 05/29/2024] [Revised: 09/09/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
Keymessage The study revealed the major biological processes occurred at three developmental stages and identified candidate genes involved in primary vein development of birch plants. Vascular tissues usually mirror the surrounding leaf shape and its development plays a fundamental role in plant performance. However, the information of vascular development in birch trees, especially primary vein development, remains unclear. Therefore, we conducted the anatomical observation on primary veins from leaves at different development stages in Betula pendula 'Dalecarlica'. With the development of primary vein, dynamic changes in mechanical tissue thickness and primary vein diameter were consistent with each other, and the sum of phloem, xylem and cambium thickness was significantly varied. Transcriptome analysis indicated that primary vein development could be divided into three stages, namely Stage I, II and III, which were in aggreement with anatomical observation. Expression of marker genes associated with vascular tissues revealed that pro-vasculature development occurred at Stage I and II, and phloem development occurred at Stage III. GO enrichment analysis of differentially expressed genes (DEGs) showed that shared DEGs at Stage II were mainly engaged in cell division and cell cycle, and shared DEGs at Stage III were mainly engaged in phosphorylation. Decreased cell division and cell cycle as well as activation of lignin biosynthesis might contribute to primary vein development. Combining phenotypic traits, we performed weighted gene co-expression network analysis and identified a cytochrome P450 84A (CYP84A) family gene (BpF5H1). Based on analyses of gene families, expression patterns and yeast-two hybrid assay results, we proposed a potential electron transfer pathway involving BpF5H1 and three cytochrome b5 proteins during primary vein development in B. pendula 'Dalecarlica'. These results could shed some light on which biological processes occurred during primary vein formation and provide some valuable clues for vascular morphogenesis in woody plants.
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Affiliation(s)
- Xiuyan Bian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University and Chinese Academy of Forestry, Harbin 150040, China
| | - Xiaoyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University and Chinese Academy of Forestry, Harbin 150040, China
| | - Chang Qu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Manman Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Danyang Li
- Core facility of Wuhan University, Wuhan 430072, China
| | - Yunjiao Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University and Chinese Academy of Forestry, Harbin 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University and Chinese Academy of Forestry, Harbin 150040, China.
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Pereyra ME, Costigliolo Rojas C, Jarrell AF, Hovland AS, Snipes SA, Nagpal P, Alabadí D, Blázquez MA, Gutiérrez RA, Reed JW, Gray WM, Casal JJ. PIF4 enhances the expression of SAUR genes to promote growth in response to nitrate. Proc Natl Acad Sci U S A 2023; 120:e2304513120. [PMID: 37725643 PMCID: PMC10523462 DOI: 10.1073/pnas.2304513120] [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: 03/18/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023] Open
Abstract
Nitrate supply is fundamental to support shoot growth and crop performance, but the associated increase in stem height exacerbates the risks of lodging and yield losses. Despite their significance for agriculture, the mechanisms involved in the promotion of stem growth by nitrate remain poorly understood. Here, we show that the elongation of the hypocotyl of Arabidopsis thaliana, used as a model, responds rapidly and persistently to upshifts in nitrate concentration, rather than to the nitrate level itself. The response occurred even in shoots dissected from their roots and required NITRATE TRANSPORTER 1.1 (NRT1.1) in the phosphorylated state (but not NRT1.1 nitrate transport capacity) and NIN-LIKE PROTEIN 7 (NLP7). Nitrate increased PHYTOCHROME INTERACTING FACTOR 4 (PIF4) nuclear abundance by posttranscriptional mechanisms that depended on NRT1.1 and phytochrome B. In response to nitrate, PIF4 enhanced the expression of numerous SMALL AUXIN-UP RNA (SAUR) genes in the hypocotyl. The growth response to nitrate required PIF4, positive and negative regulators of its activity, including AUXIN RESPONSE FACTORs, and SAURs. PIF4 integrates cues from the soil (nitrate) and aerial (shade) environments adjusting plant stature to facilitate access to light.
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Affiliation(s)
- Matías Ezequiel Pereyra
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1417, Argentina
- Fundaciόn Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1405, Argentina
| | - Cecilia Costigliolo Rojas
- Fundaciόn Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1405, Argentina
| | - Anne F. Jarrell
- Department of Biology, University of North Carolina, Chapel Hill, NC27599-3280
| | - Austin S. Hovland
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - Stephen A. Snipes
- Department of Biology, University of North Carolina, Chapel Hill, NC27599-3280
| | - Punita Nagpal
- Department of Biology, University of North Carolina, Chapel Hill, NC27599-3280
| | - David Alabadí
- Instituto de Biologίa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia46022, Spain
| | - Miguel A. Blázquez
- Instituto de Biologίa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia46022, Spain
| | - Rodrigo A. Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago8331150, Chile
| | - Jason W. Reed
- Department of Biology, University of North Carolina, Chapel Hill, NC27599-3280
| | - William M. Gray
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - Jorge José Casal
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1417, Argentina
- Fundaciόn Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1405, Argentina
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Baker CR, Stewart JJ, Amstutz CL, Ching LG, Johnson JD, Niyogi KK, Adams WW, Demmig‐Adams B. Genotype-dependent contribution of CBF transcription factors to long-term acclimation to high light and cool temperature. PLANT, CELL & ENVIRONMENT 2022; 45:392-411. [PMID: 34799867 PMCID: PMC9299779 DOI: 10.1111/pce.14231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
When grown under cool temperature, winter annuals upregulate photosynthetic capacity as well as freezing tolerance. Here, the role of three cold-induced C-repeat-binding factor (CBF1-3) transcription factors in photosynthetic upregulation and freezing tolerance was examined in two Arabidopsis thaliana ecotypes originating from Italy (IT) or Sweden (SW), and their corresponding CBF1-3-deficient mutant lines it:cbf123 and sw:cbf123. Photosynthetic, morphological and freezing-tolerance phenotypes, as well as gene expression profiles, were characterized in plants grown from the seedling stage under different combinations of light level and temperature. Under high light and cool (HLC) growth temperature, a greater role of CBF1-3 in IT versus SW was evident from both phenotypic and transcriptomic data, especially with respect to photosynthetic upregulation and freezing tolerance of whole plants. Overall, features of SW were consistent with a different approach to HLC acclimation than seen in IT, and an ability of SW to reach the new homeostasis through the involvement of transcriptional controls other than CBF1-3. These results provide tools and direction for further mechanistic analysis of the transcriptional control of approaches to cold acclimation suitable for either persistence through brief cold spells or for maximisation of productivity in environments with continuous low temperatures.
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Affiliation(s)
- Christopher R. Baker
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jared J. Stewart
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
| | - Cynthia L. Amstutz
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Lindsey G. Ching
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jeffrey D. Johnson
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Krishna K. Niyogi
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - William W. Adams
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
| | - Barbara Demmig‐Adams
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
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Han S, Cho H, Noh J, Qi J, Jung HJ, Nam H, Lee S, Hwang D, Greb T, Hwang I. BIL1-mediated MP phosphorylation integrates PXY and cytokinin signalling in secondary growth. NATURE PLANTS 2018; 4:605-614. [PMID: 29988154 DOI: 10.1038/s41477-018-0180-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 05/17/2018] [Indexed: 05/03/2023]
Abstract
Vascular cambium proliferation in plants is crucial for the generation of vascular tissues and for mechanical strength. Phytohormones and mobile peptides are key regulators of vascular cambial activity during secondary growth; however, the signalling cross-talk underlying their coordinated action is largely unknown. Here, we reveal that BIN2-LIKE 1 (BIL1), a glycogen synthase kinase 3, integrates the PHLOEM INTERCALATED WITH XYLEM/tracheary element differentiation inhibitory factor (TDIF) RECEPTOR (PXY/TDR) module into MONOPTEROS/AUXIN RESPONSE FACTOR 5 (MP/ARF5) transcription factor action during secondary growth. BIL1-mediated phosphorylation of MP/ARF5 enhances its negative effect on vascular cambial activity, which upregulates the negative regulators of cytokinin signalling ARABIDOPSIS RESPONSE REGULATOR 7 (ARR7) and ARR15. PXY/TDR inhibits BIL1 activity, which attenuates the effect of MP/ARF5 on ARR7 and ARR15 expression, thus increasing vascular cambial activity. Together, these results suggest that BIL1 is a key mediator that links peptide signalling with auxin-cytokinin signalling for the maintenance of cambial activity.
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Affiliation(s)
- Soeun Han
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Hyunwoo Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Jaegyun Noh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Jiyan Qi
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Hee-Jung Jung
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Korea
| | - Heejae Nam
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Seungchul Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Daehee Hwang
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Korea
| | - Thomas Greb
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea.
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Jackson MDB, Duran-Nebreda S, Bassel GW. Network-based approaches to quantify multicellular development. J R Soc Interface 2017; 14:20170484. [PMID: 29021161 PMCID: PMC5665831 DOI: 10.1098/rsif.2017.0484] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/14/2017] [Indexed: 12/26/2022] Open
Abstract
Multicellularity and cellular cooperation confer novel functions on organs following a structure-function relationship. How regulated cell migration, division and differentiation events generate cellular arrangements has been investigated, providing insight into the regulation of genetically encoded patterning processes. Much less is known about the higher-order properties of cellular organization within organs, and how their functional coordination through global spatial relations shape and constrain organ function. Key questions to be addressed include: why are cells organized in the way they are? What is the significance of the patterns of cellular organization selected for by evolution? What other configurations are possible? These may be addressed through a combination of global cellular interaction mapping and network science to uncover the relationship between organ structure and function. Using this approach, global cellular organization can be discretized and analysed, providing a quantitative framework to explore developmental processes. Each of the local and global properties of integrated multicellular systems can be analysed and compared across different tissues and models in discrete terms. Advances in high-resolution microscopy and image analysis continue to make cellular interaction mapping possible in an increasing variety of biological systems and tissues, broadening the further potential application of this approach. Understanding the higher-order properties of complex cellular assemblies provides the opportunity to explore the evolution and constraints of cell organization, establishing structure-function relationships that can guide future organ design.
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Affiliation(s)
| | | | - George W Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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