Coarse-Grained Simulations Reveal Mechanisms of Bacterial Morphogenesis

Abstract

How cells maintain their characteristic shapes throughout generations of growth is a fundamental question in bacterial cell biology. In most rod-shaped bacteria, the cell shape is determined by a peptidoglycan (PG) sacculus that surrounds the cell preventing lysis from turgor pressure. Despite decades of experiments, how the activities of PG synthesis enzymes are coordinated at the molecular and cellular levels to preserve the integrity and rod shape of the sacculus remains elusive. To explore different mechanistic models of sacculus growth, we have developed a coarse-grained simulation method that allows us to vary the properties and coordination of PG-remodeling enzymes while mechanical properties of the coarse-grained PG are derived from all-atom MD simulations of isolated PG. (Nguyen et al., PNAS. 112, E3689 (2015)). For the first time to our knowledge, individual enzymes, including transglycosylases, transpeptidases and endopeptidases, are explicitly represented. We have revealed the challenges a cell might face while remodeling its sacculus. For example, lysis can easily occur during bond cleavage because of turgor pressure; aggregation of new PG material can occur if enzymes are not processive; and the regular order and rod shape of the sacculus is easily lost if enzymatic activities are not coordinated. Exploring ways a cell might overcome these challenges, we find that local spatial and temporal coordination of the enzymes alone can be sufficient to maintain rod shape. Our results rationalize several experimental results, for instance explaining why the monofunctional transpeptidase PBP2 is essential and suggesting why different enzymes must exist in a complex that inserts new strands in pairs. Our approach also generates testable biological hypotheses. For instance, we predict a role for a housekeeping glycosidase; while our manuscript was in revision, just such a glycosidase was identified in cells (Cho et al., Cell 159, 1300 (2014)).

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