Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape

Abstract

Bacteria are surrounded by a peptidoglycan (PG) cell wall that must be remodeled to allow cell growth. While many structural details and properties of PG and the individual enzymes involved are known, how the process is coordinated to maintain cell integrity and rod shape is not understood. We have developed a coarse-grained method to simulate how individual transglycosylases, transpeptidases, and endopeptidases could introduce new material into an existing unilayer PG network. We find that a simple model with no enzyme coordination fails to maintain cell wall integrity and rod shape. We then iteratively analyze failure modes and explore different mechanistic hypotheses about how each problem might be overcome by the macromolecules involved. In contrast to a current theory, which posits that long MreB filaments are needed to coordinate PG insertion sites, we find that local coordination of enzyme activities in individual complexes can be sufficient to maintain cell integrity and rod shape. We also present possible molecular explanations for the existence of monofunctional transpeptidases and glycosidases (glycoside hydrolases), trimeric peptide crosslinks, cell twisting during growth, and synthesis of new strands in pairs.coarse-grained modeling | cell wall synthesis | morphogenesis T he cytoplasmic membrane of Gram-negative rod-shaped bacteria is surrounded by a peptidoglycan (PG) sacculus that protects the cell from internal turgor pressure, and its architecture determines the cell's shape (1, 2). The sacculus is composed of long glycan strands crosslinked by peptides into a mesh-like network. The glycan repeating unit is a disaccharide of an N-acetylglucosamine and an N-acetylmuramic acid attached to a stem pentapeptide L-Ala-D-iGlu-m-A 2 pm-D-Ala-D-Ala. Crosslinks are formed between peptides on adjacent strands-most at the fourth (D-Ala) residues of the donors and the third (m-A 2 pm) residues of the acceptors. While it is now understood that, in Gram-negative cells, the glycan strands run parallel to the cell surface, how the strands are arranged in this plane is still debated. While recent atomic force microscopy images of purified sacculi were interpreted to indicate that glycan strands had random orientations (3), electron cryotomography of sacculi (4) and other evidence from both Gramnegative (1, 5) and -positive (6, 7) sacculi have, instead, pointed to a universal "circumferential" model, in which the stiff glycan strands are circumferentially around the rod and the flexible peptide crosslinks parallel to the rod's long axis.Cell growth requires that the sacculus be elongated without losing its integrity or characteristic shape. This remodeling process requires the presence of not only transglycosylases and transpeptidases, also known as penicillin-binding proteins (PBPs), to polymerize and crosslink new glycan strands into the existing network (2, 8) but also, endopeptidases to cleave covalent bonds to open space for the new material (9). How these small enzymes work together to maintain the order and...

Cell-wall remodeling drives engulfment during Bacillus subtilis sporulation

“…Here the angle between neighboring stem peptides that belong to a single glycan is assumed to be 90°. Therefore, every other stem peptide is in plane with glycan sheet (Nguyen et al, 2015, Huang et al, 2008). The role of effective glycan persistence length on engulfment is negligible (see Figure 4—figure supplement 3).…”

“…( B ) Simulations for different values of effective peptide $k_{\mathrm{pep}}$ and glycan $k_{\mathrm{gly}}$ spring constants are compared with experimentally measured forespore surface area, volume and engulfment using mutual ${\chi }^2$ statistics (Equation 2). Arrows point to effective literature $k_{\mathrm{pep}}$ and $k_{\mathrm{gly}}$ (Nguyen et al, 2015). Dark blue region corresponds to simulation parameters that best fit experimental data (Figure 4—figure supplement 4, Video 3).…”

MreB Orientation Correlates with Cell Diameter in Escherichia coli

“…Although this model is able to predict conditions for rod-shaped growth, it fails to predict the MreB-dependent chiral organization of the glycan strands. Other recent attempts to model cell growth do not use chiral polymers, but instead hypothesize that MreB's role is to colocalize cell wall growth factors randomly on the cell surface (14). This work also fails to predict the cell wall chirality and invokes a global geometric sensing of the cell's long-axis direction, either by the MreB or the cell wall synthesizing enzymes, without an explanation of how a nonpolymeric molecule might achieve this.…”

Bacterial cell division is involved in the damage of gram-negative bacteria on a nano-pillar titanium surface

“…Generally, the murein sacculus (peptidoglycan layer) is the essential determinant of the shape of E. coli which has to be preserved during cell divisions. Cell growth requires that the sacculus be elongated by a complex remodeling process which requires the coordinated action of transglycosylases, transpeptidases and endopepidases [13]. Obviously, the growth occurred at multiple domains of the cylindrical part of E. coli [20].…”

“…Thus, besides the initial attachment of the E. coli to a cicada wing-like surface an ongoing cell division process will induce additional strain for cell wall rupture. For every division of the E. coli the elongation of the rod structure is necessary [13]. This elongation process will obviously induce additional strain on the bacterial cell wall when the living cell is somehow fixed by the tips of the nano-pillars.…”