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Santos Teixeira J, van den Berg T, ten Tusscher K. Complementary roles for auxin and auxin signalling revealed by reverse engineering lateral root stable prebranch site formation. Development 2022; 149:279332. [PMID: 36314783 PMCID: PMC9793420 DOI: 10.1242/dev.200927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022]
Abstract
Priming is the process through which periodic elevations in auxin signalling prepattern future sites for lateral root formation, called prebranch sites. Thus far, the extent to which elevations in auxin concentration and/or auxin signalling are required for priming and prebranch site formation has remained a matter of debate. Recently, we discovered a reflux-and-growth mechanism for priming generating periodic elevations in auxin concentration that subsequently dissipate. Here, we reverse engineer a mechanism for prebranch site formation that translates these transient elevations into a persistent increase in auxin signalling, resolving the prior debate into a two-step process of auxin concentration-mediated initial signal and auxin signalling capacity-mediated memorization. A crucial aspect of the prebranch site formation mechanism is its activation in response to time-integrated rather than instantaneous auxin signalling. The proposed mechanism is demonstrated to be consistent with prebranch site auxin signalling dynamics, lateral inhibition, and symmetry-breaking mechanisms and perturbations in auxin homeostasis.
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Affiliation(s)
- Joana Santos Teixeira
- Computational Developmental Biology Group, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Thea van den Berg
- Computational Developmental Biology Group, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Kirsten ten Tusscher
- Computational Developmental Biology Group, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands,Author for correspondence ()
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van den Herik B, ten Tusscher K. Undirected Sucrose Efflux Mitigation by the FT-Like SP6A Preferentially Enhances Tuber Resource Partitioning. Front Plant Sci 2022; 13:817909. [PMID: 35615135 PMCID: PMC9125184 DOI: 10.3389/fpls.2022.817909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/18/2022] [Indexed: 06/15/2023]
Abstract
The yield of harvestable plant organs depends on overall photosynthetic output and the subsequent distribution of the produced assimilates from source leaves across different sink organs. In this study, we aimed to obtain, using a two-sink transport model, mechanistic understanding of how the interplay between sink and pathway properties together determines sink resource partitioning. As a working example, we analyzed the partitioning of resources within potato plants, investigating the determinants of tuber sink yield. Our results indicated that, contrary to earlier studies, with a spatially explicit biophysically detailed model, transport pathway properties significantly affect sink resource partitioning within the physiologically relevant domain. Additionally, we uncovered that xylem flow, through its hydraulic coupling to the phloem, and sucrose efflux along the phloem, also significantly affected resource partitioning. For tubers, it is the cumulative disadvantage compared to sink leaves (distance, xylem flow, and sucrose efflux) that enable an undirected SP6A-mediated reduction of sucrose efflux to preferentially benefit tuber resource partitioning. Combined with the SP6A-mediated sink strength increase, undirected SP6A introduction significantly enhances tuber resource partitioning.
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van Schijndel L, Snoek BL, ten Tusscher K. Embodiment in distributed information processing: "Solid" plants versus "liquid" ant colonies. Quant Plant Biol 2022; 3:e27. [PMID: 37077985 PMCID: PMC10095861 DOI: 10.1017/qpb.2022.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 05/02/2023]
Abstract
Information processing is an essential part of biology, enabling coordination of intra-organismal processes such as development, environmental adaptation and inter-organismal communication. Whilst in animals with specialised brain tissue a substantial amount of information processing occurs in a centralised manner, most biological computing is distributed across multiple entities, such as cells in a tissue, roots in a root system or ants in a colony. Physical context, called embodiment, also affects the nature of biological computing. While plants and ant colonies both perform distributed computing, in plants the units occupy fixed positions while individual ants move around. This distinction, solid versus liquid brain computing, shapes the nature of computations. Here we compare information processing in plants and ant colonies, highlighting how similarities and differences originate in, as well as make use of, the differences in embodiment. We end with a discussion on how this embodiment perspective may inform the debate on plant cognition.
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Affiliation(s)
- Laura van Schijndel
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Basten L. Snoek
- Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Kirsten ten Tusscher
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Author for correspondence: K. ten Tusscher, E-mail:
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van den Herik B, Bergonzi S, Bachem CWB, ten Tusscher K. Modelling the physiological relevance of sucrose export repression by an Flowering Time homolog in the long-distance phloem of potato. Plant Cell Environ 2021; 44:792-806. [PMID: 33314152 PMCID: PMC7986384 DOI: 10.1111/pce.13977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 05/31/2023]
Abstract
Yield of harvestable plant organs depends on photosynthetic assimilate production in source leaves, long-distance sucrose transport and sink-strength. While photosynthesis optimization has received considerable interest for optimizing plant yield, the potential for improving long-distance sucrose transport has received far less attention. Interestingly, a recent potato study demonstrates that the tuberigen StSP6A binds to and reduces activity of the StSWEET11 sucrose exporter. While the study suggested that reducing phloem sucrose efflux may enhance tuber yield, the precise mechanism and physiological relevance of this effect remained an open question. Here, we develop the first mechanistic model for sucrose transport, parameterized for potato plants. The model incorporates SWEET-mediated sucrose export, SUT-mediated sucrose retrieval from the apoplast and StSP6A-StSWEET11 interactions. Using this model, we were able to substantiate the physiological relevance of the StSP6A-StSWEET11 interaction in the long-distance phloem for potato tuber yield, as well as to show the non-linear nature of this effect.
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Affiliation(s)
- Bas van den Herik
- Computational Developmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Sara Bergonzi
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
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Autran D, Bassel GW, Chae E, Ezer D, Ferjani A, Fleck C, Hamant O, Hartmann FP, Jiao Y, Johnston IG, Kwiatkowska D, Lim BL, Mahönen AP, Morris RJ, Mulder BM, Nakayama N, Sozzani R, Strader LC, ten Tusscher K, Ueda M, Wolf S. What is quantitative plant biology? Quant Plant Biol 2021; 2:e10. [PMID: 37077212 PMCID: PMC10095877 DOI: 10.1017/qpb.2021.8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.
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Affiliation(s)
- Daphné Autran
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - George W. Bassel
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Daphne Ezer
- The Alan Turing Institute, London, United Kingdom
- Department of Statistics, University of Warwick, Coventry, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | - Christian Fleck
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Breisgau, Germany
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, École normale supérieure (ENS) de Lyon, Université Claude Bernard Lyon (UCBL), Lyon, France
- Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), CNRS, Université de Lyon, Lyon, France
- Author for correspondence: O. Hamant and A. P. Mahönen, E-mail: ,
| | | | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Dorota Kwiatkowska
- Institute of Biology, Biotechnology and Environment Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Boon L. Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Ari Pekka Mahönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Richard J. Morris
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Bela M. Mulder
- Department of Living Matter, Institute AMOLF, Amsterdam, The Netherlands
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Ross Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North CarolinaUSA
| | - Lucia C. Strader
- Department of Biology, Duke University, Durham, North Carolina, USA
- NSF Science and Technology Center for Engineering Mechanobiology, Department of Biology, Washington University in St. Louis, St. Louis, MissouriUSA
| | - Kirsten ten Tusscher
- Theoretical Biology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Minako Ueda
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Sebastian Wolf
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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Abstract
Spatial patterns of the hormone auxin are important drivers of plant development. The observed feedback between the active, directed transport that generates auxin patterns and the auxin distribution that influences transport orientation has rendered this a popular subject for modelling studies. Here we propose a new mathematical framework for the analysis of polar auxin transport and present a detailed mathematical analysis of published models. We show that most models allow for self-organised patterning for similar biological assumptions, and find that the pattern generated is typically unidirectional, unless additional assumptions or mechanisms are incorporated. Our analysis thus suggests that current models cannot explain the bidirectional fountain-type patterns found in plant meristems in a fully self-organised manner, and we discuss future research directions to address the gaps in our understanding of auxin transport mechanisms.
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Affiliation(s)
- Klaartje van Berkel
- Molecular Genetics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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