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Huang ZH, Bao K, Jing ZH, Wang Q, Duan HF, Zhang S, Tao WW, Wu QN. Euryale Small Auxin Up RNA62 promotes cell elongation and seed size by altering the distribution of indole-3-acetic acid under the light. FRONTIERS IN PLANT SCIENCE 2022; 13:931063. [PMID: 36160968 PMCID: PMC9500450 DOI: 10.3389/fpls.2022.931063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/15/2022] [Indexed: 06/01/2023]
Abstract
Euryale (Euryale ferox Salisb.) is an aquatic crop used as both food and drug in Asia, but its utilization is seriously limited due to low yield. Previously, we hypothesized that Euryale small auxin up RNAs (EuSAURs) regulate seed size, but the underlying biological functions and molecular mechanisms remain unclear. Here, we observed that the hybrid Euryale lines (HL) generate larger seeds with higher indole-3-acetic acid (IAA) concentrations than those in the North Gordon Euryale (WT). Histological analysis suggested that a larger ovary in HL is attributed to longer cells around. Overexpression of EuSAUR62 in rice (Oryza sativa L.) resulted in larger glumes and grains and increased the length of glume cells. Immunofluorescence and protein interaction assays revealed that EuSAUR62 modulates IAA accumulation around the rice ovary by interacting with the rice PIN-FORMED 9, an auxin efflux carrier protein. Euryale basic region/leucine zipper 55 (EubZIP55), which was highly expressed in HL, directly binds to the EuSAUR62 promoter and activated the expression of EuSAUR62. Constant light increased the expression of both EubZIP55 and EuSAUR62 with auxin-mediated hook curvature in HL seedlings. Overall, we proposed that EuSAUR62 is a molecular bridge between light and IAA and plays a crucial role in regulating the size of the Euryale seed.
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Affiliation(s)
- Zhi-heng Huang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Ke Bao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Zong-hui Jing
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Qian Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Hui-fang Duan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Sen Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Wei-wei Tao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Qi-nan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
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2
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Barrera M, Hiriart M, Cocho G, Villarreal C. Type 2 diabetes progression: A regulatory network approach. CHAOS (WOODBURY, N.Y.) 2020; 30:093132. [PMID: 33003944 DOI: 10.1063/5.0011125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
In order to elucidate central elements underlying type 2 diabetes, we constructed a regulatory network model involving 37 components (molecules, receptors, processes, etc.) associated to signaling pathways of pancreatic beta-cells. In a first approximation, the network topology was described by Boolean rules whose interacting dynamics predicted stationary patterns broadly classified as health, metabolic syndrome, and diabetes stages. A subsequent approximation based on a continuous logic analysis allowed us to characterize the progression of the disease as transitions between these states associated to alterations of cell homeostasis due to exhaustion or exacerbation of specific regulatory signals. The method allowed the identification of key transcription factors involved in metabolic stress as essential for the progression of the disease. Integration of the present analysis with existent mathematical models designed to yield accurate account of experimental data in human or animal essays leads to reliable predictions for beta-cell mass, insulinemia, glycemia, and glycosylated hemoglobin in diabetic fatty rats.
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Affiliation(s)
- M Barrera
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - M Hiriart
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - G Cocho
- Instituto de Física, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - C Villarreal
- Instituto de Física, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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3
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Guzmán-Herrera A, Arias Del Angel JA, Rivera-Yoshida N, Benítez M, Franci A. Dynamical patterning modules and network motifs as joint determinants of development: Lessons from an aggregative bacterium. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:300-314. [PMID: 32419346 DOI: 10.1002/jez.b.22946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 03/26/2020] [Accepted: 04/04/2020] [Indexed: 12/15/2022]
Abstract
Development and evolution are dynamical processes under the continuous control of organismic and environmental factors. Generic physical processes, associated with biological materials and certain genes or molecules, provide a morphological template for the evolution and development of organism forms. Generic dynamical behaviors, associated with recurring network motifs, provide a temporal template for the regulation and coordination of biological processes. The role of generic physical processes and their associated molecules in development is the topic of the dynamical patterning module (DPM) framework. The role of generic dynamical behaviors in biological regulation is studied via the identification of the associated network motifs (NMs). We propose a joint DPM-NM perspective on the emergence and regulation of multicellularity focusing on a multicellular aggregative bacterium, Myxococcus xanthus. Understanding M. xanthus development as a dynamical process embedded in a physical substrate provides novel insights into the interaction between developmental regulatory networks and generic physical processes in the evolutionary transition to multicellularity.
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Affiliation(s)
- Alejandra Guzmán-Herrera
- Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico.,MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Juan A Arias Del Angel
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Natsuko Rivera-Yoshida
- Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alessio Franci
- Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
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4
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Allen HR, Ptashnyk M. Mathematical Modelling of Auxin Transport in Plant Tissues: Flux Meets Signalling and Growth. Bull Math Biol 2020; 82:17. [PMID: 31970524 PMCID: PMC6976557 DOI: 10.1007/s11538-019-00685-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/02/2019] [Indexed: 11/25/2022]
Abstract
Plant hormone auxin has critical roles in plant growth, dependent on its heterogeneous distribution in plant tissues. Exactly how auxin transport and developmental processes such as growth coordinate to achieve the precise patterns of auxin observed experimentally is not well understood. Here we use mathematical modelling to examine the interplay between auxin dynamics and growth and their contribution to formation of patterns in auxin distribution in plant tissues. Mathematical models describing the auxin-related signalling pathway, PIN and AUX1 dynamics, auxin transport, and cell growth in plant tissues are derived. A key assumption of our models is the regulation of PIN proteins by the auxin-responsive ARF-Aux/IAA signalling pathway, with upregulation of PIN biosynthesis by ARFs. Models are analysed and solved numerically to examine the long-time behaviour and auxin distribution. Changes in auxin-related signalling processes are shown to be able to trigger transition between passage- and spot-type patterns in auxin distribution. The model was also shown to be able to generate isolated cells with oscillatory dynamics in levels of components of the auxin signalling pathway which could explain oscillations in levels of ARF targets that have been observed experimentally. Cell growth was shown to have influence on PIN polarisation and determination of auxin distribution patterns. Numerical simulation results indicate that auxin-related signalling processes can explain the different patterns in auxin distributions observed in plant tissues, whereas the interplay between auxin transport and growth can explain the ‘reverse-fountain’ pattern in auxin distribution observed at plant root tips.
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Affiliation(s)
- Henry R Allen
- Department of Mathematics, Fulton Building, University of Dundee, Dundee, DD1 4HN, UK
| | - Mariya Ptashnyk
- Department of Mathematics, Colin Maclaurin Building, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
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Niklas KJ, Wayne R, Benítez M, Newman SA. Polarity, planes of cell division, and the evolution of plant multicellularity. PROTOPLASMA 2019; 256:585-599. [PMID: 30368592 DOI: 10.1007/s00709-018-1325-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/22/2018] [Indexed: 05/21/2023]
Abstract
Organisms as diverse as bacteria, fungi, plants, and animals manifest a property called "polarity." The literature shows that polarity emerges as a consequence of different mechanisms in different lineages. However, across all unicellular and multicellular organisms, polarity is evident when cells, organs, or organisms manifest one or more of the following: orientation, axiation, and asymmetry. Here, we review the relationships among these three features in the context of cell division and the evolution of multicellular polarity primarily in plants (defined here to include the algae). Data from unicellular and unbranched filamentous organisms (e.g., Chlamydomonas and Ulothrix) show that cell orientation and axiation are marked by cytoplasmic asymmetries. Branched filamentous organisms (e.g., Cladophora and moss protonema) require an orthogonal reorientation of axiation, or a localized cell asymmetry (e.g., "tip" growth in pollen tubes and fungal hyphae). The evolution of complex multicellular meristematic polarity required a third reorientation of axiation. These transitions show that polarity and the orientation of the future plane(s) of cell division are dyadic dynamical patterning modules that were critical for multicellular eukaryotic organisms.
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Affiliation(s)
- Karl J Niklas
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Randy Wayne
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Mariana Benítez
- Instituto de Ecología Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- C3, Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
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Rueda-Contreras MD, Romero-Arias JR, Aragón JL, Barrio RA. Curvature-driven spatial patterns in growing 3D domains: A mechanochemical model for phyllotaxis. PLoS One 2018; 13:e0201746. [PMID: 30114231 PMCID: PMC6095518 DOI: 10.1371/journal.pone.0201746] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/20/2018] [Indexed: 11/24/2022] Open
Abstract
Here we discuss the formation of phyllotactic patterns in the shoot apical meristem (SAM) of plants, where the spatial distribution of the phytohormone auxin determines phyllotaxis in a domain that is growing and changing in time. We assume that the concentration of auxin modifies the mechanical properties of the domain and that the mechanical stress field in the SAM orients the flux of auxin. To study this problem we propose a mechanism for pattern formation in growing domains with variable curvature. The dynamics of chemicals is modeled by a reaction-diffusion system that produces a three dimensional pattern of chemical concentrations that changes the stress field in the domain while growing. The growth process is modeled by a phase-field order parameter which determines the location of the boundaries of the domain. This field is coupled to the chemical concentration through a curvature term that affects the local mechanical stress in the domain. The local stress changes in turn modify the chemical patterns. Our model constitutes a useful and novel approach in theoretical biology, as many developmental processes in organisms seem to be affected by the changes of curvature, size, mechanical stress and other physical aspects. Several patterns seen in many plants are reproduced under certain conditions by our model.
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Affiliation(s)
- Mara D. Rueda-Contreras
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro 76230, Mexico
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Juriquilla, Querétaro 76230, Mexico
| | - José R. Romero-Arias
- CONACYT - Instituto de Física y Matemáticas, Universidad Michoacana, Ciudad Universitaria, Morelia, Michoacán 58040, Mexico
- Instituto de Matemáticas, Universidad Nacional Autónoma de México, Campus Juriquilla, Juriquilla, Querétaro 76230, Mexico
| | - José L. Aragón
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Juriquilla, Querétaro 76230, Mexico
- * E-mail:
| | - Rafael A. Barrio
- Instituto de Física, Universidad Nacional Autónoma de México, 01000 Ciudad de México, Mexico
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