The prokaryotic cytoskeleton is the collective name for all structural filaments in prokaryotes. It was once thought that prokaryotic cells did not possess cytoskeletons, but advances in visualization technology and structure determination led to the discovery of filaments in these cells in the early 1990s. [2] Not only have analogues for all major cytoskeletal proteins in eukaryotes been found in prokaryotes, cytoskeletal proteins with no known eukaryotic homologues have also been discovered. [3] [4] [5] [6] Cytoskeletal elements play essential roles in cell division, protection, shape determination, and polarity determination in various prokaryotes. [7] [8]
FtsZ, the first identified prokaryotic cytoskeletal element, forms a filamentous ring structure located in the middle of the cell called the Z-ring that constricts during cell division, similar to the actin-myosin contractile ring in eukaryotes. [2] The Z-ring is a highly dynamic structure that consists of numerous bundles of protofilaments that extend and shrink, although the mechanism behind Z-ring contraction and the number of protofilaments involved are unclear. [1] FtsZ acts as an organizer protein and is required for cell division. It is the first component of the septum during cytokinesis, and it recruits all other known cell division proteins to the division site. [9]
Despite this functional similarity to actin, FtsZ is homologous to eukaryal tubulin. Although comparison of the primary structures of FtsZ and tubulin reveal a weak relationship, their 3-dimensional structures are remarkably similar. Furthermore, like tubulin, monomeric FtsZ is bound to GTP and polymerizes with other FtsZ monomers with the hydrolysis of GTP in a mechanism similar to tubulin dimerization. [10] Since FtsZ is essential for cell division in bacteria, this protein is a target for the design of new antibiotics. [11] There currently exist several models and mechanisms that regulate Z-ring formation, but these mechanisms depend on the species. Several rod shaped species, including Escherichia coli and Caulobacter crescentus, use one or more inhibitors of FtsZ assembly that form a bipolar gradient in the cell, enhancing polymerization of FtsZ at the cell center. [12] One of these gradient-forming systems consists of MinCDE proteins (see below).
MreB is a bacterial protein believed to be homologous to eukaryal actin. MreB and actin have a weak primary structure match, but are very similar in terms of 3-D structure and filament polymerization.
Almost all non-spherical bacteria rely on MreB to determine their shape. MreB assembles into a helical network of filamentous structures just under the cytoplasmic membrane, covering the whole length of the cell. [13] MreB determines cell shape by mediating the position and activity of enzymes that synthesize peptidoglycan and by acting as a rigid filament under the cell membrane that exerts outward pressure to sculpt and bolster the cell. [1] MreB condenses from its normal helical network and forms a tight ring at the septum in Caulobacter crescentus right before cell division, a mechanism that is believed to help locate its off-center septum. [14] MreB is also important for polarity determination in polar bacteria, as it is responsible for the correct positioning of at least four different polar proteins in C. crescentus. [14]
ParM is a cytoskeletal element that possesses a similar structure to actin, although it behaves functionally like tubulin. Further, it polymerizes bidirectionally and it exhibits dynamic instability, which are both behaviors characteristic of tubulin polymerization. [4] [15] It forms a system with ParR and parC that is responsible for R1 plasmid separation. ParM affixes to ParR, a DNA-binding protein that specifically binds to 10 direct repeats in the parC region on the R1 plasmid. This binding occurs on both ends of the ParM filament. This filament is then extended, separating the plasmids. [16] The system is analogous to eukaryotic chromosome segregation as ParM acts like eukaryotic tubulin in the mitotic spindle, ParR acts like the kinetochore complex, and parC acts like the centromere of the chromosome. [17]
F plasmid segregation occurs in a similar system where SopA acts as the cytoskeletal filament and SopB binds to the sopC sequence in the F plasmid, like the kinetochore and centromere respectively. [17] Lately an actin-like ParM homolog has been found in a gram-positive bacterium Bacillus thuringiensis , which assembles into a microtubule-like structure and is involved in plasmid segregation. [18]
Crenactin is an actin homologue unique to the archaeal kingdom Thermoproteota (formerly Crenarchaeota) that has been found in the orders Thermoproteales and Candidatus Korarchaeum . [19] At the time of its discovery in 2009, it has the highest sequence similarity to eukaryotic actins of any known actin homologue. [20] Crenactin has been well characterized in Pyryobaculum calidifontis ( A3MWN5 ) and shown to have high specificity for ATP and GTP. [19] Species containing crenactin are all rod or needle shaped. In P. calidifontis, crenactin has been shown to form helical structures that span the length of the cell, suggesting a role for crenactin in shape determination similar to that of MreB in other prokaryotes. [19] [21]
Even closer to the eukaryotic actin system is found in the proposed superphylum of Asgardarchaeota. They use primitive versions of profilin, gelsolin, and cofilin to regulate the cytoskeleton. [22]
Crescentin (encoded by creS gene) is an analogue of eukaryotic intermediate filaments (IFs). Unlike the other analogous relationships discussed here, crescentin has a rather large primary homology with IF proteins in addition to three-dimensional similarity - the sequence of creS has a 25% identity match and 40% similarity to cytokeratin 19 and a 24% identity match and 40% similarity to nuclear lamin A. Furthermore, crescentin filaments are roughly 10 nm in diameter and thus fall within diameter range for eukaryal IFs (8-15 nm). [23] Crescentin forms a continuous filament from pole to pole alongside the inner, concave side of the crescent-shaped bacterium Caulobacter crescentus . Both MreB and crescentin are necessary for C. crescentus to exist in its characteristic shape; it is believed that MreB molds the cell into a rod shape and crescentin bends this shape into a crescent. [1]
The MinCDE system is a filament system that properly positions the septum in the middle of the cell in Escherichia coli . According to Shih et al., MinC inhibits the formation of the septum by prohibiting the polymerization of the Z-ring. MinC, MinD, and MinE form a helix structure that winds around the cell and is bound to the membrane by MinD. The MinCDE helix occupies a pole and terminates in a filamentous structure called the E-ring made of MinE at the middle-most edge of the polar zone. From this configuration, the E-ring will contract and move toward that pole, disassembling the MinCDE helix as it moves along. Concomitantly, the disassembled fragments will reassemble at the opposite polar end, reforming the MinCDE coil on the opposite pole while the current MinCDE helix is broken down. This process then repeats, with the MinCDE helix oscillating from pole to pole. This oscillation occurs repeatedly during the cell cycle, thereby keeping MinC (and its septum inhibiting effect) at a lower time-averaged concentration at the middle of the cell than at the ends of the cell. [24]
The dynamic behavior of the Min proteins has been reconstituted in vitro using an artificial lipid bilayer as mimic for the cell membrane. MinE and MinD self-organized into parallel and spiral protein waves by a reaction-diffusion like mechanism. [25]
Bactofilin (InterPro : IPR007607 ) is a β-helical cytoskeletal element that forms filaments throughout the cells of the rod-shaped proteobacterium Myxococcus xanthus . [26] The bactofilin protein, BacM, is required for proper cell shape maintenance and cell wall integrity. M. xanthus cells lacking BacM have a deformed morphology characterized by a bent cell body, and bacM mutants have decreased resistance to antibiotics targeting the bacterial cell wall. M. xanthus BacM protein is cleaved from its full-length form to allow polymerization. Bactofilins have been implicated in cell shape regulation in other bacteria, including curvature of Proteus mirabilis cells, [27] stalk formation by Caulobacter crescentus, [28] and helical shape of Helicobacter pylori . [29]
Within the phylum Spirochaetes, a number of species share a filamentous cytoplasmic ribbon structure formed by individual filaments, composed of the coiled-coil protein CfpA (Cytoplasmic filament protein A, Q56336 ), linked together by bridging components and by anchors to the inner membrane. [30] [31] While present in genera Treponema , Spirochaeta , Pillotina, Leptonema, Hollandina and Diplocalyx , they are however, absent in some species as per the example of Treponema primitia . [32] [33] [34] [35] With a cross-section dimension of 5 x 6 nm (horizontal/vertical) they fall within diameter range of eukaryal intermediate filaments (IFs) (8-15 nm). Treponema denticola cells lacking the CfpA protein form long concatenated cells with a chromosomal DNA segregation defect, a phenotype also affecting the pathogenicity of this organism. [36] [37] The absence of another cell ultrastructure, the periplasmic flagella filament bundle, do not alter the structure of the cytoplasmic ribbon. [38]
Microtubules are polymers of tubulin that form part of the cytoskeleton and provide structure and shape to eukaryotic cells. Microtubules can be as long as 50 micrometres, as wide as 23 to 27 nm and have an inner diameter between 11 and 15 nm. They are formed by the polymerization of a dimer of two globular proteins, alpha and beta tubulin into protofilaments that can then associate laterally to form a hollow tube, the microtubule. The most common form of a microtubule consists of 13 protofilaments in the tubular arrangement.
The cytoskeleton is a complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is composed of similar proteins in the various organisms. It is composed of three main components: microfilaments, intermediate filaments, and microtubules, and these are all capable of rapid growth or disassembly depending on the cell's requirements.
Actin is a family of globular multi-functional proteins that form microfilaments in the cytoskeleton, and the thin filaments in muscle fibrils. It is found in essentially all eukaryotic cells, where it may be present at a concentration of over 100 μM; its mass is roughly 42 kDa, with a diameter of 4 to 7 nm.
Intermediate filaments (IFs) are cytoskeletal structural components found in the cells of vertebrates, and many invertebrates. Homologues of the IF protein have been noted in an invertebrate, the cephalochordate Branchiostoma.
MreB is a protein found in bacteria that has been identified as a homologue of actin, as indicated by similarities in tertiary structure and conservation of active site peptide sequence. The conservation of protein structure suggests the common ancestry of the cytoskeletal elements formed by actin, found in eukaryotes, and MreB, found in prokaryotes. Indeed, recent studies have found that MreB proteins polymerize to form filaments that are similar to actin microfilaments. It has been shown to form multilayer sheets comprising diagonally interwoven filaments in the presence of ATP or GTP.
FtsZ is a protein encoded by the ftsZ gene that assembles into a ring at the future site of bacterial cell division. FtsZ is a prokaryotic homologue of the eukaryotic protein tubulin. The initials FtsZ mean "Filamenting temperature-sensitive mutant Z." The hypothesis was that cell division mutants of E. coli would grow as filaments due to the inability of the daughter cells to separate from one another. FtsZ is found in almost all bacteria, many archaea, all chloroplasts and some mitochondria, where it is essential for cell division. FtsZ assembles the cytoskeletal scaffold of the Z ring that, along with additional proteins, constricts to divide the cell in two.
Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member proteins of that superfamily. α- and β-tubulins polymerize into microtubules, a major component of the eukaryotic cytoskeleton. Microtubules function in many essential cellular processes, including mitosis. Tubulin-binding drugs kill cancerous cells by inhibiting microtubule dynamics, which are required for DNA segregation and therefore cell division.
Spectrin is a cytoskeletal protein that lines the intracellular side of the plasma membrane in eukaryotic cells. Spectrin forms pentagonal or hexagonal arrangements, forming a scaffold and playing an important role in maintenance of plasma membrane integrity and cytoskeletal structure. The hexagonal arrangements are formed by tetramers of spectrin subunits associating with short actin filaments at either end of the tetramer. These short actin filaments act as junctional complexes allowing the formation of the hexagonal mesh. The protein is named spectrin since it was first isolated as a major protein component of human red blood cells which had been treated with mild detergents; the detergents lysed the cells and the hemoglobin and other cytoplasmic components were washed out. In the light microscope the basic shape of the red blood cell could still be seen as the spectrin-containing submembranous cytoskeleton preserved the shape of the cell in outline. This became known as a red blood cell "ghost" (spectre), and so the major protein of the ghost was named spectrin.
Crescentin is a protein which is a bacterial relative of the intermediate filaments found in eukaryotic cells. Just as tubulins and actins, the other major cytoskeletal proteins, have prokaryotic homologs in, respectively, the FtsZ and MreB proteins, intermediate filaments are linked to the crescentin protein. Some of its homologs are erroneously labelled Chromosome segregation protein ParA. This protein family is found in Caulobacter and Methylobacterium.
The cell cortex, also known as the actin cortex, cortical cytoskeleton or actomyosin cortex, is a specialized layer of cytoplasmic proteins on the inner face of the cell membrane. It functions as a modulator of membrane behavior and cell surface properties. In most eukaryotic cells lacking a cell wall, the cortex is an actin-rich network consisting of F-actin filaments, myosin motors, and actin-binding proteins. The actomyosin cortex is attached to the cell membrane via membrane-anchoring proteins called ERM proteins that plays a central role in cell shape control. The protein constituents of the cortex undergo rapid turnover, making the cortex both mechanically rigid and highly plastic, two properties essential to its function. In most cases, the cortex is in the range of 100 to 1000 nanometers thick.
In molecular biology, treadmilling is a phenomenon observed within protein filaments of the cytoskeletons of many cells, especially in actin filaments and microtubules. It occurs when one end of a filament grows in length while the other end shrinks, resulting in a section of filament seemingly "moving" across a stratum or the cytosol. This is due to the constant removal of the protein subunits from these filaments at one end of the filament, while protein subunits are constantly added at the other end. Treadmilling was discovered by Wegner, who defined the thermodynamic and kinetic constraints. Wegner recognized that: “The equilibrium constant (K) for association of a monomer with a polymer is the same at both ends, since the addition of a monomer to each end leads to the same polymer.”; a simple reversible polymer can’t treadmill; ATP hydrolysis is required. GTP is hydrolyzed for microtubule treadmilling.
In biology, a protein filament is a long chain of protein monomers, such as those found in hair, muscle, or in flagella. Protein filaments form together to make the cytoskeleton of the cell. They are often bundled together to provide support, strength, and rigidity to the cell. When the filaments are packed up together, they are able to form three different cellular parts. The three major classes of protein filaments that make up the cytoskeleton include: actin filaments, microtubules and intermediate filaments.
Treponema denticola is a Gram-negative, obligate anaerobic, motile and highly proteolytic spirochete bacterium. It is one of four species of oral spirochetes to be reliably cultured, the others being Treponema pectinovorum, Treponema socranskii and Treponema vincentii. T. denticola dwells in a complex and diverse microbial community within the oral cavity and is highly specialized to survive in this environment. T. denticola is associated with the incidence and severity of human periodontal disease. Treponema denticola is one of three bacteria that form the Red Complex, the other two being Porphyromonas gingivalis and Tannerella forsythia. Together they form the major virulent pathogens that cause chronic periodontitis. Having elevated T. denticola levels in the mouth is considered one of the main etiological agents of periodontitis. T. denticola is related to the syphilis-causing obligate human pathogen, Treponema pallidum subsp. pallidum. It has also been isolated from women with bacterial vaginosis.
Actin, cytoplasmic 2, or gamma-actin is a protein that in humans is encoded by the ACTG1 gene. Gamma-actin is widely expressed in cellular cytoskeletons of many tissues; in adult striated muscle cells, gamma-actin is localized to Z-discs and costamere structures, which are responsible for force transduction and transmission in muscle cells. Mutations in ACTG1 have been associated with nonsyndromic hearing loss and Baraitser-Winter syndrome, as well as susceptibility of adolescent patients to vincristine toxicity.
Segrosomes are protein complexes that ensure accurate segregation (partitioning) of plasmids or chromosomes during bacterial cell division.
In molecular biology, the FERM domain is a widespread protein module involved in localising proteins to the plasma membrane. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus in the majority of proteins in which it is found.
Cytoskeletal drugs are small molecules that interact with actin or tubulin. These drugs can act on the cytoskeletal components within a cell in three main ways. Some cytoskeletal drugs stabilize a component of the cytoskeleton, such as taxol, which stabilizes microtubules, or Phalloidin, which stabilizes actin filaments. Others, such as Cytochalasin D, bind to actin monomers and prevent them from polymerizing into filaments. Drugs such as demecolcine act by enhancing the depolymerisation of already formed microtubules. Some of these drugs have multiple effects on the cytoskeleton: for example, Latrunculin both prevents actin polymerization as well as enhancing its rate of depolymerization. Typically the microtubule targeting drugs can be found in the clinic where they are used therapeutically in the treatment of some forms of cancer. As a result of the lack of specificity for specific type of actin, the use of these drugs in animals results in unacceptable off-target effects. Despite this, the actin targeting compounds are still useful tools that can be used on a cellular level to help further our understanding of how this complex part of the cells' internal machinery operates. For example, Phalloidin that has been conjugated with a fluorescent probe can be used for visualizing the filamentous actin in fixed samples.
A plasmid partition system is a mechanism that ensures the stable inheritance of plasmids during bacterial cell division. Each plasmid has its independent replication system which controls the number of copies of the plasmid in a cell. The higher the copy number, the more likely the two daughter cells will contain the plasmid. Generally, each molecule of plasmid diffuses randomly, so the probability of having a plasmid-less daughter cell is 21−N, where N is the number of copies. For instance, if there are 2 copies of a plasmid in a cell, there is 50% chance of having one plasmid-less daughter cell. However, high-copy number plasmids have a cost for the hosting cell. This metabolic burden is lower for low-copy plasmids, but those have a higher probability of plasmid loss after a few generations. To control vertical transmission of plasmids, in addition to controlled-replication systems, bacterial plasmids use different maintenance strategies, such as multimer resolution systems, post-segregational killing systems, and partition systems.
FtsA is a bacterial protein that is related to actin by overall structural similarity and in its ATP binding pocket.
Cell mechanics is a sub-field of biophysics that focuses on the mechanical properties and behavior of living cells and how it relates to cell function. It encompasses aspects of cell biophysics, biomechanics, soft matter physics and rheology, mechanobiology and cell biology.