Revision as of 18:31, 25 September 2012

Module 2: Aggregation

Modelling

Our cell model for aggregation describes the pathways through which the proteins CsgA and CsgB, which make up curli fibrils, are produced on detection of microplastics. Using this we aim to find out how many curlis each cell might express, which we could then use to estimate the binding strength of our bacteria.

As with our degradation model, this SimBiology model is divided into three compartments:

1. Outside1: in this compartment we see the association, adherence, and dissociation of persistent organic pollutants (POPs) from polyethylene (PE) (R1). We rely on the POPs to induce our degradation system, increasing by (10⁵ to 10⁶ the specificity to our system.

2. Cell: NahR is a constitutively produced mRNA product (R9) of which around 3% degrades (R10). When POP diffuses into the cell (R2), it forms a complex with intact NahR (R3) which then binds to the pSal promoter (R4) to induce the curli gene cluster (R5). This starts translation of five proteins which make up curli fibrils. Here we focus on those controlled by the CsgAB operon, CsgA (R7) and CsgB (R6), as these are the most important in curli synthesis as described on our [| research page]. The CsgA and CsgB that do not degrade (R11, R12) diffuse out of the cell.

3. Outside2: Outside of the cell the polymerization of CsgA by CsgB takes place (R8) to make a curli fibril.

Species

Species	Initial value (molecules)	Notes & Assumptions
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 CsgE⁵
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	0.0	Result of CsgA and CsgB interaction

Reactions taking place in the model

Number	Reaction	Reaction rate (molecules/sec)	Notes & Assumptions
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	Rate based on membrane permeability⁴ and 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 salycilate⁷. Salycilate binds to the NahR mRNA product, which complex then binds to the pSal promoter.
R4	POPinmRNANahr ↔ POPinmRNANahr.Psal	Forward: 78200 Backward: 0.191 ¹⁰	NahR to pSal binding based on the assumption that POP-NahR binding has no effect on NahR-pSal binding
R5	POPexmRNANahr.Psal → mRNAcurli	0.054	Transcription rate of curli cluster in molecules/sec (for cluster size 1500bp¹¹, transcription rate in E.coli 80bp/sec⁹)
R6	mRNAcurli → CsgB	0.13	Translation rate of CsgB in molecules/sec (for CsgB size 151aa¹², translation rate in E.coli 20aa/sec⁹)
R7	mRNAcurli → CsgA	0.13	Translation rate of CsgA in molecules/sec (for CsgA size 151aa¹³, translation rate in E.coli 20aa/sec⁹)
R8	CsgB + CsgA -> fibril	ARGH	ARGH
R9	0 ↔ mRNA.Nahr	Forward: 0.088 Backward: 0.6	Transcription rate of NahR in molecules/sec (for NahR size 909 bp⁸, transcription rate in E.coli 80bp/sec⁹) under constitutive promoter control
R10	mRNA.Nahr → 0	0.03	Degradation rate of NahR mRNA product¹⁴
R11	CsgA → 0	0.03	Degradation rate of CsgA ¹⁴ must be taken into account due to suboptimal conditions
R12	CsgB → 0	0.03	Degradation rate of CsgB ¹⁴ must be taken into account due to suboptimal conditions

Results

The graph shows that fibrils are produced at a rate of around 1 fibril per second.

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

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

7. https://2011.igem.org/Team:Peking_S/project/wire/harvest

8. http://www.xbase.ac.uk/genome/azoarcus-sp-bh72/NC_008702/azo2419;nahR1/viewer

9. http://kirschner.med.harvard.edu/files/bionumbers/fundamentalBioNumbersHandout.pdf

10. Park H, Lim W, Shin H (2005) In vitro binding of purified NahR regulatory protein with promoter Psal. Biochimica et Biophysica Acta 1775: 247-255

11. 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

12. http://www.ecogene.org//?q=gene/EG12621

13. http://www.ecogene.org/?q=gene/EG11489

14. Kushner S (2002) mRNA Decay in Escherichia coli Comes of Age. J Bacteriol. 184: 4658-4665

Where does this go? 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

@@ Line 60: / Line 60: @@
 | R2 || POPex ↔ POPin || Forward: 0.6 <br /> Backward: 0.4 || Rate based on membrane permeability<sup>4</sup> and diffusion gradient
 |-
-| R3 || POPin + mRNA.Nahr → POPin.mRNA.Nahr || Forward: 1 <br /> Backward: 0.0001 || Based on the assumption that the chemical structure/size of POPs is similar to salycilate<sup>7</sup>.  Salycilate binds to the NahR mRNA product, which complex then binds to the pSal promoter.
+| R3 || POPin + mRNA.Nahr ↔ POPin.mRNA.Nahr || Forward: 1 <br /> Backward: 0.0001 || Based on the assumption that the chemical structure/size of POPs is similar to salycilate<sup>7</sup>.  Salycilate binds to the NahR mRNA product, which complex then binds to the pSal promoter.
 |-
-| R4 || POPinmRNANahr → POPinmRNANahr.Psal || Forward: 78200 <br /> Backward: 0.191 <sup>10</sup> || NahR to pSal binding based on the assumption that POP-NahR binding has no effect on NahR-pSal binding
+| R4 || POPinmRNANahr ↔ POPinmRNANahr.Psal || Forward: 78200 <br /> Backward: 0.191 <sup>10</sup> || NahR to pSal binding based on the assumption that POP-NahR binding has no effect on NahR-pSal binding
 |-
 | R5 || POPexmRNANahr.Psal → mRNAcurli || 0.054 || Transcription rate of curli cluster in molecules/sec (for cluster size 1500bp<sup>11</sup>, transcription rate in E.coli 80bp/sec<sup>9</sup>)
@@ Line 72: / Line 72: @@
 | R8 || CsgB + CsgA -> fibril || ARGH || ARGH
 |-
-| R9 || 0 → mRNA.Nahr || Forward: 0.088 <br /> Backward: 0.6 || Transcription rate of NahR in molecules/sec (for NahR size 909 bp<sup>8</sup>, transcription rate in E.coli 80bp/sec<sup>9</sup>) under constitutive promoter control
+| R9 || 0 ↔ mRNA.Nahr || Forward: 0.088 <br /> Backward: 0.6 || Transcription rate of NahR in molecules/sec (for NahR size 909 bp<sup>8</sup>, transcription rate in E.coli 80bp/sec<sup>9</sup>) under constitutive promoter control
 |-
 | R10 || mRNA.Nahr → 0 || 0.03 || Degradation rate of NahR mRNA product<sup>14</sup>

Team:University College London/Module 2/Modelling

From 2012.igem.org