14 NSFBIO: Bilateral NSF/BIO-BBSRC - Modeling the effects of intrinsic and extrinsic signaling on cellular differentiation in plants
Lead Research Organisation:
University of Cambridge
Department Name: Sainsbury Laboratory
Abstract
Despite the plasticity of plant development, cellular differentiation in plants is remarkably
robust, even in the presence of perturbations. Thus, a greater understanding of the complex
regulatory networks that control cellular development, and how they operate, interact, and
respond to intercellular and extracellular signals is urgently needed to generate plants with
increased biomass and stress-tolerance. We propose that emergent properties of gene regulatory
networks involved in cellular differentiation can be represented and tested mathematically
using information gained from development-specific transcriptomic signatures in response to
varying conditions. To test this hypothesis we are using as a model the Arabidopsis root phloem
sieve element, for which we have developed a unique set of molecular, mathematical, and physiological
tools. Because complete differentiation of the enucleated sieve elements takes place in a
very compressed manner, within 20 cells, SEs provide a cell differentiation model of unprecedented
cellular resolution. Our goal is to integrate development-specific transcriptomic, molecular
and imaging data, with information about known key regulators using a system of ordinary differential
equations and agent based modeling. This mathematical approach will allow us to gain a comprehensive
and quantitative perspective of the design rules governing the progression from stem cells
to their final stage of differentiation. We aim to iteratively improve the accuracy and strength
of our models by integrating additional data after exposing this cellular process to two disparate
perturbations; symplastic isolation and iron deficiency.
robust, even in the presence of perturbations. Thus, a greater understanding of the complex
regulatory networks that control cellular development, and how they operate, interact, and
respond to intercellular and extracellular signals is urgently needed to generate plants with
increased biomass and stress-tolerance. We propose that emergent properties of gene regulatory
networks involved in cellular differentiation can be represented and tested mathematically
using information gained from development-specific transcriptomic signatures in response to
varying conditions. To test this hypothesis we are using as a model the Arabidopsis root phloem
sieve element, for which we have developed a unique set of molecular, mathematical, and physiological
tools. Because complete differentiation of the enucleated sieve elements takes place in a
very compressed manner, within 20 cells, SEs provide a cell differentiation model of unprecedented
cellular resolution. Our goal is to integrate development-specific transcriptomic, molecular
and imaging data, with information about known key regulators using a system of ordinary differential
equations and agent based modeling. This mathematical approach will allow us to gain a comprehensive
and quantitative perspective of the design rules governing the progression from stem cells
to their final stage of differentiation. We aim to iteratively improve the accuracy and strength
of our models by integrating additional data after exposing this cellular process to two disparate
perturbations; symplastic isolation and iron deficiency.
Technical Summary
We propose to identify the transcriptional signature that describes the differentiation of phloem
tissue development. We currently have seven fluorescent marker lines spanning the longitudinal
axis of the root in an overlapping manner, representing different developmental time points of phloem
(SE) differentition. After protoplasting of different marker lines, gene expression profiles of
specific phloem cell populations will be obtained using fluorescence activated cell sorting (FACS)
coupled with RNA-seq.
We propose to build a mathematical model that simulates and predicts the dynamics of phloem
development from stem cells to their final stage of differentiation. A system of ODEs will model, first, at
a cellular level, the previously known regulating factors (some of them are mobile factors)
involved in phloem development. We will then implement the system of ODEs within different
cells along the same tissue into an agent based model (ABM). We will then add into the model signals
such as mobile transcription factors among cells.
We propose to quantitatively characterize SEs transcriptional changes in response to specific
perturbations, either by inhibiting cellular communication; or by challenging the system with
environmental stimuli. Hence, we will block cell-to-cell symplastic communication by depositing, in an
inducible manner, callose specifically between the developing SE cells; and we will subject plants to iron deficiency as this environmental perturbation may directly affect SE differentiation.
Gene expression analysis of cells with altered symplastic communication will allow us to
identify the genes involved in cell-intrinsic signals.
tissue development. We currently have seven fluorescent marker lines spanning the longitudinal
axis of the root in an overlapping manner, representing different developmental time points of phloem
(SE) differentition. After protoplasting of different marker lines, gene expression profiles of
specific phloem cell populations will be obtained using fluorescence activated cell sorting (FACS)
coupled with RNA-seq.
We propose to build a mathematical model that simulates and predicts the dynamics of phloem
development from stem cells to their final stage of differentiation. A system of ODEs will model, first, at
a cellular level, the previously known regulating factors (some of them are mobile factors)
involved in phloem development. We will then implement the system of ODEs within different
cells along the same tissue into an agent based model (ABM). We will then add into the model signals
such as mobile transcription factors among cells.
We propose to quantitatively characterize SEs transcriptional changes in response to specific
perturbations, either by inhibiting cellular communication; or by challenging the system with
environmental stimuli. Hence, we will block cell-to-cell symplastic communication by depositing, in an
inducible manner, callose specifically between the developing SE cells; and we will subject plants to iron deficiency as this environmental perturbation may directly affect SE differentiation.
Gene expression analysis of cells with altered symplastic communication will allow us to
identify the genes involved in cell-intrinsic signals.
Planned Impact
Who will benefit?
(1) Academic researchers interested in development
(2) The agro-biotech, forestry and plant breeding communities
(3) The general public
How will they benefit?
(1) This research is basic by nature. It explores how the "food conductive" cells, sieve elements of phloem are differentiating from the stem cell at a molecular level and how during this process the cell exchanges information with the neighbouring cells. We will use this as a paradigm for cell differentiation in plants in general. By publishing in visible journals, this research will be made widely available. Furthermore, during this work we will generate high quality datasets and submit these to public depositories so that they may be mined by other researchers to facilitate multiple research topics. Understanding vascular development is also significant for understanding evolution of terrestrial plants.
(2) Phloem is a major carbon allocation route in plants. Therefore, understanding how phloem development is controlled and how this important long-distance transport pathway is built up has important implications for various applied plant sciences, covering both field crops as well as forest trees.
(3) Plants represents an interesting adaptation for terrestrial life. Phloem is a key innovation during this adaptation. Therefore, basic understanding on how the transporting cells of phloem develop increases also general knowledge of the important, distinctive features of plants.
(1) Academic researchers interested in development
(2) The agro-biotech, forestry and plant breeding communities
(3) The general public
How will they benefit?
(1) This research is basic by nature. It explores how the "food conductive" cells, sieve elements of phloem are differentiating from the stem cell at a molecular level and how during this process the cell exchanges information with the neighbouring cells. We will use this as a paradigm for cell differentiation in plants in general. By publishing in visible journals, this research will be made widely available. Furthermore, during this work we will generate high quality datasets and submit these to public depositories so that they may be mined by other researchers to facilitate multiple research topics. Understanding vascular development is also significant for understanding evolution of terrestrial plants.
(2) Phloem is a major carbon allocation route in plants. Therefore, understanding how phloem development is controlled and how this important long-distance transport pathway is built up has important implications for various applied plant sciences, covering both field crops as well as forest trees.
(3) Plants represents an interesting adaptation for terrestrial life. Phloem is a key innovation during this adaptation. Therefore, basic understanding on how the transporting cells of phloem develop increases also general knowledge of the important, distinctive features of plants.
People |
ORCID iD |
| Yka Helariutta (Principal Investigator) |
Publications
Abou-Saleh RH
(2018)
Interactions between callose and cellulose revealed through the analysis of biopolymer mixtures.
in Nature communications
Alonso-Serra J
(2019)
Tissue-specific study across the stem reveals the chemistry and transcriptome dynamics of birch bark.
in The New phytologist
Baesso B
(2018)
Transcription factors PRE3 and WOX11 are involved in the formation of new lateral roots from secondary growth taproot in A. thaliana.
in Plant biology (Stuttgart, Germany)
Blob B
(2018)
Phloem differentiation: an integrative model for cell specification.
in Journal of plant research
Hellmann E
(2018)
Plant Vascular Tissues-Connecting Tissue Comes in All Shapes.
in Plants (Basel, Switzerland)
Heo JO
(2017)
Differentiation of conductive cells: a matter of life and death.
in Current opinion in plant biology
Kalantzi S
(2019)
General Approach for the Liquid-Phase Fragment Synthesis of Orthogonally Protected Naturally Occurring Polyamines and Applications Thereof.
in The Journal of organic chemistry
Kalmbach L
(2019)
Sieve Plate Pores in the Phloem and the Unknowns of Their Formation.
in Plants (Basel, Switzerland)
Kim H
(2020)
SHORTROOT-Mediated Intercellular Signals Coordinate Phloem Development in Arabidopsis Roots.
in The Plant cell
| Description | In this project we want to understand how gene expression is controlled when a plant cell differentiates from a stem cell to an enucleate sieve element of phloem, a major transporting conduit in plants. We have determined here that the differentiation cascade is 19 cells long. We have now been able to establish molecular markers that allow cell sorting and further analysis of dynamics in gene expression in this stretch. We have also carried out single cell transcriptomics approach. We have now also identified a set of interesting markers with which we may be able to anchor the cell identities to the transcroptional trajectory. We have also identified some key molecular players controlling the timing of gene expression along this temporal gradient.These factors include both transcriptional as well as cell polarity related effectors. |
| Exploitation Route | We are describing here in an unprecedented detail how gene expression changes when a plant cell differentiated. We will create an atlas of gene expression, which is likely to be an important source of information for others. |
| Sectors | Agriculture, Food and Drink,Education |
| Description | Together with the University of Helsinki and University of Ghent, University of Cambridge has filed a patent application "Means and methods to increasse organ size in plants" on the role of DOF transcription factors in promoting growth in plants. |
| First Year Of Impact | 2015 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic |
| Description | Modeling the effects of intrinsic and extrinsic signaling on cellular differentiation in plants |
| Organisation | North Carolina State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Yka Helariutta has expertise in genetic analysis of vascular development as well as in symplastic communication during plant morphogenesis. |
| Collaborator Contribution | Terri Long has experience in molecular analysis and mathematical modeling of plant responses to nutrient availability, Ross Sozzani provides expertise in computational analyses of cell-type specific gene regulatory networks (GRNs) and dynamic mathematical modeling. |
| Impact | null |
| Start Year | 2015 |
| Title | Means and methods to increase organ size in plants |
| Description | While apical growth in plants initiates upon seed germination, radial growth is only primed during early ontogenesis in procambium cells and activated later by the vascular cambium. Although it is not known how radial growth is organized and regulated in plants, the system resembles the development competence observed in some animal systems, in which pre-existing patterns of developmental potential are established early on. Here, we show that the initiation of radial growth occurs around early protophloem sieve element (PSE) cell files of the root procambial tissue in Arabidopsis. In this domain cytokinin signalling promotes expression of a pair of novel mobile transcription factors, PHLOEM EARLY DOF (PEAR1, PEAR2) and their four homologs (DOF6, TMO6, OBP2 and HCA2), collectively called PEAR proteins. The PEAR proteins form a short-range concentration gradient peaking at PSE and activating gene expression that promotes radial growth. The expression and function of PEAR proteins are antagonized by well-established polarity transcription factors, HD-ZIP III, whose expression is concentrated in the more internal domain of radially non-dividing procambial cells by the function of auxin and mobile miR165/166. The PEAR proteins locally promote transcription of their inhibitory HD-ZIP III genes, thereby establishing a negative feedback loop that forms a robust boundary demarking the zone of cell divisions. Taken together, we have established a network, in which the PEAR - HD-ZIP III module integrates spatial information of the hormonal domains and miRNA gradients during root procambial development, to provide adjacent zones of dividing and more quiescent cells as foundation for future radial growth. |
| IP Reference | |
| Protection | Patent application published |
| Year Protection Granted | 2018 |
| Licensed | No |
| Impact | This patent was filed, but given there was no commercial interest in the first few years, the extension has not been funded, so the official status now is 'lapsed'. Still, this was an actual filed patent from 2018 until 06-05-2020. |