22 results on '"Mellor, Nathan L."'
Search Results
2. Multiscale modelling of plant hormone signalling : auxin regulated lateral root emergence
- Author
-
Mellor, Nathan L.
- Subjects
575.5438 ,QK640 Plant anatomy ,QK710 Plant physiology - Abstract
The formation of lateral roots is an important post-embryonic developmental process that allows plants to adapt to their environment via exploitation of soil mineral resources. New lateral roots initiate as lateral root primordia (LRP) in the pericycle cell layer adjacent to the central vascular tissue in the primary root, and must pass through the outer cell layers of endodermis, cortex and epidermis to emerge as mature roots. A key regulator of emergence is the plant hormone auxin and it has been shown previously that in Arabidopsis the auxin induced expression of the auxin influx carrier LAX3 in specific cortical cells over LRP is required for emergence to occur, as this leads to the expression of cell wall remodelling enzymes such as polygalacturonase (PG). By developing mathematical models of auxin transport and LAX3 expression the work in the thesis aims to test the existing conceptual models for lateral root emergence, and provide testable hypotheses for the existence of additional gene regulatory components. An initial single cell model demonstrates that hysteresis and bistability may explain the experimentally observed 'all-or-nothing' LAX3 spatial expression pattern in cortical cells containing a gradient of auxin concentrations. By fitting model parameters against experimental data, the model is then used to show that some auxin homeostasis mechanism is present, with both endogenous and exogenous sources of homeostasis investigated. The single cell model also investigates the validity of several alternative gene regulatory networks for LAX3, and its apparent repression by a key mediator of the auxin response, ARF19. Finally, the model is extended to a multicellular context, in which the auxin distribution from a simulated LRP source cell is used as a basis for the expression of LAX3, leading to the expression of PG in specific cells between which the LRP must pass.
- Published
- 2013
3. Systems approaches reveal that ABCB and PIN proteins mediate co-dependent auxin efflux
- Author
-
Mellor, Nathan L, Ware, Alexander, Janes, George, Barrack, Duncan, Bishopp, Anthony, Bennett, Malcolm J, Geisler, Markus, Wells, Darren M, and Band, Leah R
- Subjects
Cell Biology ,Plant Science - Abstract
Members of the B family of membrane-bound ATP-binding cassette (ABC) transporters represent key components of the auxin-efflux machinery in plants. Over the last two decades experimental studies have shown that modifying ABCB expression affects auxin distribution and plant phenotypes. However, precisely how ABCB proteins transport auxin in conjunction with the more widely studied family of PIN-formed (PIN) auxin efflux transporters is unclear, and studies using heterologous systems have produced conflicting results.Here, we integrate ABCB localization data into a multicellular model of auxin transport in the Arabidopsis thaliana root tip to predict how ABCB-mediated auxin transport impacts organ-scale auxin distribution. We use our model to test five potential ABCB–PIN regulatory interactions, simulating the auxin dynamics for each interaction and quantitatively comparing the predictions with experimental images of the DII-VENUS auxin reporter in wild type and abcb single and double loss-of-function mutants. Only specific ABCB–PIN regulatory interactions result in predictions that recreate the experimentally observed DII-VENUS distributions and long-distance auxin transport. Our results suggest that ABCBs enable auxin efflux independently of PINs; however, PIN-mediated auxin efflux is predominantly through a co-dependent efflux where co-localised with ABCBs.
- Published
- 2022
4. Auxin fluxes through plasmodesmata modify root-tip auxin distribution
- Author
-
Mellor, Nathan L., primary, Voß, Ute, additional, Janes, George, additional, Bennett, Malcolm J., additional, Wells, Darren M., additional, and Band, Leah R., additional
- Published
- 2020
- Full Text
- View/download PDF
5. Dynamic regulation of auxin oxidase and conjugating enzymes AtDAO1 and GH3 modulates auxin homeostasis
- Author
-
Mellor, Nathan L., Band, Leah. R., Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Owen, Markus R., and Bennett, Malcolm J.
- Subjects
Hormone Regulation, Auxin, Metabolism, Homeostasis, Arabidopsis Thaliana ,fungi ,food and beverages ,heterocyclic compounds - Abstract
Auxin is a key hormone regulating plant growth and development. We combine experiments and mathematical modeling to reveal how auxin levels are maintained via feedback regulation of genes encoding key metabolic enzymes. We describe how regulation of auxin oxidation via transcriptional control of Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1 (AtDAO1) expression is important at low to normal auxin concentrations. In contrast, higher auxin levels lead to increased Gretchen Hagen3 expression and auxin conjugation. Integrating this understanding into a multicellular model of root auxin dynamics successfully predicts that the dao1-1 mutant has an auxin-dependent longer root hair phenotype. Our findings reveal the importance of auxin homeostasis to maintain this hormone at optimal levels for plant growth and development.
- Published
- 2016
6. Dynamic regulation of AtDAO1 and GH3 modulates auxin homeostasis
- Author
-
Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., and Owen, Markus R.
- Subjects
fungi ,food and beverages ,heterocyclic compounds - Abstract
The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by AtDAO1/2 and conjugation by GH3s. Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product oxIAA, an increase in the conjugated forms IAA-Asp and IAA-Glu of 438-fold and 240-fold respectively, while auxin remains close to wild type. By fitting parameter values to a mathematical model of these metabolic pathways we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1. We then quantified gene expression in plantae, and found that transcripts of AtDAO1 and GH3 genes are increased in response to auxin, over different time scales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, while auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues, in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1, acting in concert with GH3, to maintain auxin at optimal levels for plant growth and development.
- Published
- 2016
7. Multiscale modelling of plant hormone signalling: auxin regulated lateral root emergence
- Author
-
Mellor, Nathan L.
- Subjects
fungi ,food and beverages - Abstract
The formation of lateral roots is an important post-embryonic developmental process that allows plants to adapt to their environment via exploitation of soil mineral resources. New lateral roots initiate as lateral root primordia (LRP) in the pericycle cell layer adjacent to the central vascular tissue in the primary root, and must pass through the outer cell layers of endodermis, cortex and epidermis to emerge as mature roots. A key regulator of emergence is the plant hormone auxin and it has been shown previously that in Arabidopsis the auxin induced expression of the auxin influx carrier LAX3 in specific cortical cells over LRP is required for emergence to occur, as this leads to the expression of cell wall remodelling enzymes such as polygalacturonase (PG). By developing mathematical models of auxin transport and LAX3 expression the work in the thesis aims to test the existing conceptual models for lateral root emergence, and provide testable hypotheses for the existence of additional gene regulatory components. An initial single cell model demonstrates that hysteresis and bistability may explain the experimentally observed `all-or-nothing' LAX3 spatial expression pattern in cortical cells containing a gradient of auxin concentrations. By fitting model parameters against experimental data, the model is then used to show that some auxin homeostasis mechanism is present, with both endogenous and exogenous sources of homeostasis investigated. The single cell model also investigates the validity of several alternative gene regulatory networks for LAX3, and its apparent repression by a key mediator of the auxin response, ARF19. Finally, the model is extended to a multicellular context, in which the auxin distribution from a simulated LRP source cell is used as a basis for the expression of LAX3, leading to the expression of PG in specific cells between which the LRP must pass.
8. Dynamic regulation of AtDAO1 and GH3 modulates auxin homeostasis
- Author
-
Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., Owen, Markus R., Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., and Owen, Markus R.
- Abstract
The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by AtDAO1/2 and conjugation by GH3s. Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product oxIAA, an increase in the conjugated forms IAA-Asp and IAA-Glu of 438-fold and 240-fold respectively, while auxin remains close to wild type. By fitting parameter values to a mathematical model of these metabolic pathways we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1. We then quantified gene expression in plantae, and found that transcripts of AtDAO1 and GH3 genes are increased in response to auxin, over different time scales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, while auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues, in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1, acting in concert with GH3, to maintain auxin at optimal levels for plant growth and development.
- Full Text
- View/download PDF
9. OpenSimRoot: widening the scope and application of root architectural models
- Author
-
Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., Watt, Michelle, Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., and Watt, Michelle
- Abstract
Research Conducted and Rationale: OpenSimRoot is an open sourced, functional- structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. Description: OpenSimRoot is an extended version of SimRoot, established to simulate root system architecture, nutrient acquisition, and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient, and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species. Key results and unique features: The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate 1) resource costs of developmental and anatomical traits, 2) trait synergisms, 3) (inter species) root competition. OpenSimRoot can model 3D images from MRI and X-ray CT of roots in soil. New modules include: 1) soil water dependent water uptake and xylem flow, 2) tiller formation, 3) evapotranspiration, 4) simultaneous simulation of mobile solutes, 5) mesh refinement, and 6) root growth plasticity. Conclusion: OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and gain mechanistic understanding at system scales.
- Full Text
- View/download PDF
10. OpenSimRoot: widening the scope and application of root architectural models
- Author
-
Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., Watt, Michelle, Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., and Watt, Michelle
- Abstract
Research Conducted and Rationale: OpenSimRoot is an open sourced, functional- structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. Description: OpenSimRoot is an extended version of SimRoot, established to simulate root system architecture, nutrient acquisition, and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient, and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species. Key results and unique features: The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate 1) resource costs of developmental and anatomical traits, 2) trait synergisms, 3) (inter species) root competition. OpenSimRoot can model 3D images from MRI and X-ray CT of roots in soil. New modules include: 1) soil water dependent water uptake and xylem flow, 2) tiller formation, 3) evapotranspiration, 4) simultaneous simulation of mobile solutes, 5) mesh refinement, and 6) root growth plasticity. Conclusion: OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and gain mechanistic understanding at system scales.
- Full Text
- View/download PDF
11. Dynamic regulation of AtDAO1 and GH3 modulates auxin homeostasis
- Author
-
Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., Owen, Markus R., Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., and Owen, Markus R.
- Abstract
The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by AtDAO1/2 and conjugation by GH3s. Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product oxIAA, an increase in the conjugated forms IAA-Asp and IAA-Glu of 438-fold and 240-fold respectively, while auxin remains close to wild type. By fitting parameter values to a mathematical model of these metabolic pathways we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1. We then quantified gene expression in plantae, and found that transcripts of AtDAO1 and GH3 genes are increased in response to auxin, over different time scales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, while auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues, in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1, acting in concert with GH3, to maintain auxin at optimal levels for plant growth and development.
- Full Text
- View/download PDF
12. OpenSimRoot: widening the scope and application of root architectural models
- Author
-
Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., Watt, Michelle, Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., and Watt, Michelle
- Abstract
Research Conducted and Rationale: OpenSimRoot is an open sourced, functional- structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. Description: OpenSimRoot is an extended version of SimRoot, established to simulate root system architecture, nutrient acquisition, and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient, and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species. Key results and unique features: The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate 1) resource costs of developmental and anatomical traits, 2) trait synergisms, 3) (inter species) root competition. OpenSimRoot can model 3D images from MRI and X-ray CT of roots in soil. New modules include: 1) soil water dependent water uptake and xylem flow, 2) tiller formation, 3) evapotranspiration, 4) simultaneous simulation of mobile solutes, 5) mesh refinement, and 6) root growth plasticity. Conclusion: OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and gain mechanistic understanding at system scales.
- Full Text
- View/download PDF
13. Multiscale modelling of plant hormone signalling: auxin regulated lateral root emergence
- Author
-
Mellor, Nathan L. and Mellor, Nathan L.
- Abstract
The formation of lateral roots is an important post-embryonic developmental process that allows plants to adapt to their environment via exploitation of soil mineral resources. New lateral roots initiate as lateral root primordia (LRP) in the pericycle cell layer adjacent to the central vascular tissue in the primary root, and must pass through the outer cell layers of endodermis, cortex and epidermis to emerge as mature roots. A key regulator of emergence is the plant hormone auxin and it has been shown previously that in Arabidopsis the auxin induced expression of the auxin influx carrier LAX3 in specific cortical cells over LRP is required for emergence to occur, as this leads to the expression of cell wall remodelling enzymes such as polygalacturonase (PG). By developing mathematical models of auxin transport and LAX3 expression the work in the thesis aims to test the existing conceptual models for lateral root emergence, and provide testable hypotheses for the existence of additional gene regulatory components. An initial single cell model demonstrates that hysteresis and bistability may explain the experimentally observed `all-or-nothing' LAX3 spatial expression pattern in cortical cells containing a gradient of auxin concentrations. By fitting model parameters against experimental data, the model is then used to show that some auxin homeostasis mechanism is present, with both endogenous and exogenous sources of homeostasis investigated. The single cell model also investigates the validity of several alternative gene regulatory networks for LAX3, and its apparent repression by a key mediator of the auxin response, ARF19. Finally, the model is extended to a multicellular context, in which the auxin distribution from a simulated LRP source cell is used as a basis for the expression of LAX3, leading to the expression of PG in specific cells between which the LRP must pass.
14. OpenSimRoot: widening the scope and application of root architectural models
- Author
-
Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., Watt, Michelle, Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., and Watt, Michelle
- Abstract
Research Conducted and Rationale: OpenSimRoot is an open sourced, functional- structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. Description: OpenSimRoot is an extended version of SimRoot, established to simulate root system architecture, nutrient acquisition, and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient, and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species. Key results and unique features: The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate 1) resource costs of developmental and anatomical traits, 2) trait synergisms, 3) (inter species) root competition. OpenSimRoot can model 3D images from MRI and X-ray CT of roots in soil. New modules include: 1) soil water dependent water uptake and xylem flow, 2) tiller formation, 3) evapotranspiration, 4) simultaneous simulation of mobile solutes, 5) mesh refinement, and 6) root growth plasticity. Conclusion: OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and gain mechanistic understanding at system scales.
- Full Text
- View/download PDF
15. Multiscale modelling of plant hormone signalling: auxin regulated lateral root emergence
- Author
-
Mellor, Nathan L. and Mellor, Nathan L.
- Abstract
The formation of lateral roots is an important post-embryonic developmental process that allows plants to adapt to their environment via exploitation of soil mineral resources. New lateral roots initiate as lateral root primordia (LRP) in the pericycle cell layer adjacent to the central vascular tissue in the primary root, and must pass through the outer cell layers of endodermis, cortex and epidermis to emerge as mature roots. A key regulator of emergence is the plant hormone auxin and it has been shown previously that in Arabidopsis the auxin induced expression of the auxin influx carrier LAX3 in specific cortical cells over LRP is required for emergence to occur, as this leads to the expression of cell wall remodelling enzymes such as polygalacturonase (PG). By developing mathematical models of auxin transport and LAX3 expression the work in the thesis aims to test the existing conceptual models for lateral root emergence, and provide testable hypotheses for the existence of additional gene regulatory components. An initial single cell model demonstrates that hysteresis and bistability may explain the experimentally observed `all-or-nothing' LAX3 spatial expression pattern in cortical cells containing a gradient of auxin concentrations. By fitting model parameters against experimental data, the model is then used to show that some auxin homeostasis mechanism is present, with both endogenous and exogenous sources of homeostasis investigated. The single cell model also investigates the validity of several alternative gene regulatory networks for LAX3, and its apparent repression by a key mediator of the auxin response, ARF19. Finally, the model is extended to a multicellular context, in which the auxin distribution from a simulated LRP source cell is used as a basis for the expression of LAX3, leading to the expression of PG in specific cells between which the LRP must pass.
16. OpenSimRoot: widening the scope and application of root architectural models
- Author
-
Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., Watt, Michelle, Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., and Watt, Michelle
- Abstract
Research Conducted and Rationale: OpenSimRoot is an open sourced, functional- structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. Description: OpenSimRoot is an extended version of SimRoot, established to simulate root system architecture, nutrient acquisition, and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient, and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species. Key results and unique features: The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate 1) resource costs of developmental and anatomical traits, 2) trait synergisms, 3) (inter species) root competition. OpenSimRoot can model 3D images from MRI and X-ray CT of roots in soil. New modules include: 1) soil water dependent water uptake and xylem flow, 2) tiller formation, 3) evapotranspiration, 4) simultaneous simulation of mobile solutes, 5) mesh refinement, and 6) root growth plasticity. Conclusion: OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and gain mechanistic understanding at system scales.
- Full Text
- View/download PDF
17. Dynamic regulation of AtDAO1 and GH3 modulates auxin homeostasis
- Author
-
Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., Owen, Markus R., Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., and Owen, Markus R.
- Abstract
The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by AtDAO1/2 and conjugation by GH3s. Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product oxIAA, an increase in the conjugated forms IAA-Asp and IAA-Glu of 438-fold and 240-fold respectively, while auxin remains close to wild type. By fitting parameter values to a mathematical model of these metabolic pathways we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1. We then quantified gene expression in plantae, and found that transcripts of AtDAO1 and GH3 genes are increased in response to auxin, over different time scales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, while auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues, in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1, acting in concert with GH3, to maintain auxin at optimal levels for plant growth and development.
- Full Text
- View/download PDF
18. OpenSimRoot: widening the scope and application of root architectural models
- Author
-
Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., Watt, Michelle, Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan L., Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., and Watt, Michelle
- Abstract
Research Conducted and Rationale: OpenSimRoot is an open sourced, functional- structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. Description: OpenSimRoot is an extended version of SimRoot, established to simulate root system architecture, nutrient acquisition, and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient, and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species. Key results and unique features: The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate 1) resource costs of developmental and anatomical traits, 2) trait synergisms, 3) (inter species) root competition. OpenSimRoot can model 3D images from MRI and X-ray CT of roots in soil. New modules include: 1) soil water dependent water uptake and xylem flow, 2) tiller formation, 3) evapotranspiration, 4) simultaneous simulation of mobile solutes, 5) mesh refinement, and 6) root growth plasticity. Conclusion: OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and gain mechanistic understanding at system scales.
- Full Text
- View/download PDF
19. Dynamic regulation of AtDAO1 and GH3 modulates auxin homeostasis
- Author
-
Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., Owen, Markus R., Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., and Owen, Markus R.
- Abstract
The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by AtDAO1/2 and conjugation by GH3s. Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product oxIAA, an increase in the conjugated forms IAA-Asp and IAA-Glu of 438-fold and 240-fold respectively, while auxin remains close to wild type. By fitting parameter values to a mathematical model of these metabolic pathways we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1. We then quantified gene expression in plantae, and found that transcripts of AtDAO1 and GH3 genes are increased in response to auxin, over different time scales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, while auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues, in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1, acting in concert with GH3, to maintain auxin at optimal levels for plant growth and development.
- Full Text
- View/download PDF
20. Dynamic regulation of AtDAO1 and GH3 modulates auxin homeostasis
- Author
-
Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., Owen, Markus R., Mellor, Nathan L., Band, Leah. R., Pěnčík, Aleš, Novak, Ondrej, Rashed, Afaf, Holman, Tara, Wilson, Michael H., Voss, Ute, Bishopp, Antony, King, John R., Ljung, Karin, Bennett, Malcolm J., and Owen, Markus R.
- Abstract
The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by AtDAO1/2 and conjugation by GH3s. Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product oxIAA, an increase in the conjugated forms IAA-Asp and IAA-Glu of 438-fold and 240-fold respectively, while auxin remains close to wild type. By fitting parameter values to a mathematical model of these metabolic pathways we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1. We then quantified gene expression in plantae, and found that transcripts of AtDAO1 and GH3 genes are increased in response to auxin, over different time scales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, while auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues, in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1, acting in concert with GH3, to maintain auxin at optimal levels for plant growth and development.
- Full Text
- View/download PDF
21. Systems approaches reveal that ABCB and PIN proteins mediate co-dependent auxin efflux.
- Author
-
Mellor NL, Voß U, Ware A, Janes G, Barrack D, Bishopp A, Bennett MJ, Geisler M, Wells DM, and Band LR
- Subjects
- ATP-Binding Cassette Transporters genetics, ATP-Binding Cassette Transporters metabolism, Adenosine Triphosphate metabolism, Biological Transport, Indoleacetic Acids metabolism, Plant Roots metabolism, Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism
- Abstract
Members of the B family of membrane-bound ATP-binding cassette (ABC) transporters represent key components of the auxin efflux machinery in plants. Over the last two decades, experimental studies have shown that modifying ATP-binding cassette sub-family B (ABCB) expression affects auxin distribution and plant phenotypes. However, precisely how ABCB proteins transport auxin in conjunction with the more widely studied family of PIN-formed (PIN) auxin efflux transporters is unclear, and studies using heterologous systems have produced conflicting results. Here, we integrate ABCB localization data into a multicellular model of auxin transport in the Arabidopsis thaliana root tip to predict how ABCB-mediated auxin transport impacts organ-scale auxin distribution. We use our model to test five potential ABCB-PIN regulatory interactions, simulating the auxin dynamics for each interaction and quantitatively comparing the predictions with experimental images of the DII-VENUS auxin reporter in wild-type and abcb single and double loss-of-function mutants. Only specific ABCB-PIN regulatory interactions result in predictions that recreate the experimentally observed DII-VENUS distributions and long-distance auxin transport. Our results suggest that ABCBs enable auxin efflux independently of PINs; however, PIN-mediated auxin efflux is predominantly through a co-dependent efflux where co-localized with ABCBs., (© American Society of Plant Biologists 2022. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
- Published
- 2022
- Full Text
- View/download PDF
22. The Virtual Root : Mathematical Modeling of Auxin Transport in the Arabidopsis Root Tip Using the Open-Source Software SimuPlant.
- Author
-
Collis H, Band LR, Fozard JA, Ghetiu T, Wilson MH, Mellor NL, Bennett MJ, and Owen MR
- Subjects
- Arabidopsis Proteins metabolism, Biological Transport, Gene Expression Regulation, Plant, Hormones, Indoleacetic Acids, Meristem metabolism, Models, Theoretical, Plant Roots metabolism, Plants metabolism, Software, Arabidopsis metabolism
- Abstract
Hormone signals like auxin play a critical role controlling plant growth and development. Determining the mechanisms that regulate auxin distribution in cells and tissues is a vital step in understanding this hormone's role during plant development. Recent mathematical models have enabled us to understand the essential role that auxin influx and efflux carriers play in auxin transport in the Arabidopsis root tip (Band et al., Plant Cell 26(3):862-875, 2014; Grieneisen et al., Nature 449(7165):1008-1013, 2007; van den Berg et al., Development 143(18):3350-3362, 2016). In this chapter, we describe SimuPlant: The Virtual Root (SimuPlant, University of Nottingham. https://www.simuplant.org/ . Accessed 20 Sept 2019); an open source software suite, built using the OpenAlea (Pradal et al., Funct Plant Biol 35(10):751-760, 2008) framework, that is designed to simulate vertex-based models in real plant tissue geometries. We provide guidance on how to install SimuPlant, run 2D auxin transport models in the Arabidopsis root tip, manipulate parameters, and visualize model outputs.SimuPlant features a graphical user interface (GUI) designed to allow users with no programming experience to simulate auxin dynamics within the Arabidopsis root tip. Within the user interface, users of SimuPlant can select from a range of model assumptions and can choose to manipulate model and simulation parameter values. Users can then investigate how their choices affect the predicted distribution of auxin in the Arabidopsis root tip. The results of the model simulations are shown visually within the root geometry and can be exported and saved as PNG image files., (© 2022. Springer Science+Business Media, LLC, part of Springer Nature.)
- Published
- 2022
- Full Text
- View/download PDF
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