Module 2: Aggregation

Modelling

In addition to our gene network model for this module, we have come up with a system of equations which describe the strength of our adhesive biofilms under shear force stress.

Species

Species	Initial value (molecules)	Notes
PE	0.044	Polyethylene found in North Pacific Gyre (value per cubic metre)^1,2
POPex	0.0	Persistent organic pollutants (ex = extracellular) that are not adhered to plastic surface
PEPOPex	9.24E-5	Persistent organic pollutants (ex = extracellular) that are adhered to the plastic surface³
POPin	0.5	Persistent organic pollutants (in = intracellular) assumed from E. coli membrane permeability ⁴
mRNANahR	0.0	NahR mRNA product
POPinNahR	0.0	Complex of the above two molecules
POPinNahRpSal	0.0	Complex of the above molecule and pSal (promoter that induces laccase transcription)
mRNACurli	0.0	Polycistronic mRNA as it codes for more than one protein, in reality curli cluster contains five or more proteins, in our model mRNA is present as ??CsgE??⁵
CsgA	0.0	One of the polypeptides that is coded for in curli cluster, it is a structural component secreted in subunits outside of the cell
CsgB	0.0	One of the polypeptides that is coded for in curli cluster, it is secreted outside of the cell allowing polymerization of CsgA
Fibril	Result of CsgA and CsgB interaction

Reactions taking place in the model

Number	Reaction	Reaction rate (molecules/sec)	Notes
R1	PE + POPex ↔ PEPOPex	Forward: 1000 Backward: 1	Pops have 1000 to 10000 times greater tendency to adhere to plastic than float free in the ocean⁶
R2	POPex ↔ POPin	Forward: 0.6 Backward: 0.4	Based on membrane permeability⁴: diffusion gradient
R3	POPin + mRNA.Nahr → POPin.mRNA.Nahr	Forward: 1 Backward: 0.0001	Based on the assumption that the chemical structure/size of POPs is similar to salycilate⁶. Salycilate binds to the NahR mRNA product, which complex then binds to the pSal promoter.
R7	0 → mRNA.Nahr	Forward: 0.088 Backward: 0.6	Transcription rate of NahR in molecules/sec (for NahR size 909 bp⁷, transcription rate in E.coli 80bp/sec⁸) under constitutive promoter control
R4	POPinmRNANahr → POPinmRNANahr.Psal	Forward: 78200 Backward: 0.191 ⁹	NahR to pSal binding based on the assumption that POP-NahR binding has no effect on NahR-pSal binding
R5	POPexmRNANahr.Psal → GFP.mRNA	0.11	Transcription rate of GFP in molecules/sec (for GFP size 720bp¹⁰, transcription rate in E.coli 80bp/sec⁸)
R6	GFP.mRNA → GFP	0.084	Translation rate of GFP in molecules/sec (for GFP size 240aa¹⁰, translation rate in E.coli 20aa/sec⁸)
R9	GFP.mRNA → 0	0.03	Degradation rate of GFP mRNA product¹¹ must be taken into account due to suboptimal conditions

Results

To follow

References

1. Goldstein M, Rosenberg M, Cheng L (2012) Increased oceanic microplastic debris enhances oviposition in an endemic pelagic insect. Biology Letters 10.1098

2. Andrady AL (2011) Microplastics in the marine environment. Marine Pollution Bulletin 62: 1596-1605 Shala AA, Restrepo S, Gonzalez Barrios AF (2011) A network model for biofilm development in Escherichia coli K-12. Theoretical Biology and Medical Modelling 8: 34 doi:10.1186/1742-4682-8-34

3. To follow

4. To follow

5. Nenninger AA, Robinson LS, Hammer ND, Epstein EA, Badtke MP, Hultgren SJ, Chapman MR (2011) CsgE is a curli secretion specificity factor that prevents amyloid fibre aggregation. Mol Microbiol 81: 486-499

6. Mato Y, Isobe T, Takada H, Kanehiro H, Ohtake C, Kaminuma T (2001) Plastic Resin Pellets as a Transport Medium for Toxic Chemicals in the Marine Environment. Environ. Sci. Technol. 35: 318-324

Walsh DM, Lomakin A, Benedek GB, Condron MM, Teplow DB (1997) Amyloid b-Protein Fibrillogenesis: Detection of a protofibrillar intermediate. The Journal of Biological Chemistry 272: 22364–22372

Team:University College London/Module 2/Modelling

From 2012.igem.org

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