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Prokaryotic Cytoskeletons: Protein Filaments Organizing Small Cells

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Prokaryotic Cytoskeletons: Protein Filaments Organizing Small Cells REVIEWS Prokaryotic cytoskeletons: protein filaments organizing small cells James Wagstaff and Jan Löwe Abstract | Most, if not all, bacterial and archaeal cells contain at least one protein filament system. Although these filament systems in some cases form structures that are very similar to eukaryotic cytoskeletons, the term ‘prokaryotic cytoskeletons’ is used to refer to many different kinds of protein filaments. Cytoskeletons achieve their functions through polymerization of protein monomers and the resulting ability to access length scales larger than the size of the monomer. Prokaryotic cytoskeletons are involved in many fundamental aspects of prokaryotic cell biology and have important roles in cell shape determination, cell division and nonchromosomal DNA segregation. Some of the filament-forming proteins have been classified into a small number of conserved protein families, for example, the almost ubiquitous tubulin and actin superfamilies. To understand what makes filaments special and how the cytoskeletons they form enable cells to perform essential functions, the structure and function of cytoskeletal molecules and their filaments have been investigated in diverse bacteria and archaea. In this Review, we bring these data together to highlight the diverse ways that linear protein polymers can be used to organize other molecules and structures in bacteria and archaea. 16–18 Endomembrane Eukaryotic cytoskeletons are canonically defined by as well as entirely new classes of filaments , leading to Membrane binding internal their constitutive protein components: actin, tubulin an expanded concept of what a cytoskeleton is (BOX 1). compartments in eukaryotic and intermediate filaments. These three families of We now know that even at their comparatively small typ- cells. filament- forming proteins are involved in diverse cellu- ical cell sizes, bacteria and archaea require the function of Segregation lar processes, providing long-range organization of sub- protein filaments and their ability to act as large and often The active partitioning of a cellular components across broad time and length scales. dynamic cytoskeletons in order to accomplish cellular cellular component into In particular, protein filaments are used in eukaryotes processes at large length scales (reviewed in REF. 19). This daughter cells at division. to control cell and endomembrane morphology (dynam- is because prokaryotic cells are still extremely large when ically and for long-term maintenance of shape), as a compared with individual proteins or even large com- Superfamily TABLE 1 In proteins, the largest group scaffold for long-range organization of cytoplasmic pro- plexes, such as ribosomes. summarizes the that can be determined to have cesses (including as a support matrix for cytoskeleton- diversity of the prokaryotic cytoskeletons that are dis- a common ancestor. associated motor proteins, which remain undiscovered cussed in this Review. Like eukaryotic cytoskeletons, in prokaryotes) and for pushing and pulling other mol- prokaryotic cytoskeletons rely on interactions between ecules in the cytoplasm (particularly for the segregation filament-forming proteins and a vast number of other of DNA during cell division). proteins to modulate or provide function; these accessory The existence of a prokaryotic cytoskeleton that is factors are not discussed extensively in this Review. analogous to eukaryotic cytoskeletons was first hypoth- The various filaments of the prokaryotic cytoskel- esized more than 25 years ago when a member of the eton collectively demonstrate how conserved proteins tubulin superfamily, cell division protein FtsZ, was dis- and their filaments have been preserved during evolu- covered in bacteria and archaea and was found to have tion owing to their usefulness in many different cellular Medical Research Council 1–6 (BOX 2) Laboratory of Molecular a role in cytokinesis . The identification of rod shape- processes that require long-range organization . Biology, Francis Crick Avenue, determining protein MreB as a ‘prokaryotic actin’ fol- In this Review, we summarize our knowledge of the Cambridge CB2 0QH, UK. lowed ~5 years later when a role for MreB in cell shape molecular biology of known filament-forming proteins Correspondence to J.L. maintenance was linked to its polymerization prop- in bacteria and archaea, placing them into evolutionar- [email protected] erties7–9. Many other components of the prokaryotic ily or structurally related classes where possible. This doi:10.1038/nrmicro.2017.153 cytoskeleton have been discovered since then, including classification reveals that diverse biological functions Published online 22 Jan 2017 more homologues of eukaryotic cytoskeletal filaments10–15 are carried out by strikingly similar filaments and also NATURE REVIEWS | MICROBIOLOGY ADVANCE ONLINE PUBLICATION | 1 ©2018 Mac millan Publishers Li mited, part of Spri nger Nature. All ri ghts reserved. REVIEWS Box 1 | Filament-forming proteins and cytoskeletons: key terms Overall, we have a good understanding of the struc- ture of the conserved tubulin protofilament architecture Filaments: self-association into linear polymers (FIG. 1a). This basic protofilament structure has been Many proteins self-associate to form regular linear polymers: filaments. Importantly, adopted by diverse cellular genomes and by mobile filaments are just one way that the self-association of proteins is used to extend the genetic elements, including plasmids and viruses, often geometric capabilities of the proteome, and large protein structures are just one way (FIG. 1b) to organize cells at large length scales. forming higher-order filaments in these cases . In many cases, filament formation is mediated through serial head-to-tail interactions between monomers, which gives the resulting single-subunit-thick protofilament (or FtsZ: the organizer of bacterial cell division. Cell strand) a structural polarity (the two ends are different). Protofilaments can also be division protein FtsZ was the first component of a nonpolar if monomers associate head-to-head and tail-to-tail. Individual protofilaments prokaryotic cytoskeleton to be identified1–4. FtsZ has (or strands) can be associated further to form mature functional filaments. When the common tubulin bipartite globular domain at the filaments further associate in a nonregular manner, this is typically described as a bundle, N-terminus, which is separated by a disordered linker although this is a term that is used inconsistently. Filaments often associate to form of variable length from a short, conserved, C-terminal regular higher-order structures, the most prominent example being ordered sheets of region that is responsible for mediating interactions with adjacent filaments. In many cases, filament formation in vivo occurs on a supporting other proteins (reviewed in REF. 21). matrix, such as a membrane, DNA or another protein filament. We have previously termed these filaments ‘collaborative’ (REF. 166). FtsZ is localized near the membrane at future division sites in almost all bacteria and most archaeal phyla6,22 and Cytoskeleton: a gradually expanded term with no good definition forms a ring-like structure known as the Z-ring, which Defining prokaryotic cytoskeletons is an evergreen problem. Taken literally, ‘cytoskeleton’ contracts during cytokinesis. In bacteria, FtsZ is among implies inclusion of only those filament systems that are relatively static and perform a scaffolding function exclusively; however, the term is generally implied to also include the first molecules to arrive during the assembly of a dynamic systems that push or pull cellular components. We have previously proposed a poorly characterized macromolecular complex known as distinct term for this second class of filaments that are dynamic: ‘cytomotive’ (REF. 167). the divisome, which incorporates many of the enzymatic The ambiguity of ‘cytoskeleton’ and the problem that in initial stages of research it can be activities and other functional modules that are needed unclear whether a system adheres to a given definition have led some researchers of to carry out cytokinesis and to remodel the cell wall filament systems to abandon the term altogether168. One recent review169 proposed an (reviewed in REF. 23). Although the central role of FtsZ in expansive definition: “all cytoplasmic protein filaments and their super-structures that cell division of bacteria is well established23, it has recently either move or scaffold (stabilize or position or recruit) materials within the cell”, although been better characterized using new light microscopy even this helpful definition does not fully reflect our understanding of the term. For techniques24–28. Higher-resolution imaging of the Z-ring example, in this Review, we include a discussion of the periplasmic polymer CrvA and in live bacteria using improved pulsed labelling of newly exclude cytoplasmic Type VI secretion systems. We believe a precise definition of the peptidoglycan prokaryotic cytoskeleton would be of limited use but that the current usage of the term synthesized suggests a new model for FtsZ does meaningfully group diverse cell biological phenomena with filaments at their heart. function whereby relatively short FtsZ filaments tread- More importantly, the term ‘prokaryotic cytoskeleton’ does provide a helpful rallying mill circumferentially around the division plane to drive point for researchers trying to gain a global understanding of the diverse and cell wall remodelling
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