Computational modeling of cambium activity provides a regulatory framework for simulating radial plant growth
- Centre for Organismal Studies, Heidelberg University, Germany
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, Italy
- Gregor Mendel Institute, Vienna Biocenter, Austria
- Mathematical Institute, Leiden University, Netherlands
- Institute of Biology, Leiden University, Netherlands
- BioQuant, Heidelberg University, Germany
Figures
Figure 1
Generation of the initial model.
(A) Tissue template used to run VirtualLeaf simulations. Phloem* is depicted in purple, xylem* in red. Cambium cells* are colored according to their levels of PXY* and PXY-active*. Cambium* is …
Figure 2 with 1 supplement
Implementing phloem formation into the model.
(A) Cross-section of a wild-type hypocotyl expressing PXYpro:CFP (blue) and SMXL5pro:YFP (green). Cell walls are stained by Direct Red 23, mainly visualizing xylem (red). Only a sector of the …
Figure 2—figure supplement 1
Wild type control for fluorescent reporter analyses and color-blind modes for images shown in main figures.
(A) A hypocotyl cross-section from a wild-type plant not carrying any transgene, which was stained and imaged in the same way as, for example, the section shown in Figure 2A. The signal detected in …
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Figure 2—figure supplement 1—source data 1
Raw image data collected for Figure 2—figure supplement 1.
- https://cdn.elifesciences.org/articles/66627/elife-66627-fig2-figsupp1-data1-v2.zip
Figure 3 with 6 supplements
Comparing the effect of perturbing cambium activity in the model and in plants.
(A) Cross-section of a hypocotyl carrying PXYpro:CFP (blue), SMXL5pro:YFP (green) markers, and the IRX3pro:CLE41 transgene. Cell walls are stained by Direct Red 23 visualizing mostly xylem (red). …
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Figure 3—source data 1
Source data for cell type classification using ilastik.
- https://cdn.elifesciences.org/articles/66627/elife-66627-fig3-data1-v2.zip
Figure 3—figure supplement 1
First example revealing the dynamics of PXYpro:CFP/SMXL5pro:YFP activities during radial hypocotyl growth in wild-type, IRX3pro:CLE41, and pxy plants.
(A–D) PXYpro:CFP (blue) and SMXL5pro:YFP (green) activities at different stages of wild-type hypocotyl development from young (A)to old (D).(E–H) PXYpro:CFP (blue) and SMXL5pro:YFP (green) …
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Figure 3—figure supplement 1—source data 1
Raw image data collected for Figure 3—figure supplement 1, first part.
- https://cdn.elifesciences.org/articles/66627/elife-66627-fig3-figsupp1-data1-v2.zip
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Figure 3—figure supplement 1—source data 2
Raw image data collected for Figure 3—figure supplement 1, second part.
- https://cdn.elifesciences.org/articles/66627/elife-66627-fig3-figsupp1-data2-v2.zip
Figure 3—figure supplement 2
Second example revealing the dynamics of PXYpro:CFP/SMXL5pro:YFP activities during radial hypocotyl growth in wild-type, IRX3pro:CLE41, and pxy plants.
(A–D) PXYpro:CFP (blue) and SMXL5pro:YFP (green) activities at different stages of wild-type hypocotyl development from young (A)to old (D).(E–H) PXYpro:CFP (blue) and SMXL5pro:YFP (green) …
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Figure 3—figure supplement 2—source data 1
Raw image data collected for Figure 3—figure supplement 2, first part.
- https://cdn.elifesciences.org/articles/66627/elife-66627-fig3-figsupp2-data1-v2.zip
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Figure 3—figure supplement 2—source data 2
Raw image data collected for Figure 3—figure supplement 2, second part.
- https://cdn.elifesciences.org/articles/66627/elife-66627-fig3-figsupp2-data2-v2.zip
Figure 3—figure supplement 3
First example revealing the dynamics of PXYpro:CFP/SMXL5pro:YFP activities during radial hypocotyl growth in wild-type, IRX3pro:CLE41, and pxy plants (color-blind mode).
(A–D) PXYpro:CFP (blue) and SMXL5pro:YFP (green) activities at different stages of wild-type hypocotyl development from young (A)to old (D).(E–H) PXYpro:CFP (blue) and SMXL5pro:YFP (green) …
Figure 3—figure supplement 4
Second example revealing the dynamics of PXYpro:CFP/SMXL5pro:YFP activities during radial hypocotyl growth in wild-type, IRX3pro:CLE41, and pxy plants (color-blind mode).
(A–D) PXYpro:CFP (blue) and SMXL5pro:YFP (green) activities at different stages of wild-type hypocotyl development from young (A)to old (D).(E–H) PXYpro:CFP (blue) and SMXL5pro:YFP (green) …
Figure 3—figure supplement 5
Close-up revealing the dynamics of PXYpro:CFP/SMXL5pro:YFP activities in hypocotyls in wild-type and pxy plants.
(A–C) Three examples showing PXYpro:CFP (top, bottom, in magenta) and SMXL5pro:YFP (middle, bottom, in green) activities in the cambium zone of wild-type plants. Scale bar in (A): 20µm. Same …
Figure 3—figure supplement 6
Overview and magnifications of sections used for cell-type classification shown in Figure 3.
Original toluidine-stained cross-sections (A, D), cross-section with cell-type classifications (B, E), and magnifications of regions indicated by black rectangles in (B) and (E) (C, F)for wild type …
Figure 4 with 3 supplements
An extended model for simulating genetic perturbations of cambium activity.
(A) Regulatory network proposed based on experimental observations. (B) Result of the simulation run for Model 3A. This model implements the network interactions described in (A). Color coding at …
Figure 4—figure supplement 1
Overview of cell types*, regulatory interactions and expression* profiles in Model 3.
Schemes include representations for Models 3B and C. Color code shown at the bottom of the figure.
Figure 4—figure supplement 2
Determination of cell wall thickness across the radial sequence of hypocotyl tissues.
(A) Cross-section of a 4.5-week-old plant stained by Direct Red 23. Radius and circumference used by the ‘Radial Profile’ function of the Fiji image analysis tool (Schindelin et al., 2012) are …
Figure 4—figure supplement 3
Behavior of the different model parameterizations (Model 4:2–5).
(A) Overview of parameter values of the different parameter sets. Shown are the relative values of the estimated parameter compared to the original parameter values. Horizontal lines indicate the …
Figure 5 with 4 supplements
Effect of xylem cell wall stiffness* on the radiality of cambium-derived cell lineages*.
(A) Final output of Model 4 and parameter set 1. (B) Visualization of the relative levels of chemicals* and division rates* in different bins. Bin colors along the x-axis correspond to the different …
Figure 5—figure supplement 1
Distribution of cell* properties under different xylem ‘stiffness’ regimes.
(A) Cell* size in arbitrary units. (B) Major axis lengths of cells* in arbitrary units. (C) Numbers of nodes (vertexes) per cell*. (D) Number of cells* among cell types and stiffness values for n = …
Figure 5—figure supplement 2
Distribution of cell* properties under different tissue boundary (=epidermis*) ‘stiffness’ regimes.
(A) Cell* size in arbitrary units. (B) Major axis lengths of cells* in arbitrary units. (C) Numbers of nodes (vertexes) per cell*. (D) Number of cells* among cell types and stiffness values for n = …
Figure 5—figure supplement 3
Fraction of median relative amount of cell lineages for parameter sets 2–5 for n = 30 simulations and n ≥ 60 lineages.
(A) With increasing xylem* ‘stiffness’.(B) With increasing epidermis* ‘stiffness’. KW-significance is indicated as follows: (*) p-value ≤ 0.05, (**) p-value ≤ 0.001 and (***) p value ≤ 1 E-5.
Figure 5—figure supplement 4
Fraction of median relative amount of cell lineages at different parameters governing cell wall* dynamics.
The model parameters cell walls’ target length and yielding threshold were varied by± 50%and the behavior at different cell wall stiffness values simulated. The statistical analysis was done as …
Appendix 1—figure 1
Cell wall calculations during node movement.
Node 5 is moved to a new position. During calculations, the change in wall elements between nodes 5 and 6, 5 and 7, as well as 5 and 4 is considered. The cell-specific stiffness of the wall elements …
Videos
Video 1
Model 1 output, visualizing xylem (red) and phloem (purple), and accumulation of PXY* (blue) and PXYactive* (green).
Video 2
Model 1 output, visualizing CLE41* (yellow) accumulation.
Video 3
Model 1 output, visualizing cell divisions (red).
Video 4
Model 1 output, visualizing PXYactive*.
Video 5
Model 1 output, visualizing PXY*.
Video 6
Model 2A output, visualizing xylem (red) and phloem (purple), and accumulation of PXY* (blue) and PXY-active* (green).
Video 7
Model 2A output, visualizing CLE41* (yellow) accumulation.
Video 8
Model 2A output, visualizing cell divisions (red).
Video 9
Model 2A output, visualizing cell divisions (red) together with PXY* (blue) and PXY-active* (green) accumulation.
Video 10
Model 2A output, visualizing PXYactive*.
Video 11
Model 2A output, visualizing PXY*.
Video 12
Model 2B output, visualizing xylem (red) and phloem (purple), and accumulation of PXY* (blue), and PXY-active* (green).
Video 13
Model 2B output, visualizing CLE41* (yellow) accumulation.
Video 14
Model 2B output, visualizing cell divisions (red).
Video 15
Model 2B output, visualizing accumulation of PXY* (blue) and PXY-active* (green).
Video 16
Model 2B output, visualizing PXYactive*.
Video 17
Model 2B output, visualizing PXY*.
Video 18
Model 3A output, visualizing xylem (red), phloem parenchyma (light purple), and phloem poles (dark purple), and accumulation of PXY* (blue) and the division chemical (DF)* (green).
Video 19
Model 3A output, visualizing CLE41* (yellow) accumulation.
Video 20
Model 3A output, visualizing cell divisions (red).
Video 21
Model 3A output, visualizing accumulation of PXY* (blue) and PXYactive* (green).
Video 22
Model 3A output, visualizing PXYactive*.
Video 23
Model 3A output, visualizing PXY*.
Video 24
Model 3B output, visualizing xylem (red), phloem parenchyma (light purple), and phloem poles (dark purple), and accumulation of PXY* (blue) and the division chemical (DF)* (green).
Video 25
Model 3B output, visualizing CLE41* (yellow) accumulation.
Video 26
Model 3B output, visualizing cell divisions (red).
Video 27
Model 3B output, visualizing accumulation of PXY* (blue) and PXYactive* (green).
Video 28
Model 3B output, visualizing PXYactive*.
Video 29
Model 3B output, visualizing PXY*.
Video 30
Model 3C output, visualizing xylem (red), phloem parenchyma (light purple), and phloem poles (dark purple), and accumulation of PXY* (blue) and the division chemical (DF)* (green).
Video 31
Model 3C output, visualizing CLE41* (yellow) accumulation.
Video 32
Model 3C output, visualizing cell divisions (red).
Video 33
Model 3C output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green).
Video 34
Model 3C output, visualizing PXYactive*.
Video 35
Model 3C output, visualizing PXY*.
Video 36
Model 4 output, parameter Set 1, visualizing xylem (red), phloem parenchyma (light purple), and phloem poles (dark purple), and accumulation of PXY* (blue) and the division chemical (DF)* (green).
Video 37
Model 4 output, parameter set 1, visualizing CLE41* (yellow) accumulation.
Video 38
Model 4 output, parameter set 1, cell divisions (red).
Video 39
Model 4 output, parameter set 1, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green).
Video 40
Model 4 output, parameter set 1, visualizing PXYactive*.
Video 41
Model 4 output, parameter set 1, visualizing PXY*.
Video 42
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green) implementing a 0.1-fold change in xylem* cell wall stiffness.
Video 43
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green) implementing a 0.5-fold change in xylem* cell wall stiffness.
Video 44
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green) at experimentally determined xylem cell wall stiffness.
Video 45
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green), implementing a 5-fold increase in xylem* cell wall stiffness.
Video 46
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green), a tenfold increase in xylem* cell wall stiffness.
Video 47
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green), a 50-fold increase in xylem* cell wall stiffness.
Video 48
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green) implementing a 0.1-fold change in epidermis* cell wall stiffness.
Video 49
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green) implementing a 0.5-fold change in epidermis* cell wall stiffness.
Video 50
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green) at experimentally determined epidermis* cell wall stiffness.
Video 51
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green), implementing a fivefold increase in epidermis* cell wall stiffness.
Video 52
Model 4 output, visualizing accumulation of PXY* (blue) and the division chemical (DF)* (green), a tenfold increase in epidermis* cell wall stiffness.
Additional files
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Supplementary file 1
Table listing cell* behavior rules for Models 1–4.
- https://cdn.elifesciences.org/articles/66627/elife-66627-supp1-v2.docx
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Supplementary file 2
Table listing parameter values and chemical thresholds after parameter estimation.
- https://cdn.elifesciences.org/articles/66627/elife-66627-supp2-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/66627/elife-66627-transrepform1-v2.pdf
