Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations

Dimer dynamics and filament organization of the bacterial cell division protein FtsA

FtsA is a bacterial actin homolog and one of the core proteins involved in cell division. While previous studies have demonstrated the capability of FtsA to polymerize, little is known about its polymerization state in vivo or if polymerization is necessary for FtsA function. Given that one function of FtsA is to tether FtsZ filaments to the membrane, in vivo polymerization of FtsA imposes geometric constraints and requires a specific polymer curvature direction. Here, we report a series of molecular dynamics simulations probing the structural dynamics of FtsA as a dimer and as a tetrameric single filament. We found that the FtsA polymer exhibits a preferred bending direction that would allow for its placement parallel with FtsZ polymers underneath the cytoplasmic membrane. We also identified key interfacial amino acids that mediate FtsA-FtsA interaction and propose that some amino acids play more critical roles than others. We performed in silico mutagenesis on FtsA and demonstrated that, while a moderate mutation at the polymerization interface does not significantly affect polymer properties such as bending direction and association strength, more drastic mutations change both features and could lead to non-functional FtsA.

A flexible C-terminal linker is required for proper FtsZ assembly in vitro and cytokinetic ring formation in vivo

Assembly of the cytoskeletal protein FtsZ into a ring-like structure is required for bacterial cell division. Structurally, FtsZ consists of four domains: the globular N-terminal core, a flexible linker, 8-9 conserved residues implicated in interactions with modulatory proteins, and a highly variable set of 4-10 residues at its very C terminus. Largely ignored and distinguished by lack of primary sequence conservation, the linker is presumed to be intrinsically disordered. Here we employ genetics, biochemistry and cytology to dissect the role of the linker in FtsZ function. Data from chimeric FtsZs substituting the native linker with sequences from unrelated FtsZs as well as a helical sequence from human beta-catenin indicate that while variations in the primary sequence are well tolerated, an intrinsically disordered linker is essential for Bacillus subtilis FtsZ assembly. Linker lengths ranging from 25 to 100 residues supported FtsZ assembly, but replacing the B. subtilis FtsZ linker with a 249-residue linker from Agrobacterium tumefaciens FtsZ interfered with cell division. Overall, our results support a model in which the linker acts as a flexible tether allowing FtsZ to associate with the membrane through a conserved C-terminal domain while simultaneously interacting with itself and modulatory proteins in the cytoplasm.

Probing the conformational flexibility of monomeric FtsZ in GTP-bound, GDP-bound, and nucleotide-free states

The mechanism of nucleotide-regulated assembly and disassembly of the prokaryotic cell division protein FtsZ is not yet clearly understood. In this work, we attempt to characterize the functional motions in monomeric FtsZ through molecular dynamics simulations and essential dynamics (ED) analyses and correlate those motions to FtsZ assembly and disassembly. Results suggest that the nucleotide binding subdomain of FtsZ can switch between multitudes of curved conformations in all nucleotide states, but it prefers to be in an assembly competent less curved conformation in the GTP-bound state. Further, the GDP to GTP exchange invokes a subtle conformational change in the nucleotide binding pocket that tends to align the top portion of core helix H7 along the longitudinal axis of the protein. ED analyses suggest that the longitudinal movements of H7 and the adjacent H6-H7 region modulate the motions of C-domain elements coherently. These longitudinal movements of functionally relevant H7, H6-H7, T3, T7, and H10 regions are likely to facilitate the assembly of GTP-FtsZ into straight filament. On the other hand, the observed radial or random movements of FtsZ residues in the GDP state might not allow the monomers to assemble as efficiently as GTP-bound monomers and could produce curved filaments. Our results correlate very well with recent mutagenesis data that inferred FtsZ conformational flexibility and the involvement of the H6-H7 region in assembly.

The bacterial cytoskeleton: more than twisted filaments

Far from being simple 'bags' of enzymes, bacteria are richly endowed with ultrastructures that challenge and expand standard definitions of the cytoskeleton. Here we review rods, rings, twisted pairs, tubes, sheets, spirals, moving patches, meshes and composites, and suggest defining the term 'bacterial cytoskeleton' as all cytoplasmic protein filaments and their superstructures that move or scaffold (stabilize/position/recruit) other cellular materials. The evolution of each superstructure has been driven by specific functional requirements. As a result, while homologous proteins with different functions have evolved to form surprisingly divergent superstructures, those of unrelated proteins with similar functions have converged.

Comparing contractile apparatus-driven cytokinesis mechanisms across kingdoms

Cytokinesis is the final stage of the cell cycle during which a cell physically divides into two daughters through the assembly of new membranes (and cell wall in some cases) between the forming daughters. New membrane assembly can either proceed centripetally behind a contractile apparatus, as in the case of prokaryotes, archaea, fungi, and animals or expand centrifugally, as in the case of higher plants. In this article, we compare the mechanisms of cytokinesis in diverse organisms dividing through the use of a contractile apparatus. While an actomyosin ring participates in cytokinesis in almost all centripetally dividing eukaryotes, the majority of bacteria and archaea (except Crenarchaea) divide using a ring composed of the tubulin-related protein FtsZ. Curiously, despite molecular conservation of the division machinery components, division site placement and its cell cycle regulation occur by a variety of unrelated mechanisms even among organisms from the same kingdom. While molecular motors and cytoskeletal polymer dynamics contribute to force generation during eukaryotic cytokinesis, cytoskeletal polymer dynamics alone appears to be sufficient for force generation during prokaryotic cytokinesis. Intriguingly, there are life forms on this planet that appear to lack molecules currently known to participate in cytokinesis and how these cells perform cytokinesis remains a mystery waiting to be unravelled.