Gram_negative_wall

The Gram Negative Cell Envelope

The diagram above shows a bacterial envelope. It contains an inner membrane, resembling the 'skin' or membrane of an animal cell, in that it is a typical phospholipid bilayer, but then wrapped around this is a cell wall layer of tough but flexible peptidoglycan and then wrapped around this is the outer membrane.

The labelled version of the diagram, followed by a key, is shown below. This type of envelope belongs to bacteria known as
Gram negative bacteria. Gram's stain is a dye used to stain bacteria - if the bacteria
stain purple then they are said to be Gram positive, but if they do not stain then they are said to be Gram negative and many Gram negative bacteria have the envelope structure shown here. This is important as it drastically narrows down the choices when one is attempting to identify a strain of bacterium - the first things we determine are the cell shape and the Gram stain reaction.

Whereas an animal cell, such as the cells that make up your body, have a single membrane skin consisting of a
double layer of phospholipids, Gram negative bacteria have two such double-layered membranes. Each membrane can be divided into an outer and an inner leaflet - a leaflet is a single layer
of lipids (such as phospholipids) and two opposing leaflets are needed to make a stable membrane. The
outer membrane(OM) - the outermost of the two - is often the surface-most layer of a bacterial cell - the
layer that faces the outside world. The inner leaflet is made up of phospholipids (shown in green), like a typical biological membrane, but the outer leaflet is made up of a type of lipid (fat) unique to Gram negative bacteria, called
lipopolysaccharide (LPS) - shown in orange. LPS is also called endotoxin, as the bacteria shed some of it into their environment and if they are inside the human body, then the LPS
has toxic effects on the human body and is a primary inducer of fever when a person is infected by bacteria such as
Salmonella typhi which causes typhoid fever.

Gram negative wall labelled

Gram_negative_wall_key

The inner membrane (IM) has two phospholipids (just as in the animal cell membrane). Beneath this membrane, at the bottom of the digram, we have the internal parts of the cell (the cell cytoplasm), so the inner membrane (or cytoplasmic membrane) is the innermost layer of the bacteria's 'skin'. To add a scale, the inner membrane has the usual membrane thickness of about 7.5 nanometres (7.5 millionths of a millimetre). This is extremely thin, but compared to the size of the bacterium (typically one thousandth of a millimetre in diameter) this is not so thin and biological membranes are also very strong and more importantly they automatically repair themselves (unless the damage is too severe). However, the world is a rough place and so most bacteria have additional structures to protect them. In particular the layer of material called peptidoglycan forms a very strong wall around the cell. Peptidoglycan is a tough, rigid and fibrous material, though in Gram negatives it is quite thin and so quite flexible and elastic and maintains the shape of the cell. The peptidoglycan sits in the 'space' between the inner and outer membranes. This space is called the periplasmic space and is actually filled with a gelatinous substance called periplasm. Periplasm contains many proteins (not shown in the diagram) including lipoproteins (proteins that connect to lipids in the membranes) that connect the peptidoglycan to the inner membrane, anchoring everything in place. The periplasm is typically 13 to 25 nm thick ( 1 nm = 1 nanometre = 1 millionth of a millimetre) depending on growth conditions and contains a 5 to 8 nm thick layer of peptidoglycan which is closely associated with the OM.

Both membranes contain proteins that float in the lipid sheets. However, the proteins of the inner
membrane are especially diverse and three are shown in the diagram. These proteins may span the
membrane (so-called transmembrane proteins that cross the membrane) or sit in one or other leaflet or
even flip from one side to the other. They have very diverse functions, including the import of nutrients
into the cell and the export of unwanted materials. Others function as sensors that monitor the
environment. The outer membrane contains proteins that form pores called porins that allow nutrients
into the periplasm where they may be processed by periplasmic proteins and then transported into the
cell by inner membrane proteins.

The lipopolysaccharide of the outer leaflet of the outer membrane may have chains of sugars
(
polysaccharides) attached to it. Depending on the strain and species these chains may be of variable
length, but they form a thin layer of protective slime over the cell surface. In addition much longer
polysaccharides may also be present, which form a thick
slime capsule around the cell
(polysaccharides may form a slimy gel when mixed with water). This capsule may as thick as the
bacterium and offers superb protection against many threats. Whether or not there is a slime capsule,
there may be a layer of crystalline protein on top of the outer membrane, called an S-layer, which may
offer additional protection. All those structures that occur on the surface may be involved in adhesion -
allowing the bacteria to stick to surfaces and also provide protection from host defenses in pathogenic bacteria. For example, slime capsules can repel the efforts of immune cells to phagocytose (eat) bacteria. Slime capsules also protect bacteria in the environment from desiccation, since they act as a buffer and store of water.

A fringe of
pili may also cover the cell and flagella may also project through the envelope.

Gram negative cell envelope - detailed version

Above: a more detailed model of the gram-negative cell envelope. (Another version of this diagram appeared in Pumbwe et al., 2006. The Bacteroides fragilis cell envelope: quarterback, linebacker, coach-or all three? Anaerobe 12(5-6):211-20). On the left-hand side of the diagram the LPS (orange) making up the outer leaflet of the outer membrane consists of a lipid core and polysaccharide chain (shorter orange chains). These carbohydrate chains form a slimy layer called the glycocalyx. Some species, such as Bacteroides fragilis, have additional organic chains attached (longer chains, shown here are the two types typical of B. fragilis) which make up a slime capsule.

On the right a different configuration is shown: the outermost wall layer in this case consists of a coat of porous S-proteins forming the S-layer. An S-layer is found in some Gram-negative bacteria, some Gram-positives and some archaebacteria (archaea). In this instance it is attached to a smooth variant of LPS (smooth LPS has much shorter carbohydrate chains attached to it). The S-proteins are packaged into a sqaure or helical lattice that spirals around the bacterium, completely covering its surface. These proteins self-assemble and may consist of one or two protein types. The pores in the S-proteins means that the S-layer acts as a molecular sieve, only allowing through molecules below a certain size, though in some S-layers more than one pore diameter may be present (but generally in the 2 nm to 8 nm diameter range). S-layers may function as ion stores and buffers, as attachment sites for secreted enzymes, in adhesion to surfaces, and in pathogenic bacteria they provide protection against host defenses, such as complement proteins which disrupt the cell membranes of foreign cells. In the center is a pilus.


Bacteroides fragilis showing outer membrane vesicle (OMV)

Above:a cross-section through the rod-shaped Gram-negative bacterium Bacteroides fragilis. The double layers of the outer and inner membrane can be clearly seen and also some layers of peptidoglycan in the periplasm. In the bottom left, an outer membrane vesicle (OMV) has been budded off. These OMVs serve many different functions in bacteria, including communication. B. fragilis is a gut commensal of humans. One such function in B. fragilis is communication with the host: the OMV carries a biochemical signal to the epithelial cells lining the intestinal lumen of the host to inform the host that the bacterium is friendly and beneficial, causing the host to turn off the immune response against the gut contents. If this communication system fails, or a bacterium like B. fragilis is not present in sufficient numbers in the gut flora, then the host may mount an immune response against the gut contents, resulting in an inflammatory bowel disease.


The Gram Positive Cell Wall

The Gram positive envelope lacks the outer membrane altogether, and like an animal cell has a single membrane which is a double layer of phospholipids. However, on top of this is a very thick wall of peptidoglycan (10-80 nanometres thick). There may also be an S-layer on top of the peptidoglycan and there may be a slime capsule also on top of the peptidoglycan. The structure of Gram positive bacterial envelopes is shown below:

Gram_positive_wall

Gram_positive_wall_labelled

Gram_positive_wall

Gram_positive_wall

The common core components of the Gram-positive cell wall are shown above and below. Teichoic acids are of two classes: lipotechoic acids (LTA) or membrane teichoic acids are anchored to a glycolipid in the cell membrane; wall teichoic acids (WTA) are anchored to N-acetyl-muramic acid (NAM) via the hydroxyl group of carbon-6 (through a phosphodiester linkage); the peptidoglycan (PG) is generally much thicker than depicted here, with more layers, but the glycosylated chains of some of the teichoic acids emerge from its surface; phospholipid bilayer (PLB); lipoproteins (LP) are also present in Gram-negative envelopes and contain a membrane lipid anchor attached to a cysteine residue; membrane proteins (MP) are very diverse with a multitude of functions.

Additional, and often very long, polymer chains may be attached to the peptidoglycan and extend from the cell surface to form a slime capsule (not shown). The chemical nature of these capsules is extremely variable. In Bacillus anthracis, for example, the capsule consists of polymer chains of D-glutamic acid attached to some of the peptide chains in the peptidoglycan (the remaining peptide chains form cross-bridges that strengthen the peptidoglycan as explained below (see the structure of peptidoglycan)).

Gram_positive_wall

Additionally the peptidoglycan layer may contain long chain molecules called teichoic acids (TAs) and lipoteichoic acids (LTAs). Lipoteichoic acids (LTAs) are attached to the cytoplasmic membrane and pass through the peptidoglycan to emerge from its surface as a fringe. The peptidoglycan is a fibrous mesh and some fibres also stand up on the surface, giving the cell a hairy appearance (though this would be slimy in real life). The teichoic acids do not attach to the lipids in the membrane but are present on the outer surface of the peptidoglycan layer and also within it. The thick peptidoglycan layer forms a rigid and very tough wall that protects the bacterium and maintains its shape.

Teichoic acids may make up as much as 60% of the total cell wall mass of Gram-positive bacteria. each consists of a basal pair of modified hexose ring sugars, joined together and to either peptidoglycan (wall teichoic acids, WTA) via a phosphodiester link (-O-P-O-) or to a glycolipid in the cell membrane (lipoteichoic acids or membrane teichoic acids). The rest of the molecule consists of a long chain of carbon atoms, with -O- and -O-P-O- replacing carbon atoms at regular intervals and sugar molecules and/or D-alanine side-groups decorating the chain.Teichoic acids not only strengthen the cell wall, but may act to store and buffer ions and in attachment to surfaces and are an important virulence factor allowing gram-positive bacteria to colonize the body. However, some bacteriophages (viruses that attack bacteria) recognise and bind to teichoic acids prior to inserting their genetic material into the bacterium.

Gram's stain contains a dye that stains peptidoglycan purple. Peptidoglycan is unique to bacteria, but in Gram negative bacteria the outer membrane stops the dye molecules from reaching the peptidoglycan, and so it does not get stained. Some Gram negative bacteria also have no peptidoglycan at all, they may have a single membrane, perhaps with some slime on top, and no rigid wall, or they may have rigid walls composed of different materials. There is in fact a very wide range of envelope types in bacteria, but the two discussed here are the two most commonly encountered.

Gram_positive_wall

Importance of the cell envelope

First of all the cell envelope is protective. It protects against both toxic chemicals and physical trauma. Mechanically, even the envelope of Gram negative bacteria, with a thin peptidoglycan layer, is immensely strong. For example, the pressure needed to collapse Gram negative bacteria varies from 30 to 100 atmospheres, depending upon species. Compare this  with the pressure needed to collapse the hull of a military submarine: 20-25 atmospheres for a WWII U-boat and about 73 atmospheres for a modern nuclear submarine! Usually the inside of the cell will be maintained at a higher pressure than the outside. The strength of the cell wall also maintains the shape of the cell.

The slime capsule protects the bacteria from noxious chemicals and from predators such as
amoebae (or in the case of pathogens the white blood cells). The slime may be so extensive as to encapsulate a whole colony of bacteria. Such slime mats and biofilms and balls of millions of bacteria may form quite large and easily visible structures.

The lipid membranes act as selective barriers, allowing only certain materials in and out of the cell, rather like a passport control (but probably more rigorous!). Nutrients are allowed into the cell and unwanted waste and toxins are removed. In this way the cell can maintain an internal environment different from that outside the cell - inside is salty, even if the cell is in fresh water and the salts may be different to those in sea water. Lipid membranes are disrupted by detergents (lipids are fats) and when this happens the cell contents mix with the surroundings and the cell is destroyed.

The envelope must also sense the environment - the envelope of a cell is its interface with the outside world. It does this with specific proteins that are designed to detect and respond to specific signals, such as the presence of nearby food or signals from other bacteria.

In a later update we shall look at how cells, such as bacteria, import and export materials.

How strong is the cell envelope?

The envelope of a Gram-negative bacterium, such as Salmonella typhimurium, can withstand pressures of about 100 atmospheres before breaching. In comparison, the hull of a nuclear submarine would breach at around 70 atmospheres. Under normal conditions, however, turgor pressure (due to osmosis swelling the cell with water) generates an internal pressure of 3 to 5 atmospheres in Escherichia coli and presumably this increases with depth so as to counteract external pressures.

Other Variants

The mollicutes are a strange group of bacteria which lack a rigid cell wall and simply have a single typical
bilayered phospholipid membrane. Carbohydrate chains are attached to the outer surface of the membrane, giving it a protective slimy covering. These cells, like animal cells, are sensitive to
osmotic
lysis
. The contents of cells are quite salty, for example animal cell cytoplasm has a salt content similar to that of sea water, and when a cell lacking a rigid wall is placed in pure water, then the salts inside it draws water through the membrane and the cell swells and bursts. This movement of water across the membrane is called osmosis and the bursting of the cell is lysis. Mollicutes and animal cells burst when immersed in
fresh (non-salty) water. Cells with a rigid wall, such as plant cells and the typical bacteria described above do not burst since their rigid walls prevent the cell from swelling too much. Mollicutes are also
pleomorphic - meaning that they are capable of assuming a variety of shapes, since they lack a rigid wall
and are somewhat plastic and elastic. The mollicute
Spiroplasma, however, adopts a helical form (0.2
micrometres in diameter and 3 to 5 micrometres long) as they contain contractile cylindrical protein rods that both maintain shape and move the cell.

Mollicutes are parasitic on other creatures.
Spiroplasma is a parasite of plants and arthropods.
Mycoplasma is a mollicute that lives in the mucous membranes of animals (such as the mucous lining the
repiratory and genital tracts and the synovial membranes of joints) and may cause pneumonia or arthritis.
Acholeplasma is a mollicute that infects various animal tissues. Anaeroplasma inhabits the rumen of
ruminants and secretes enzymes that destroy the rigid walls of other bacteria and lyses them, allowing the
Acholeplasma to feed on the bacterial cell contents. Ureaplasma need urea as a source of energy and normally inhabit the mouth, respiratory and genital tracts of humans and other animals. The phytoplasmas cause more than 600 recognised plant diseases and are spread by insects that feed on the phloem of plants (such as aphids).

Most mollicutes incorporate sterols from the host into their membranes, which increases the strength and rigidity of their membranes.
Acholeplasma may synthesise carotenoids to strengthen its membrane in a
similar way. The mollicutes survive without cell walls because of their parasitic nature - their host provides an osmotically stable environment (the saltiness of animal and plant bodies is well regulated) and so  they can survive without a rigid cell wall, but would soon be lysed in the external environment.

The
archaebacteria are an ancient group of bacteria that are distant relatives of the bacteria we have considered so far (the eubacteria or 'true' bacteria). In fact, biochemically all the eukaryotes (animals, plants, fungi and protoctistans) are more closely related to eubacteria than eubacteria are to archaebacteria! Archaebacteria probably represent the most ancient life forms on Earth that still exist. Although quite widespread and turning up all the time in common places, archaebacteria are best known as inhabitants of extreme environments, such as hot volcanic ponds and extremely salty lakes and highly acidic waters.

The membranes of eukaryotes and eubacteria all have the same basic structure - they are composed of two leaflets of phospholipids with proteins embedded and are about 8 nanometres thick - what we call the
unit membrane. These phospholipids all consist of  lipids joined to a phosphate head by ester linkages (-O-(C=O)-). However, the phospholipids of archaebacteria are unique in that the lipids are joined to the phosphate head by ether linkages (-O-). This fundamental difference suggest that archaebacteria and eubacteria diverged early in the Earth's history (maybe 3 billion years ago or so) or had separate origins and that all other cellular life as we know it ion Earth, evolved from the eubacteria (yes, humans evolved from bacteria!).

Archaebacteria may possess a rigid cell wall, but whereas the cell wall of eubacteria (usually called simply bacteria) is usually made of peptidoglycan (murein) the archaebacterial cell wall contains a different chemical called pseudomurein (pseudopeptidoglycan), but is otherwise similar to the Gram positive arrangement - with a wall overlying a single unit membrane. Some archaebacteria have a flexible wall of polysaccharides (long chain sugars) and lipoproteins (proteins with attached lipids) rather than a rigid cell wall.

Planctomycetes are unusual bacteria with a single unit membrane and a rigid wall made of glycoprotein (protein with sugars attached). In short, the bacteria exhibit a very wide range of cell envelope structures, which is a reflection of their diverse evolutionary relationships and diverse biochemistry.

Note on the thickness of biological membranes

It has been pointed out to use that the textbook value of membrane thickness, which is obtained from standard transmission electron microscopy (TEM) using chemical fixatives, which is some 6-8 nm, is larger than that measured with techniques like diffraction or predicted on the basis of computed dimensions of membrane-spanning proteins. The latter give values of around 3 nm (though these measurements may also be subject to larger errors than usually assumed).

Electron microscopy likely exaggerates the apparent thickness of membranes - chemical fixation may cause them to swell, and staining with electron-dense reagents will certainly add to their thickness. There is possibly also observer bias - selecting areas for measurement where the membrane is more readily visible (although stereology can help address these issues). There is also a difficult issue of defining the 'membrane'. In reality membranes have attached carbohydrate chains, forming the glycocalyx, and some of these may be incorporated in crude measurements. We conclude that the smaller value, using less disruptive techniques like neutron diffraction, are likely to be the more accurate measure of the actual phospholipid bilayer thickness (excluding glycocalyx). To conclude, the average thickness of the bacterial inner membrane (meaning the lipid bilayers of inner and outer membranes) is probably closer to 3.5 to 4 nm, as obtained by X-ray diffraction. Measurements of the outer membrane give a thickness of 12-14 nm, based on cryo-fixation TEM, which avoids the problems of chemical fixation and staining.

That said the official value for a mammalian cell membrane is given as 7.5 nm (not sure what method was used here). Animal cell membranes are different, with different cholesterol components, for example, and variation between different cell types is to be expected. Textbooks often do not cite their sources and early biologists often applied 7.5 nm as a ball-park figure to any phospholipid bilayer, possibly without attempting accurate measurements.

Figures with references can be found in the
bionumbers database.

Outer Membrane Proteins (OMPs)

OMPs. It's easier to understand the bacterial envelope if one has some examples of proteins associated with it and their functions. Outer membrane contains proteins (OMPs) are either an integral part of the outer membrane or attached or embedded in its surface. Since the Om interfaces with the external environment, the functions of these proteins are often readily apparent. In addition there are periplasmic proteins in the periplasm and inner membrane proteins (IMPs). Often all three classes of proteins assemble in groups which work together. e.g. to transport materials into or out of the cell. OMPs are also exposed on the surface of the cell and so are a target for host antibodies during infection by pathogenic strains of bacteria.

Porins. A major class of OMP is the porin. These associate in triplets (trimers) to form a channel or pore across the outer membrane. They may be specific or non-specific. For example LamB is a porin in Escherichia coli which allows maltose and maltodextrin sugars, nutrients, to pass from the external medium into the periplasm. OprB is a sugar-specific porin in Pseudomonas aeruginosa. In LamB The maltose binds to a specific site within the porin channel before diffusing across (essentially one-dimensional diffusion). LamB consists of a trimer of three proteins, each barrel-shaped (a beta-barrel) and acting as a pore (so there are 3 pores per unit, which is typical of porins) and there are about 10 000 such units per cell. Inside each channel there is a hydrophobic track (of amino acid residues) and a hydrophilic track (of amino acid residues). The hydrophobic face of the sugar molecule to be imported is thought to align with the hydrophobic track, the hydrophilic -OH groups of the sugar with the hydrophilic track and the sugar molecule is thought to translocate through the channel by making and breaking hydrogen-bonds as it goes.

Above: The E. coli porin OmpC as seen in plan view, showing the classic porin trimer of barrels structure. (The source file for OmpC was downloaded from the NCBI protein databank (PDB, National Library of Medicine (NLM)) and was originally uploaded by Basle et al. 2006 and obtained by X-ray diffraction of crystallised OmpC.) The smaller central 'channel' in between the 3 trimers possibly binds a molecule of LPS in the outer membrane, or possibly functions as a gas channel for gas exchange (as it apparently does in mammalian porins).

Non-specific porins. Some porins, however, are largely non-specific, allowing any substance small enough to fit inside to cross. OprF is a major OMP in Pseudomonas and is non-specific. It is also multifunctional, acting as a structural protein, giving the outer membrane strength, and binds the outer membrane to the peptidoglycan in the periplasm. It forms channels of two different sizes but is downregulated in some multidrig resistant strains, reducing the permeability of the OM to antibiotics. The OM of Pseudomona aeruginosa is generally only 8% as permeable as that of Escherichia coli, though its porins allow larger molecules to cross the membrane (up to a molecular mass of 3000 in Pseudomonas aeruginosa compared to 500 in Escherichia coli).

Efflux porins. Simply reducing membrane permeability is not sufficient to keep drugs and toxins out of the bacterial cell, however, and some porins are efflux porins which are coupled to efflux systems which pump unwanted materials out of the bacterium. These include OprJ and OprM in Pseudomonas. Although more copies of these efflux porins may be found in bacteria exposed to antibiotics in a clinical or human-made environmental setting, conferring antibiotic resistance, it is important to understand that they have other more natural efflux functions, removing plant toxins and naturally occurring antibiotics, for example. These pumps often recognise and expel a wide variety of toxins, and in at least one case it has been shown that they tend to recognise a wide range of compounds, but especially those with activated benzene rings, or similar charge distributions, which are a common feature of many plant secondary metabolites. This wide specificity also gives them the ability to expel novel toxins, including antibiotics.

OprP is a
Pseudomonas porin specific for phosphate (an essential mineral nutrient). Phosphate starvation induces the production of these porins which act as electrical wires conducting negatively charged phosphate ions along a series of binding sites inside the channel before passing them onto a periplasmic phosphate-binding protein.

Gated porins and iron transport. Some porins are gated, meaning they can be opened and closed. One example involves iron uptake. Iron is an essential nutrient for aerobic organisms. Since iron is tightly bound to carrier molecules in the human body it is hard for pathogenic bacteria to acquire optimum levels of iron and iron often limits their growth. To overcome these problems bacteria may import haemoglobin, and related molecules, e.g. in Pseudomonas an OMP called PhuR binds to haemoglobin and haem groups and initiates their import into the bacterium. Pseudomonas, and many other bacteria, can also secrete its own high affinity iron carriers or chelators called siderophores. In commensals and pathogens living in the
body, these siderophores attempt to steal iron from the body's own carrier proteins. Once they are bound to iron, specific OMPs recognise the iron-bound siderophore and initiate its transport into the bacterium.
Pseudomonas typically produces up to two siderophores: pyoverdine and pyochelin. Pyoverdin is the main siderophore used to steal iron from transferrin, the mammalian blood plasma protein which transports iron around the body. Once bound to iron, pyoverdin binds to its specific receptor, an outer membrane protein called FpvA. This protein is TonB-dependant, meaning that it complexes to TonB which is essential for its function. TonB is a periplasm-spanning inner membrane protein (IMP) involved in passing signals across the cell envelope. TonB will then open the gate, allowing the iron-pyoverdin to cross the envelope and enter the bacterial cell.

Pyochelin binds to its own receptor, an OMP called FptA, which is a virulence factor, meaning that its presence is associated with virulent disease-causing strains, suggesting that it is especially useful in stealing iron from the host.

Other gated porins include BtuB, an
Escherichia coli receptor for vitamin B12, and is also TonB-dependant. OprH is a Pseudomonas OMP thought to act as a gated porin for the import of magnesium and calcium ions.

Inner Membrane Proteins (IMPs)

Crossing the OM through porins is not the whole story since molecules must also cross the periplasm and the inner membrane (IM). The inner membrane requires its own transport proteins. Often, however, the various OM, periplasmic and IM components form a serial transport system in which three proteins are arranged in series: an OM transporter/porin connects to a periplasmic transport protein (periplasmic permease) which connects to an IM transporter, allowing molecules to more easily cross the whole cell envelope. It is not always clear whether the proteins connect physically or whether they are distinctly separate (for example materials entering the periplasm may need to diffuse across the periplasm to reach the IM transporter). Below we consider some inner membrane proteins (IMPs) though our survey will not be exhaustive. When the three components of a serial transport system are in close proximity or physically connected then this clearly speeds up the transport process by restricting diffusion of the solute being transported to one dimension rather than three.

ABC Transporters. ABC (ATP-binding cassette) proteins have an ATP binding domain to utilise energy. ABC proteins are usually transporters. ABC transporters are ATP-driven transport systems (see energy systems) that transport molecules across the cell envelope using cell-derived energy in the form of ATP. They occur in prokaryotes and eukaryotes, but here we shall focus on prokaryotes only. They contain two membrane-spanning regions that span the inner membrane (which possibly form a channel to transport materials across the IM) and two regions that extend into the cytoplasm and utilise the ATP. Binding and hydrolysis of ATP to ADP and inorganic phosphate releases chemical energy which causes a conformational (shape) change in the transporter.

Uptake ABC transporters (ABC importers) are involved in importing useful materials into the cell. They utilise a high-affinity solute binding protein in the periplasm (a periplasmic permease). In Gram positive bacteria they may be tethered to the cell surface or fused to the transporter protein. These import nutrients and osmoprotectants (small molecules which ensure that the cell has the correct osmotic potential, see membranes) into the bacterial cell. They import molecules like sugars, diamino acids, small peptides, metal ions, anions, siderophores and vitamin B12. There are some 80 types of ABC transporter in Escherichia coli alone!

This leads to some complex arrangements which are still being elucidated. For example, in the
Helicobacter pylori, which lives in the mammalian stomach, nickel and cobalt can cross the outer membrane via the protein transporter NikH, which is associated with TonB, and so is a gated porin of sorts. TonB provides the energy for transport across the OM (it opens the gate). These ions can then cross the inner membrane through the NixA transporter, an inner membrane protein. They can also cross the IM, however, by using an ABC transporter called FecDE, which appears independent of TonB rather than being bound to it in a complex. Whether the FecDE ABC transporter requires its own OM transporter, or whether it uses nickel and cobalt ions that have diffused through the periplasm, perhaps after entering via NikH, is not clear.

ABC exporters transport materials out into the periplasm (where they may subsequently be exported across the outer membrane). These may export slime capsule polysaccharides, lipopolysaccharides,teichoic acids, siderophores, antibiotics, toxins and unwanted drugs that have entered the bacterial cell, etc. They may contribute to antibiotic resistance (although there other transporters than may do this).

RND (resistance-nodulation-division) Efflux Pumps. RND efflux pumps are another class of exporters that are also implicated in resistance to antibiotics. Examples include MexAB-OprM and MexXY-OprM in Pseudomonas aeruginosa. These three-component export pumps consist of an outer membrane efflux
protein (OEP), an efflux porin (such as oprM spanning the outer membrane) an RND protein  (e.g. MexB) and a membrane fusion protein (MFP, e.g. MexA) which spans the periplasm and apparently joins the OEP to the RND and possibly forms a channel. Thus we can envisage molecules crossing all three proteins in series as they are transported across the envelope. In addition to their role in pumping out antibiotics and other toxins, RND transporters possibly export siderophores and homoserine lactone autoinducer used in
quorum sensing, amongst other things.

Ion Symporters and Antiporters. These transporters are more like those that are likely to be familiar to
college students (see
membranes). Symporters transport two different ion species together in the same direction across the membrane. They harness a concentyration gradient of one ion species to drag the other one along with it. As bacteria respire they generate a proton gradient across the inner membrane (which acts as an electrical capacitor storing electric charge) - they pump protons into the periplasm by using energy liberated by oxidising fuels such as glucose. These ions are used for a variety of purposes, from making ATP to driving flagella rotation. They can also be used for transport. For example, the LacY transporter of Escherichia coli imports lactose. It is a proton/lactose symporter, allowing a proton flowing passively down its concentration gradient (diffusion) to cross the inner membrane and enter the cytosol, along with a lactose molecule which is pulled in with it.

In contrast antiporters also pump two different ion species together, harnessing the concentration gradient of one of the species, but transport the two ions in opposite directions. For example, the sodium/proton antiporter of
Escherichia coli expels one sodium ion for every proton taken in.

Periplasmic Proteins

The functions of the periplasm include the detection and processing of nutrients, nutrient transport, the biogenesis of certain proteins, slime capsules, lipopolysaccharide. In addition to proteins, the periplasm
also contains carbohydrate
glucans, short highly-branched chains of glucose molecules which are produced under hypo-osmotic conditions; that is when the cell contents are too dilute, which would cause the loss of water by osmosis, but the presence of glucans in the periplasm rectifies this. These glucans probably make the periplasm more gelatinous.

Many periplasmic proteins are solute or ion-binding proteins which couple with ABC transporters to import nutrients (such as amino acids, sugars, vitamins, peptides and ions). These
periplasmic solute-binding proteins have a high affinity for their specific solute, and so are able to concentrate a solute that is otherwise at low concentration outside the bacterial cell. They are typically monomers consisting of two globular domains joined by a flexible stalk or hinge. The two globules come together to 'pincer' the solute. The binding protein then interacts with an ABC transporter (permease) to translocate the solute into the cell.

Periplasmic binding-proteins also function to detect solutes in
chemotaxis. For example, the maltose sugar receptor (sensor) in Escherichia coli consists of the maltose-binding protein (MBP) MalE and the Tar signal transducer. MalE binds the maltose and then interacts with Tar, which spans the inner membrane and relays the signal to the cytoplasm.

Conclusion on envelope proteins

Hopefully this summary of envelope proteins gives you some feel for the sorts of functions of proteins in the bacterial envelope and how OMPs, IMPs and periplasmic proteins interact to provide useful functions. The more we learn about cells the more we move away from the old idea of cells as 'bags of chemicals' diffusing and mixing at random, to one where processes occur in a much more ordered fashion, often restricted to small compartments or molecular machines, such as in the three-component serial transport systems which speed-up the process of diffusion. We also increasingly see not simple enzymes and chemicals but molecular machines with moving parts, such as the gated porins. This theme will become increasingly apparent if you read the other cell biology and microbiology articles on ww.cronodon.com.

For more information on some special envelope proteins see the sections on
flagella and pili.

The chemical structure of peptidoglycan

The peptidoglycan in the walls of bacteria is a polysaccharide, that is it is made up of chains of sugar molecules and so is a carbohydrate. It is a polymer (made up of molecular chains) of a disaccharide. Recall that a disaccharide is a sugar made up of two sugar monosaccharide (single sugar) units joined together. In this instance the sugars are N-acetyl-glucosamine (NAG) and N-acetyl-muramic acid (NAM). Thus peptidoglycan is made up of chains of alternating -NAG-NAM- units.

Both these sugars are derived from glucose, specifically the isomer beta-D-glucose, see
carbohydrates.
D-glucose or dextrose (grape sugar) is the usual form of glucose found in plants and utilised as fuel by animal and plant cells. Dextrose contains six carbon atoms and forms an hexagonal ring using five of the carbon atoms plus an oxygen atom. The carbon atoms (C) are numbered clockwise from the oxygen atom (O), 1 through 6, in the diagrams below. Dextrose can exist in two isomers that concern us: alpha and beta, depending whether the hydrogen atom on carbon atom number 1 (rightmost corner of the hexagon shown below) is above the plane of the ring (alpha-dextrose) or below the plane of the ring (beta-dextrose) as shown below (where for clarity hydrogen atoms are represented as small balls and a C atom is situated at each of the five unlabelled corners of the ring):

The constituents of peptidoglycan

Notice how beta-D-glucose is modified:

In NAG there is a nitrogen containing
amine group (NH2) added to the second carbon atom, hence
glucosamine. This amine group has an acetic acid (ethanoic acid CH3COOH) joined to it: the acetyl
group (CH3CO-), joined to glucosamine with the loss of water (H2O) hence acetyl-glucosamine. Since this
acetyl group is joined to the glucosamine via the nitrogen (N) atom of the amine we call the molecule
N-acetyl-glucosamine.

NAM is NAG with a lactic acid derivative (the lactyl group) joined to the third carbon atom (the bent bond is
for clarity). Since this lactyl group connects to the NAG via an O bridge (-O-) it is an ether and we say that
NAM is a
lactyl ether of glucosamine. To this lactyl group is added four amino acids. Recall an amino
acid is an organic molecule with both a carboxylic acid group, -COOH, and an amine group, NH2, attached
to it.

The sequence of amino acids joined to NAM varies, but the sequence shown above is the most common
one and is found in most Gram negative bacteria and some Gram positives. These amino acids are:
L-alanine, D-glutamic acid,
meso-diaminopimelic acid (DAP) and D-alanine. The usual amino acids found in proteins are 20 or so L-amino acids. L and D amino acids are mirror images of one another, they are isomers or different forms of the same chemical. Bacterial envelopes are unusual in containing two D-amino acid isomers. Most biological systems use L-amino acids only. Also unusual is meso-diaminopimelic acid, which is a diamino acid, meaning it contains a carboxylic acid group and two amine groups.

These amino acids are joined to one-another in a short side-chain by peptide bonds (-NH-CO-) between the amino group of one amino acid and the carboxylic acid group of another (with the loss of one molecule of water per peptide bond formed). See
proteins for more information on peptide bonds. Thus, NAM has a short peptide side-chain attached to it.

The sugars in each peptidoglycan are joined by
beta-(1,4)-glycosidic links or bonds. This means they are joined by an O atom (one water molecule, H2O, being removed from the bonding sugars for each glycosidic link formed) bridging carbon atom 1 on one sugar (left-hand sugar in our diagram) to carbon 4 of the adjacent sugar (right-hand sugar in our diagram) as shown below:

peptidoglycan chain

In our example 4 sugars, or two disaccharide units are shown linked together. In bacteria each chain typically contains between 10 and 65 disaccharide units joined together in this fashion. The many chains making up the bacterial cell wall do not just flop about! Rather, they are bonded to one-another to form a fairly rigid 3D structure or giant molecule. This is where the spare amino group on DAP comes in handy, since it can bind to the unused carboxylic acid group of D-alanine, forming a peptide bond between two adjacent chains, a cross-link. Not all DAPs form these cross-links, but many do and they can cross-link with chains, above, below, or to the sides, so that all the chains are cross-linked together. The more cross-links that form teh more rigid and stronger the cell wall, but some flexibility is needed is the cell wall is to stretch as the cell grows and bacteria can regulate the degree of cross-linking.

This type of peptidoglycan, the most common type, is called the
m-Dpm-direct type, since cross-links occur directly to meso-diaminopimelic acid (m-Dpm or DAP). This is a group A (or type 1) peptidoglycan.

Group A peptidoglycans are those in which the crosslinks utilise the third amino acid in the side-chain (DAP in this case). In non-direct Group A peptidoglycans, D-alanine crosslinks to the third amino acid (e.g. lysine in place of DAP) indirectly through a variable number of additional amino acids, forming a peptide bridge.

In
group B (or type 2) peptidoglycans the cross-links involve the second amino acid of the side-chain,
D-glutamic acid which, like the terminal D-alanine, also has a spare carboxylic acid group for peptide bond formation.

Variations in the side-chain generally occur in the third amino acid which must be a diamino acid to form the cross-link in the direct crosslink types. In the indirect cross-links a diamino acid (e.g. lysine) must occur in the peptide bridge to link the carboxylic acid ends of the two peptide side-chains.

peptidoglycan chain

Lysozyme is an enzyme found in tears, milk, mucus, saliva and inside cells of the immune system called phagocytes (which ingest and digest bacteria and other foreign or waste bodies). Lysozyme breaks the -C-O-C- bonds between each NAG and NAM unit (beta-1,4 links). This weakens the cell wall causing bacteria to lyse (burst open due to a loss of osmotic control). Gram-negative bacteria have the outer membrane protetcting their peptidoglycan and can not be attacked by peptidoglycan alone.

Peptidoglycan growth

Bacteria need to synthesise more peptidoglycan when they grow and divide. Divisomes are molecular machines involved in cell division and these contribute to cell growth by synthesising new cell wall material at the plane where cell division is destined to occur, for example at the middle of a rod-shaped bacterium or the equator of a spherical bacterium. This requires elongating peptidoglycan chains. To do this enzymes called autolysins break the beta 1-4 glycosdic bonds and peptide cross-links to allow new sugar units to be inserted. Then enzymes called transglycosidases insert and link new sugar units into the breaks. A further set of enzymes, the transpeptidases reform the peptide cross-links. Penicillin type antibiotics inactivate the transpeptidases, preventing the formation of new cross-links in growing cells resulting in failed growth and a weakened cell wall which is prone to rupture, killing the cell.


This page was updated on 12/9/2013, 27 Aug 2020.

The Bacterial Cell Envelope
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