Many Gram-negative and Gram-positive bacteria, as well a many archaea, possess a regularly structured layer called an S-layer attached to the outermost portion of their cell wall. It is composed of protein or glycoprotein and in electron micrographs, has a pattern resembling a tiled surface. Transmission electron micrograph of a freeze-etched, metal shadowed preparation of a bacterial cell with an S-layer with hexagonal lattice symmetry. Bar = 100nm.
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S-layers have been associated with a number of possible functions that relate to pathogenicity. S-layers can function as adhesins, enabling the bacterium to adhere to host cell membranes and tissue surfaces in order to colonize. Many of the cell-associated protein adhesins used by pathogens are components of the S-layer. The S-layer may protect bacteria from harmful enzymes or changes in pH. Like many other surface components, S-layers contribute to virulence by protecting the bacterium against complement and attack by phagocytes.

The cell wall of a bacterium is an essential structure that protects the delicate cell protoplast from osmotic lysis. The cell wall of Bacteria consists of a polymer of disaccharides cross-linked by short chains of amino acids (peptides). This molecule is a type of peptidoglycan called murein. Murein is unique to the Domain, Bacteria. In the Gram-positive bacteria, the cell wall is thick (15-80 nanometers), consisting of several layers of peptidoglycan complexed with molecules called teichoic acids. In the Gram-negative bacteria, the cell wall is relatively thin (10 nanometers) and is composed of a single layer of peptidoglycan surrounded by a membranous structure called the outer membrane. 

The structure of the muramic acid subunit in the peptidoglycan Escherichia. coli. The molecule consists of N-acetyl glucosamine (NAG) attached (via a beta 1,4 link) to N-acetyl-muramic acid (NAM). Attached to the NAM is a peptide chain, which (in the case of E. coli, as illustrated) consists of L-alanine, D-glutamate, diaminopimelic acid and D-alanine. Some antibiotics, including bacitracin, act by blocking the synthesis of the muramic acid subunit. Penicillin and related antibiotics (beta lactams), as well as vancomycin, block the assembly of the muropeptide subunits into the peptidoglycan polymer.

The cell wall, more properly the cell envelope, is a complicated structure, fundamentally different in Gram-positive and Gram-negative bacteria. Cell wall components are major determinants of virulence in both groups of bacteria. Endotoxin, inherent to all Gram-negative bacteria, is toxic to animals in a variety of ways. Peptidoglycan and LPS, as well as some teichoic acids, induce the alternate complement pathway leading to inflammation. Teichoic acids and O-specific polysaccharides may be used as adhesins by Gram-positive and Gram-negative bacteria, respectively. Some cell wall components protect against phagocytic engulfment or digestion. Variations in the macromolecular structure of cell wall components may be at the basis of antigenic variation as well as specific host resistance to pathogens.

E. coli 0157. Transmission electron micrograph (CDC). O157 refers to the antigenic type of E. coli which, in this case, is based on the precise molecular structure of the O-specific polysaccharide in the cell wall LPS.

The essential outer membrane of Gram-negative bacteria is the target for attack by complement, hydrophobic agents and certain antibiotics. Murein (peptidoglycan) is dismantled by a host enzyme, lysozyme, found in most body fluids. Several antibiotics, mainly the beta lactams, exert their antimicrobial effect by blocking the synthesis and assembly of peptidoglycan.

Schematic drawing the outer membrane of a Gram-negative bacterium.

The membranes of bacteria are structurally similar to the cell membranes of eucaryotes, except that bacterial membranes consist of saturated or monounsaturated fatty acids (rarely polyunsaturated fatty acids) and do not normally contain sterols. The plasma membrane is an exceptionally dynamic structure in bacteria which mediates permeability, transport, secretion and energy generation. In terms of pathogenesis of a bacterium, it is often dependent upon the integrity and function of its plasma membrane. The membrane might be responsible for secretion of toxins, resistance to antimicrobial agents, tactic responses or sensing other environmental signals to turn on genes for virulence.

Endospores are bacterial structures (resting cells) formed by a few groups of bacteria as intracellular structures, but ultimately they are released as free endospores. Biologically, endospores are a fascinating type of cell. Endospores exhibit no signs of life, being described as cryptobiotic. They are highly resistant to environmental stresses such as high temperature (some endospores can be boiled for hours and retain their viability), irradiation, strong acids, disinfectants, etc. They are thought to be the most durable cell produced in nature. Although cryptobiotic, they retain viability indefinitely, such that under appropriate environmental conditions, they germinate back into vegetative cells.

Endospores are formed mainly by two genera of Gram-positive bacteria: Bacillus, the aerobic sporeformers, and Clostridium, the anaerobic sporeformers. Both genera contain pathogens, and the endospores produced by these bacteria invariably play some role in the toxicity, transmission or survival of the pathogen.

Spore stain of a Bacillus species. (CDC). Mature spores stain green whether free or still inside the vegetative sporangium. Vegetative cells and sporangia stain red. The Schaeffer-Fulton stain technique was applied. The primary stain, malachite green, is forced into the spores by heating the prepared slide to boiling for 4-5 minutes. After washing, the vegetative cells are counterstained with safranine.