Pathway Model

1 Overview

Curli is the main proteinaceous component of the extracellular matrix naturally produced by E. coli. Although the main structural component is the self-assembling csgA monomer, there are a number of other proteins involved in its production and export. The curli production pathway can be broken down into two main modules: gene expression and translocation. The first, gene expression, is comprised of transcription and translation. Translocation can be further broken down into periplasmic export and extracellular secretion.

2 Gene Expression

2.1 Transcription

The naturally occurring genes corresponding to curli are organized into csgBAC and csgDEFG operons. csgD is a regulatory protein, and thus is not applicable for the expression of foreign plasmids. Additionally, due to the additional protein domains fused to the csgA monomer, it is placed on a plasmid on its own (\(g_{csgA}\)). The remaining genes are placed on another plasmid (\(g_{csgCEFG}\)). The rate of transcription is primarily governed by the plasmid copy number and promoter strength. $$g_{csgA} + RNA_{pol} \overset{\alpha_{1}}{\rightarrow} g_{csgA} + RNA_{pol} + mRNA_{csgA}$$ $$g_{csgBCEFG} + RNA_{pol} \overset{\alpha_{2}}{\rightarrow} g_{csgBCEFG} + RNA_{pol} + mRNA_{csgBCEFG}$$ $$mRNA_{csgA} \overset{\zeta_{1}}{\rightarrow} \varnothing$$ $$mRNA_{csgBCEFG} \overset{\zeta_{1}}{\rightarrow} \varnothing$$

2.2 Translation

Each of the coding sequences in the two transcripts described above are preceded by an RBS sequence that determines the rate of translation of each protein. The relative RBS strengths determine the stoichiometry between the proteins involved in the curli pathway. $$mRNA_{csgA} + ribosome \overset{\beta_{1}}{\rightarrow} mRNA_{csgA} + ribosome + csgA_{cyt}$$ $$mRNA_{csgBCEFG} + ribosome \overset{\beta_{2}}{\rightarrow} mRNA_{csgBCEFG} + ribosome + csgB_{cyt}$$ $$mRNA_{csgBCEFG} + ribosome \overset{\beta_{3}}{\rightarrow} mRNA_{csgBCEFG} + ribosome + csgC_{cyt}$$ $$mRNA_{csgBCEFG} + ribosome \overset{\beta_{4}}{\rightarrow} mRNA_{csgBCEFG} + ribosome + csgE_{cyt}$$ $$mRNA_{csgBCEFG} + ribosome \overset{\beta_{5}}{\rightarrow} mRNA_{csgBCEFG} + ribosome + csgF_{cyt}$$ $$mRNA_{csgBCEFG} + ribosome \overset{\beta_{6}}{\rightarrow} mRNA_{csgBCEFG} + ribosome + csgG_{cyt}$$ $$csgA_{cyt} \overset{\zeta_{1}}{\rightarrow} \varnothing$$ $$csgB_{cyt} \overset{\zeta_{1}}{\rightarrow} \varnothing$$ $$csgC_{cyt} \overset{\zeta_{1}}{\rightarrow} \varnothing$$ $$csgE_{cyt} \overset{\zeta_{1}}{\rightarrow} \varnothing$$ $$csgF_{cyt} \overset{\zeta_{1}}{\rightarrow} \varnothing$$ $$csgG_{cyt} \overset{\zeta_{1}}{\rightarrow} \varnothing$$

3 Translocation

Although the ultimate destination of the csgA monomer is the extracellular space, not all of the other proteins involved in the pathway have the same fate. csgB and csgF do operate in the extracellular space, but csgC and csgE are chaperone proteins that remain in the periplasm, whereas csgG forms a channel in the outer membrane.

3.1 Periplasmic export

Since none of the curli proteins remain in the cytoplasm, all must translocate into the cell's periplasm. The mechanism by which this occurs is the Sec secretion pathway. The main actors in this secretion pathway are SecYEG, the protein conducting channel (PCC), SecA which acts as an ATPase driving the translocation, and SecB, a chaperone protein that keeps proteins in an unfolded state (Driessen et al., 2007). As a protein emerges from the ribosome, SecB, a homotetramer, binds and stabilizes it in its unfolded conformation. SecB binds to SecA, a homodimer which also recruits SecYEG to assemble a dimeric PCC. $$csgA_{cyt} + 4 SecB + 2 SecA + SecYEG \overset{\gamma_{1}}{\rightarrow} 4 SecB + 2 SecA + SecYEG + csgA_{per}$$ $$csgB_{cyt} + 4 SecB + 2 SecA + SecYEG \overset{\gamma_{2}}{\rightarrow} 4 SecB + 2 SecA + SecYEG + csgB_{per}$$ $$csgC_{cyt} + 4 SecB + 2 SecA + SecYEG \overset{\gamma_{3}}{\rightarrow} 4 SecB + 2 SecA + SecYEG + csgC_{per}$$ $$csgE_{cyt} + 4 SecB + 2 SecA + SecYEG \overset{\gamma_{4}}{\rightarrow} 4 SecB + 2 SecA + SecYEG + csgE_{per}$$ $$csgF_{cyt} + 4 SecB + 2 SecA + SecYEG \overset{\gamma_{5}}{\rightarrow} 4 SecB + 2 SecA + SecYEG + csgF_{per}$$ $$csgG_{cyt} + 4 SecB + 2 SecA + SecYEG \overset{\gamma_{6}}{\rightarrow} 4 SecB + 2 SecA + SecYEG + csgG_{per}$$

3.2 Extracellular secretion

Analysis of the crystal structure of csgG and has revealed that it assembles into a double-nonameric form in D9 symmetry (Taylor and Matthews 2015). CsgE has also been shown to form a nonamer at the base of the csgG structure in the periplasm, providing selectivity for the substrates that are secreted (Goyal et al., 2014). CsgG and csgE participate in the translocation fo csgF into the extracellular matrix, which then folds and binds csgG to the membrane. Meanwhile, csgC interacts with csgA and csgB monomers to prevent the formation of oligomers (Taylor and Matthews 2015). When the monomers interact with csgE, they become trapped in the periplasmic cavity and are transported across the outer membrane. CsgB then interacts with csgF to initiate the nucleation of csgA fibers. $$9 csgG_{per} \overset{\delta_{1}}{\rightarrow} csgG_{9}$$ $$9 csgE_{per} \overset{\delta_{2}}{\rightarrow} csgE_{9}$$ $$2 csgF_{per} \overset{\delta_{3}}{\rightarrow} 2 csgF_{ECM}$$ $$ csgG_{9} + 2 csgF_{ECM} + csgE_{9} \overset{\delta_{4}}{\rightarrow} csgGEF$$ $$csgA_{per} + csgGEF \overset{\delta_{5}}{\rightarrow} csgGEF + csgA_{ECM}$$ $$csgB_{per} + csgGEF \overset{\delta_{6}}{\rightarrow} csgGEF + csgB_{ECM}$$

4 Aggregation and Polymerization

5 Differential Equations