Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis

Abstract

Abstract. The Stochastic Calculus of Wrapped Compartments (SCWC)is a recently proposed variant of the Stochastic Calculus of Looping Sequences (SCLS), a language for the representation and simulation of biological systems. In this work we apply SCWC to model a newly discovered ammonium transporter. This transporter is believed to play a fundamental role for plant mineral acquisition, which takes place in the arbuscular mycorrhiza, the most wide-spread plant-fungus symbiosis on earth. Investigating this kind of symbiosis is considered one of the most promising ways to develop methods to nurture plants in more natural manners, avoiding the complex chemical productions used nowadays to produce artificial fertilizers. In our experiments the passage of N H3 / N H + 4 from the fungus to the plant has been dissected in known and hypothetical mechanisms; with the model so far we have been able to simulate the behavior of the system under different conditions. Our simulations confirmed some of the latest experimental results about the LjAMT2;2 transporter. Moreover, by comparing the behaviour of LjAMT2;2 with the behaviour of another ammonium transporter which exists in plants, viz. LjAMT1;1, our simulations support an hypothesis about why LjAMT2;2 is so selectively expressed in arbusculated cells.

Functional genomics and signaling events in mycorrhizal symbiosis

“…The ammonium transporter binds to charged ammonium in the apoplastic interface compartment and releases the uncharged NH 3 molecule into the cytoplasm. The role of ammonium transporter LjAMT2 is confirmed by stochastic calculus of wrapped compartment (SCWC) (Variant of stochastic calculus of looping sequence) in mycorrhizal symbiosis (Coppo et al 2011). The X-ray structure study of ammonium transporter revealed the conduction mechanism of Amt/Rh (rhesus) protein that involved in the single-file diffusion of NH 3 molecule (Zheng et al 2004;Andrade et al 2005;Lamoureux et al 2010).…”

On Designing Multicore-Aware Simulators for Biological Systems

“…The Calculus of labelled Wrapped Compartments (CWC) (see [9], [11]) is based on a nested structure of ambients delimited by membranes with specific proprieties. Biological entities like cells, bacteria and their interactions can be easily described in CWC.…”

Modelling Spatial Interactions in the Arbuscular Mycorrhizal Symbiosis using the Calculus of Wrapped Compartments

“…The Calculus of Wrapped Compartments (CWC) (see [19,17]) is based on a nested structure of ambients delimited by membranes with specific proprieties. Biological entities like cells, bacteria and their interactions can be easily described in CWC.…”