Chromosome driven spatial patterning of proteins in bacteria

Abstract

The spatial patterning of proteins in bacteria plays an important role in many processes, from cell division to chemotaxis. In the asymmetrically dividing bacteria Caulobacter crescentus, a scaffolding protein, PopZ, localizes to both poles and aids the differential patterning of proteins between mother and daughter cells during division. Polar patterning of misfolded proteins in Escherichia coli has also been shown, and likely plays an important role in cellular ageing. Recent experiments on both of the above systems suggest that the presence of chromosome free regions along with protein multimerization may be a mechanism for driving the polar localization of proteins. We have developed a simple physical model for protein localization using only these two driving mechanisms. Our model reproduces all the observed patterns of PopZ and misfolded protein localization--from diffuse, unipolar, and bipolar patterns and can also account for the observed patterns in a variety of mutants. The model also suggests new experiments to further test the role of the chromosome in driving protein patterning, and whether such a mechanism is responsible for helping to drive the differentiation of the cell poles.

Figure 1. Schematics of observed patterns and model for protein localization in bacteria.

(a) Schematic of PopZ localization during cell cycle of Caulobacter crescentus. PopZ starts localized in a scaffold at one pole and then during division forms at the 2nd pole. Upon division the two daughter cells both inherit PopZ localized to one pole. (b) Model for protein localization due to nucleoid. Protein freely diffuses throughout the cytoplasm in the presence of the bacterial nucleoid. The nucleoid acts as a region of excluded volume that occupies a space that is smaller than the cellular volume. This creates regions that are empty of DNA at the cell poles. Proteins such as PopZ or misfolded proteins are able to interact with themselves and depending on density can form growing domains in chromosome free regions of the cell.

Figure 2. Representative low energy configurations of protein in cylindrical cells.

From (a) low concentration of protein (upper) to high (lowest). Protein localization transitions from diffuse (upper, ) to unipolar (middle, ), to bipolar (lower, ) as the concentration increases for fixed DNA volume fraction . In these figures, the diameter of DNA monomers is , the diameter of PopZ subunits is , the length of the cell is and the diameter is . (b) Decreasing the interaction between PopZ monomers, here , leads to freely diffusing protein monomers. (c) Increasing the protein-protein interaction, , causes protein to form multiple domains. (d) Effect of fragmenting the chromosome into 10 equal fragments. In all the above simulations the nucleoid was modeled using an attractive Lennard-Jones potential with .

Figure 3. Classifying patterns based on protein distribution in cell.

(a) Protein probability density as a function of position along the cell, measured in . Shown are the densities for diffuse (GAS), unipolar on the right (UNI_R) and bipolar (BI). (b) Shown are the resulting frequencies of protein patterns from 50 separate simulations at each value of for the cell geometry and DNA density described in Fig. 2a. (c) Same as in (b) except using a DNA volume fraction of . The frequencies of both unipolar patterns have been combined into a single unipolar classification, ‘UNI’ and patterns that result in domains elsewhere than at the poles are classified as ‘OTHER’.

Figure 4. Effect on protein patterning by changing the aspect ratio.

(a) In (a), protein and DNA volume fractions are fixed at and with a cell diameter of . (top) Cell with and an aspect ratio of 2.0 and a typical unipolar pattern. (middle) Cell with and a aspect ratio of 3.0 showing a unipolar pattern. (bottom) Cell with , giving an aspect ratio of 3.5 showing the likely bipolar pattern. (b) Affect on patterning by altering cell shape. In (b) the total amount of protein and DNA are fixed using volume fractions are and respectively for a cell with and a diameter of . (left) A cell with showing unipolar patterning. (right) A cell with showing a destabilization of the protein domain. For simulations in both (a) and (b) the nucleoid was modeled using an attractive Lennard-Jones potential with (c) Summary of results for the frequency of the various patterns over 50 simulations at each aspect ratio.

Figure 5. Protein distribution in spherical cells.

From left to right, (a) diffuse protein at low concentration (left), to unispot (center), to multi-spot at higher concentrations (right), . The radius of the cell is , using and all other bead sizes and interactions are as given in Fig. 2. Beneath each pattern are shown the frequencies of observing the patterns: diffuse (green), unispot (red), bipolar (blue). Compact refers to a nucleoid modeled using an attractive Lennard-Jones potential with and non-compact is for a nucleoid with only the repulsive portion of the Lennard-Jones potential considered.

Figure 6. Protein distribution in multi-chromosomal cells.

(a) Cell possessing two chromosomes. The cell diameter was taken to be with the length of a single cell having , using to determine the size of a single chromosome. Protein concentration increases from top to bottom, from (top) to (bottom), and cell's length is varied, from (left) to (right). (b) Cell containing three chromosomes using the same individual chromosome size as in (a), with a cell length of . At lower concentrations (), protein forms only at poles (top). At higher protein concentrations, poles and interchromosomal regions can be occupied by protein domains (bottom) and at even higher concentrations () all chromosome free regions can be occupied by a protein domain.

Figure 7. Summary of frequencies of observed patterns in multi-chromosomal cells.

Results for a cell possessing two chromosomes with (a) length or (b) length . Diameter and DNA volume fraction are as in Fig. 6a. ‘MULTI_2’ corresponds to 2 protein domains, one in between the two chromosomes and one at a pole. ‘MULTI_3’ corresponds to all chromosome free regions being occupied by a protein domain. (c) Results for cells possessing three chromosomes. Here ‘MULTI_2’ are patterns with two protein domains that are not at both poles, ‘MULTI_3’ cells possess three domains and ‘MULTI_4’ cells have all chromosome free regions occupied by a protein domain. Frequecencies of patterns were found as a function of over 25 independent simulations at each value of and length, .