2.1 Prokaryote Cell Structure

Prokaryotes are living entities with a characteristic size and distinct cell structure. They are surrounded by complex multilayered envelopes that serve as a protective boundary between the inside and outside of individual cells (Konhauser, 2007; Kleanthous and Armitage, 2015). The cell envelope also provides physical strength and shape to bacteria, supports the generation of energy for growth and division, permits selective passage of nutrients from the outside and waste products from the inside, facilitates motility, and allows cells to interact with their surroundings. The cell envelope of almost all bacteria consists of two principal layers: an inner cytoplasmic membrane (also known as the plasma membrane) and an external cell wall.

The cytoplasmic membrane consists of a bilayer of lipids, as well as proteins that contribute to active solute transport, metabolic processes, and communication between the cell and the environment. Most of the lipids are phospholipids composed of fatty acids that are attached to a glycerol phosphate backbone by ester bonds in Bacteria and ether bonds in Archaea. Small polar molecules can diffuse through the lipid bilayer, but the passage of ions and large polar molecules is restricted and depends on specific transport proteins embedded in the membrane. The viability of prokaryotic cells depends critically on the physical integrity of the cytoplasmic membrane because structural failure results in cell death.

Two basic types of prokaryotic cells walls are distinguished by their response to the Gram stain, a long-standing test for the classification of bacteria by light microscopy (Figure 2). The cell walls of bacteria staining Gram-positive consist of peptidoglycan (a meshwork of mucopolysaccharides cross-linked in three dimensions by peptide bridges) and a variety of secondary polymers (teichoic or teichuronic acids and proteins). In contrast, Gram-negative walls contain lipopolysaccharides, phospholipids, and proteins arranged in a membrane bilayer (the outer membrane). Sandwiched between the outer membrane and cytoplasmic membrane is a thin layer of peptidoglycan. Some bacteria have cell walls that are neither Gram-­positive nor Gram-negative. The cell walls of Archaea lack the kind of peptidoglycan that is found in Bacteria and instead contain either pseudopeptidoglycan, glycoproteins, or proteins alone. Moreover, prokaryotic cell walls are different from those of eukaryotic plants and fungi, which are made from cellulose and chitin, respectively.

Thin-section transmission electron micrographs showing examples of Gram-positive and Gram-negative bacterial cells.

Figure 2 Thin-section transmission electron micrographs showing examples of Gram-positive a) and Gram-negative b) bacterial cells. The cells are enclosed by a plasma membrane (PM). A peptidoglycan cell wall (PG) surrounds the Gram-positive cell, whereas the Gram-negative cell wall has an outer membrane (OM); sandwiched between the outer membrane and cytoplasmic membrane is a thin layer of peptidoglycan. Extracellular polymeric substances (EPS), which are produced by many types of bacteria, are evident on the Gram-positive cell. A proteinaceous regularly structured surface layer (RS) exists on the Gram-negative bacteria cell. Scale bars = 80 nm.

The cell wall is responsible for providing mechanical strength and shape to prokaryotic cells. If agents such as lysozymes or antibiotics damage the stress-bearing peptidoglycan layer, cell lysis (break down of the membrane of a cell) will occur owing to the turgor pressure of the cytoplasm. A good analogy for turgor pressure is the force pushing outwards in a balloon filled with water. When it comes to cell shape, most bacteria display one of three basic morphologies: spherical coccus, rod-shaped bacilli, or curved varieties that range from comma-shaped vibrio to elongated spirals. While many exist as solitary cells, some remain linked together in pairs, cuboidal tetrads, chains, or random clusters depending on the geometry of cell division (Figure 3).

An epifluorescence photomicrograph of coccoid-shaped bacterial cells growing in tetrads and a differential interference contrast photomicrograph of rod-shaped bacteria growing in a chain among empty filamentous bacterial sheaths.

Figure 3 a) An epifluorescence photomicrograph of coccoid-shaped bacterial cells growing in tetrads. b) A differential interference contrast photomicrograph of rod-shaped bacteria growing in a chain among empty filamentous bacterial sheaths. Scale bars = 4.0 μm.

Extracellular polymeric substances (EPS) composed mainly of acidic polysaccharides (carbohydrates of bonded sugar molecules) and proteins are often secreted in copious amounts by prokaryotes to form external hydrated coatings around cells (Figure 2a). These EPS layers display a high degree of structural variability, ranging from diffuse slime layers to highly organized capsules and sheaths. Two physicochemical properties of EPS contribute to their functions. First, these cell surface coatings are highly hydrated and protect against moisture deficits and water loss. Second, deprotonation (the transfer of a proton in an acid-base reaction) of acidic functional groups fosters the development of a net negative surface charge. This allows EPS to work like an ion exchange resin (sorbent) for the capture of dissolved nutrients and protection against toxic chemical agents. EPS serves additional important functions, which include assisting in cell recognition, attachment to surfaces, and formation of biofilms.

Many prokaryotes possess proteinaceous regularly structured surface arrays (RS or S-layers) on the outside of their cell walls (Figure 2b). These are assemblies of protein subunits arranged into either linear, square, tetragonal, or hexagonal packing formats. Pores are located between the protein subunits that extend completely through the array, providing open channels that are 2 to 3 nm in diameter to the underlying cell wall. This allows RS-layers to function as a molecular sieve, allowing passage of small molecules while excluding large deleterious agents such as wall-degrading enzymes, as well as protecting cells from attack by bacteriophage viruses or predatory bacteria such as Bdellovibrio.

Among Bacteria, flagella are helical protein filaments about 20 nm in diameter and up to 20 μm in length that are responsible for swimming motility (Figure 4a). They can be located at either one or both ends of a cell or be arranged in a uniform (peritrichous) manner about a cell. The basal bodies of flagella are anchored in the cytoplasmic membrane and consist of ring structures that act as a miniature electric motor. Flagellar rotation is driven by energy obtained from the active transport of ions across the cytoplasmic membrane. When flagella rotate in a clockwise direction, cells swim in a forward direction, whereas counter-clockwise rotation produces a tumbling motion.

Pili (sometimes called fimbriae) are fine filamentous protein appendages that are 2 to 10 nm in diameter and up to several micrometers in length (Figure 4b). They extend outwards from the cytoplasmic membrane through the cell wall, but do not have complex anchoring structures analogous to flagellar basal bodies. Some pili play a role in facilitating prokaryotic attachment to surfaces, while others allow for the transfer of genetic material between cells in a process called conjugation. Another group, referred to as type IV pili, are capable of contraction and cause a twitching motion that is sometimes exhibited by cells attached to surfaces. Additional evidence suggests the gliding motility of some bacteria over solid surfaces is at least partially dependent on the production of type IV pili. Further indications suggest the flagella of Archaea resemble type IV pili, in contrast to those of Bacteria.

An epifluorescence photomicrograph of Bacillus subtilis cells with peritrichous flagella labeled with a green fluorescent stain and a transmission electron micrograph negative stain of type IV pili on Pseudomonas aeruginosa.

Figure 4 a) An epifluorescence photomicrograph of Bacillus subtilis cells with peritrichous flagella labeled with a green fluorescent stain (reproduced under the terms of Creative Commons Attribution 3.0 license from Wang et al., 2017). b) A transmission electron micrograph negative stain of type IV pili (arrow) on Pseudomonas aeruginosa (reproduced under the terms of Creative Commons Attribution 3.0 license from Chanyi and Koval, 2014). Scale bars = 500 nm.

To survive periods of environmental stress, some genera of Bacteria (such as Bacillus and Clostridium) form dormant, resistant, non-reproductive structures called endospores. Archaea are not known to form endospores. Individual cells that undergo sporulation produce a single endospore internally within the cytoplasm. Once assembled, an endospore contains a core of DNA and ribosomes surrounded by a protective coat with multiple layers of peptidoglycan and proteins. Endospores are inactive and show no detectable metabolism. They can survive extreme physical and chemical stresses such as ultraviolet radiation, extreme temperatures, disinfectants, and desiccation. In this inanimate state, endospores may remain viable for hundreds to thousands, perhaps even millions, of years.

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