Which organisms contain peptidoglycan

What is most notable about the gram negative cell wall is the presence of a plasma membrane located outside of the peptidoglycan layers, known as the outer membrane. This makes up the bulk of the gram negative cell wall. The outer membrane is composed of a lipid bilayer, very similar in composition to the cell membrane with polar heads, fatty acid tails, and integral proteins.

It differs from the cell membrane by the presence of large molecules known as lipopolysaccharide LPS , which are anchored into the outer membrane and project from the cell into the environment. LPS is made up of three different components: 1 the O-antigen or O-polysaccharide , which represents the outermost part of the structure , 2 the core polysaccharide , and 3 lipid A , which anchors the LPS into the outer membrane. LPS is known to serve many different functions for the cell, such as contributing to the net negative charge for the cell, helping to stabilize the outer membrane, and providing protection from certain chemical substances by physically blocking access to other parts of the cell wall.

In addition, LPS plays a role in the host response to pathogenic gram negative bacteria. The O-antigen triggers an immune response in an infected host, causing the generation of antibiotics specific to that part of LPS think of E. Lipid A acts as a toxin, specifically an endotoxin , causing general symptoms of illness such as fever and diarrhea.

A large amount of lipid A released into the bloodstream can trigger endotoxic shock, a body-wide inflammatory response which can be life-threatening. The outer membrane does present an obstacle for the cell. While there are certain molecules it would like to keep out, such as antibiotics and toxic chemicals, there are nutrients that it would like to let in and the additional lipid bilayer presents a formidable barrier.

Large molecules are broken down by enzymes, in order to allow them to get past the LPS. Instead of exoenzymes like the gram positive bacteria , the gram negative bacteria utilize periplasmic enzymes that are stored in the periplasm. Where is the periplasm, you ask? It is the space located between the outer surface of the cell membrane and the inner surface of the outer membrane, and it contains the gram negative peptidoglycan. Once the periplasmic enzymes have broken nutrients down to smaller molecules that can get past the LPS, they still need to be transported across the outer membrane, specifically the lipid bilayer.

Gram negative cells utilize porins , which are transmembrane proteins composed of a trimer of three subunits, which form a pore across the membrane. Some porins are non-specific and transport any molecule that fits, while some porins are specific and only transport substances that they recognize by use of a binding site.

Once across the outer membrane and in the periplasm, molecules work their way through the porous peptidoglycan layers before being transported by integral proteins across the cell membrane.

At one end the lipoprotein is covalently bound to the peptidoglycan while the other end is embedded into the outer membrane via its polar head. Lipoteichoic acids anchor the cell wall to the cell membrane. Gram-negative bacteria have a relatively thin cell wall composed of a few layers of peptidoglycan only 10 percent of the total cell wall , surrounded by an outer envelope containing lipopolysaccharides LPS and lipoproteins.

This outer envelope is sometimes referred to as a second lipid bilayer. The chemistry of this outer envelope is very different, however, from that of the typical lipid bilayer that forms plasma membranes.

Which of the following statements is true? There are four different types of archaean cell walls. One type is composed of pseudopeptidoglycan , which is similar to peptidoglycan in morphology but contains different sugars in the polysaccharide chain. The other three types of cell walls are composed of polysaccharides, glycoproteins, or pure protein. Other differences between Bacteria and Archaea are seen in Figure. Note that features related to DNA replication, transcription and translation in Archaea are similar to those seen in eukaryotes.

Reproduction in prokaryotes is asexual and usually takes place by binary fission. Recall that the DNA of a prokaryote is a single, circular chromosome. Prokaryotes do not undergo mitosis; instead, the chromosome is replicated and the two resulting copies separate from one another, due to the growth of the cell.

The prokaryote, now enlarged, is pinched inward at its equator and the two resulting cells, which are clones , separate. Binary fission does not provide an opportunity for genetic recombination or genetic diversity, but prokaryotes can share genes by three other mechanisms. In transformation , the prokaryote takes in DNA shed by other prokaryotes into its environment. If a nonpathogenic bacterium takes up DNA for a toxin gene from a pathogen and incorporates the new DNA into its own chromosome, it too may become pathogenic.

In transduction , bacteriophages, the viruses that infect bacteria, may move short pieces of chromosomal DNA from one bacterium to another.

Transduction results in a recombinant organism. Archaea also have viruses that may translocate genetic material from one individual to another. In conjugation , DNA is transferred from one prokaryote to another by means of a pilus , which brings the organisms into contact with one another, and provides a channel for transfer of DNA. The DNA transferred can be in the form of a plasmid or as a composite molecule, containing both plasmid and chromosomal DNA.

These three processes of DNA exchange are shown in Figure. Reproduction can be very rapid: a few minutes for some species. This short generation time coupled with mechanisms of genetic recombination and high rates of mutation result in the rapid evolution of prokaryotes, allowing them to respond to environmental changes such as the introduction of an antibiotic very quickly.

Evolution Connection The Evolution of Prokaryotes How do scientists answer questions about the evolution of prokaryotes? Unlike with animals, artifacts in the fossil record of prokaryotes offer very little information. Fossils of ancient prokaryotes look like tiny bubbles in rock.

Some scientists turn to genetics and to the principle of the molecular clock, which holds that the more recently two species have diverged, the more similar their genes and thus proteins will be. Conversely, species that diverged long ago will have more genes that are dissimilar.

Scientists at the NASA Astrobiology Institute and at the European Molecular Biology Laboratory collaborated to analyze the molecular evolution of 32 specific proteins common to 72 species of prokaryotes. Actinobacteria are a group of very common Gram-positive bacteria that produce branched structures like fungal mycelia, and include species important in decomposition of organic wastes. You will recall that Deinococcus is a genus of bacterium that is highly resistant to ionizing radiation.

It has a thick peptidoglycan layer in addition to a second external membrane, so it has features of both Gram-positive and Gram-negative bacteria. Cyanobacteria are photosynthesizers, and were probably responsible for the production of oxygen on the ancient earth.

The timelines of divergence suggest that bacteria members of the domain Bacteria diverged from common ancestral species between 2. Eukarya later diverged from the archaean line. The work further suggests that stromatolites that formed prior to the advent of cyanobacteria about 2. Prokaryotes domains Archaea and Bacteria are single-celled organisms that lack a nucleus.

They have a single piece of circular DNA in the nucleoid area of the cell. Likewise, archaea do not produce walls of cellulose as do plants or chitin as do fungi. The cell wall of archaeans is chemically distinct. Methanogens are the only exception and possess pseudopeptidoglycan chains in their cell wall that lacks amino acids and N-acetylmuramic acid in their chemical composition. The most striking chemical differences between Archaea and other living things lie in their cell membrane.

There are four fundamental differences between the archaeal membrane and those of all other cells: 1 chirality of glycerol, 2 ether linkage, 3 isoprenoid chains, and 4 branching of side chains. The cell wall is responsible for bacterial cell survival and protection against environmental factors and antimicrobial stress. The cell wall is the principal stress-bearing and shape-maintaining element in bacteria. Its integrity is thus of critical importance to the viability of a particular cell.

In both gram-positive and gram-negative bacteria, the scaffold of the cell wall consists of a cross-linked polymer peptidoglycan. The cell wall of gram-negative bacteria is thin approximately only 10 nanometers in thickness , and is typically comprised of only two to five layers of peptidoglycan, depending on the growth stage. In gram-positive bacteria, the cell wall is much thicker 20 to 40 nanometers thick.

This affects murein hydrolase activity, resistance to antibacterial peptides, and adherence to surfaces. Although both of these molecules are polymerized on the surface of the cytoplasmic membrane, their precursors are assembled in the cytoplasm.

Any event that interferes with the assembling of the peptidoglycan precursor, and the transport of that object across the cell membrane, where it will integrate into the cell wall, would compromise the integrity of the wall. Damage to the cell wall disturbs the state of cell electrolytes, which can activate death pathways apoptosis or programmed cell death.

Regulated cell death and lysis in bacteria plays an important role in certain developmental processes, such as competence and biofilm development. They also play an important role in the elimination of damaged cells, such as those irreversibly injured by environmental or antibiotic stress.

An example of an antibiotic that interferes with bacterial cell wall synthesis is Penicillin. Penicillin acts by binding to transpeptidases and inhibiting the cross-linking of peptidoglycan subunits. A bacterial cell with a damaged cell wall cannot undergo binary fission and is thus certain to die. Penicillin mechanism of action : Penicillin acts by binding to penicillin binding proteins and inhibiting the cross-linking of peptidoglycan subunits.

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The Cell Wall of Bacteria Bacteria are protected by a rigid cell wall composed of peptidoglycans. Learning Objectives Recall the characteristics of a bacterial cell wall. Key Takeaways Key Points A cell wall is a layer located outside the cell membrane found in plants, fungi, bacteria, algae, and archaea.

A peptidoglycan cell wall composed of disaccharides and amino acids gives bacteria structural support. The bacterial cell wall is often a target for antibiotic treatment. Key Terms binary fission : The process whereby a cell divides asexually to produce two daughter cells. Gram-Negative Outer Membrane The Gram-negative cell wall is composed of an outer membrane, a peptidoglygan layer, and a periplasm.

Made of glycan strands cross-linked by short peptides, the sacculus forms a closed, bag-shaped structure surrounding the cytoplasmic membrane. There is a high diversity in the composition and sequence of the peptides in the peptidoglycan from different species. Furthermore, in several species examined, the fine structure of the peptidoglycan significantly varies with the growth conditions. Limited number of biophysical data on the thickness, elasticity and porosity of peptidoglycan are available.

The different models for the architecture of peptidoglycan are discussed with respect to structural and physical parameters. Peptidoglycan murein is an essential and specific component of the bacterial cell wall found on the outside of the cytoplasmic membrane of almost all bacteria Rogers et al. Its main function is to preserve cell integrity by withstanding the turgor. Indeed, any inhibition of its biosynthesis mutation, antibiotic or its specific degradation e.

Peptidoglycan also contributes to the maintenance of a defined cell shape and serves as a scaffold for anchoring other cell envelope components such as proteins Dramsi et al. It is intimately involved in the processes of cell growth and cell division. Peptidoglycan and the genetic arsenal necessary to its biosynthesis is absent in Mycoplasmas, Planctomyces and the scrub typhus agent Orientia Rickettsia tsutsugamushi Moulder et al.

It has never been detected in Chlamidiae although most biosynthetic genes exist Chopra et al. A few biosynthetic genes but no peptidoglycan have been found in the green plant Arabidopsis thaliana five genes and the moss Physcomitrella patens nine genes ; these genes would be involved in chloroplast division Machida et al.

This review provides a brief overview on the diversity and variability of the chemical structure of peptidoglycan in different bacteria, and summarizes the available data on the biophysical properties of the cell wall. Finally, structural aspects required for modelling the architecture of the peptidoglycan sacculus are discussed.

The main structural features of peptidoglycan are linear glycan strands cross-linked by short peptides Rogers et al. Cross-linking of the glycan strands generally occurs between the carboxyl group of d -Ala at position 4 and the amino group of the diamino acid at position 3, either directly or through a short peptide bridge.

Structure of the peptidoglycan of Escherichia coli. The yellowish labelled part represents the basic disaccharide tetrapeptide subunit monomer , which is also written with the conventional amino acid and hexosamine abbreviations on the left-hand side. The middle part shows a cross-linked peptide, with the amide group connecting both peptide stems drawn in red.

The structural features outlined in the preceding paragraph are retrieved in all bacterial species known to date. However, a certain degree of variation exists either in the peptide stem, in the glycan strands or in the position or composition of the interpeptide bridge.

In the next sections, this study will present an overview of the different types of variations encountered. The glycan strands are formed by oligomerization of monomeric disaccharide peptide units lipid II by transglycosylation reactions. Secondary modifications in the glycan strands such as N -deacetylation, O -acetylation and N -glycolylation are frequently found and are the topic of another review in this issue Vollmer, In the Gram-positive Staphylococcus aureus , the glycan strands may contain either a Mur N Ac or a Glc N Ac residue at the reducing end; the latter residue indicates that cleavage of the strand by an N -acetylglucosaminidase had occurred Boneca et al.

In all Gram-negative and some Gram-positive species e. It is not known whether the 1,6-anhydroMur N Ac residues present in the sacculi have been formed during termination of glycan strand synthesis, or whether they are the result of degradation by lytic transglycosylases, or both. In species with high activity of glycan strand-cleaving enzymes glucosaminidases and muramidases , the peptidoglycan may contain glycan strands with all possible combinations of Glc N Ac and Mur N Ac residues at the ends.

These hydrolytic enzymes must be inactivated rapidly and removed quantitatively when peptidoglycan is prepared for glycan strand length analysis to avoid cleavage of the strands after peptidoglycan isolation Ward, Different methods have been applied to determine the average length of the glycan strands and the length distribution: 1 quantification of the fraction of the reducing hexosamine residues after chemical reduction Rogers, ; Ward, , 2 enzymatic addition of galactosamine residues to the Glc N Ac end and their quantification Schindler et al.

The latter method is restricted to the separation of glycans from 1 to 30 disaccharide units. Glycans that are longer than 30 disaccharide units elute together in one peak. There are only limited data on the average chain length and the chain length distribution of the glycan strands in different species. Remarkably, the average chain length of the glycan strands does not correlate with the thickness of the peptidoglycan layer, as there are Gram-positive species with a thick cell wall with either short S.

Similarly, there are Gram-negative species with either short Helicobacter pylori or long Proteus morganii glycan strands. The glycan strands in the peptidoglycan of Bacilli B. In contrast, the glycan strands of S. Separation of the staphylococcal glycan strands by HPLC revealed that the predominant chain length was between 3 and 10 disaccharide units. The l -ornithine-containing peptidoglycan of Deinococcus radiodurans Sark, a Gram-positive bacterium that is extremely resistant to ionizing radiations, had glycan strands terminated by 1,6-anhydroMur N Ac residues with an average chain length of about 20 disaccharide units Quintela et al.

The average chain length of the glycan strands in Gram-negative bacteria can be calculated from the fraction of 1,6-anhydroMur N Ac residues containing disaccharide peptide subunits.

Different species differ in the average chain length of the glycan strands but the normal range lies between 20 and 40 disaccharide units Tuomanen et al.

As shown for Escherichia coli , the average chain length of the glycan strands also varies to some extent with the strain and growth conditions Glauner, Escherichia coli glycan strands of up to 30 disaccharide units have been separated by HPLC Harz et al.

The average chain length of the glycan strands from 1 to 30 disaccharide units was 8. The average chain length of all glycan strands was estimated as 21 disaccharide units, which is slightly less than the average chain length of 25—35 disaccharide units calculated from the fraction of 1,6-anhydroMur N Ac residues Gmeiner et al.

The average glycan chain length is greater ca. The glycan strands from H. It might be important for the integrity of the peptidoglycan net that the glycan strand ends are hyper-cross-linked in H. The variations of the peptide stem can be divided into two categories: 1 those due to the specificity of the Mur ligases, the enzymes responsible for its biosynthesis, and 2 those occurring at a later step of the biosynthesis [see accompanying chapters in this issue Barreteau et al.

These variations are enumerated in Table 1. These residues result from reactions occurring posterior to the action of Mur ligases. The first amino acid of the peptide stem is added by the MurC ligase. In most bacterial species, this amino acid is l -Ala; in rare cases, Gly or l -Ser is added instead Table 1. Two interesting cases deserve to be mentioned.

First, the enzymes from Mycobacterium tuberculosis and Mycobacterium leprae have the same in vitro specificity pattern towards l -Ala and Gly; however, the amino acid found at the first position of the peptide stem is different l -Ala for the former and Gly for the latter. This appears to be due to the growth conditions Mahapatra et al. The second case is that of Chlamydia trachomatis : the MurC activity adds l -Ala, l -Ser and Gly with similar in vitro efficiencies.

This absence of specificity prevents from deducing the nature of the first amino acid of the putative chlamydial peptidoglycan Hesse et al. The amino acid at the second position is added by the MurD ligase. In all species this enzyme adds d -Glu, the modifications encountered Table 1 occurring at a later step. The greatest variation is found at position 3. The addition of the third amino acid is catalyzed by the MurE ligase. This amino acid is generally a diamino acid, either meso -A 2 pm most Gram-negative bacteria, Mycobacteria, Bacilli or l -Lys most Gram-positive bacteria ; in certain species, other diamino acids l -Orn, ll -A 2 pm, meso -lanthionine, l -2,4-diaminobutyric acid, d -Lys or monoamino acids l -homoserine, l -Ala, l -Glu are encountered Table 1.

As for the second position, further modifications of the third amino acid occur posterior to MurE action Table 1. In most cases, the MurE enzyme is highly specific for the relevant amino acid; this has been demonstrated for the meso -A 2 pm-adding and l -Lys-adding enzymes from E. However, the MurE enzyme sometimes seems to be devoid of strict specificity, and this affects the final composition of peptidoglycan.

As a matter of fact, it has been shown that MurE from Bifidobacterium globosum can incorporate both diamino acids indifferently Hammes et al. MurE from Thermotoga maritima , a Gram-negative species whose peptidoglycan contains similar proportions of both enantiomers of lysine, but no meso -A 2 pm Huber et al.

The absence of meso -A 2 pm in T. Amino acids at positions 4 and 5 are added as a dipeptide, in most cases d -Ala- d- Ala. The synthesis of the dipeptide is carried out by the Ddl enzyme and its incorporation into the peptide stem by the MurF ligase.

It has been established that the latter has a high degree of specificity for the C-terminal amino acid Duncan et al. A certain proportion of Gly, presumably escaping from the double-sieving mechanism, is often found at position 4 or 5 in lieu of d -Ala.

The proportion is low ca. Other variations in peptidoglycan composition amidation, hydroxylation, acetylation, attachment of amino acids or other groups, attachment of proteins occur after the action of the Mur ligases, often at the level of lipid II. These modifications concern essentially positions 2 and 3. It should be mentioned that most enzymes responsible for these modifications are still unknown.

It has been shown in Mycobacterium smegmatis that lipid II is the substrate for amidation reactions; in fact, lipid II in this species appears as a mixture of non-, mono- and di-amidated molecules Mahapatra et al. The hydrocarbon chain of d -Glu, meso -A 2 pm or l -Lys is hydroxylated in some species.

In the case of d -Glu, it was demonstrated that hydroxylation occurs after the cytoplasmic steps Schleifer et al. In certain organisms, an amino acid or another amine-containing moiety, such as glycine Micrococcus luteus , Arthrobacter tumescens , glycine amide Arthrobacter athrocyaneus , d -alanine amide Arthrobacter sp.

The peptide stem constitutes the point of covalent anchoring of cell envelope proteins to peptidoglycan Dramsi et al. It is a amino acid protein whose N-terminal glyceryl-cysteine residue is modified by the addition of three fatty acids.

Lately, it has been demonstrated that in E. Gram-positive bacteria contain many surface proteins e. The anchoring reaction is catalyzed by a membrane protein called sortase A Marraffini et al. Sortase A from S. It has been demonstrated that the acceptor substrate of sortase A is lipid II. Most variations of the peptide moiety of peptidoglycan occur in its mode of cross-linkage and in the composition of the interpeptide bridge Fig.

In the first group 3—4 cross-linkage , the cross-linkage extends from the amino group of the side-chain of the residue at position 3 of one peptide subunit acyl acceptor to the carboxyl group of d -Ala at position 4 of another acyl donor. As mentioned above, this is the most common kind of cross-linkage.

It can be either direct most Gram-negative bacteria or through an interpeptide bridge most Gram-positive bacteria. In this case, for the first subunit to be an acceptor, an interpeptide bridge containing a diamino acid must be present.

The cross-linking reactions are catalyzed by the transpeptidase domain of penicillin-binding proteins, enzymes that have been studied extensively, in particular in human pathogenic bacteria Sauvage et al. Examples of cross-linkage and interpeptide bridge.

G, N -acetylglucosamine; M, N -acetylmuramic acid. Characterized branching enzymes, and nature of the interpeptide bridges synthesized. FemX catalyses the addition of the first amino acid residue l -Ala of the side chain; the second l -Ser and third l -Ala residues are added by unknown Fem transfereases Villet et al. The size of the interpeptide bridge ranges from one to seven amino acid residues.

As already mentioned, the interpeptide bridges of 2—4 cross-links contain necessarily but not exclusively a diamino acid l - or d -Lys, d -Orn, d -2,4-diaminobutyrate.

In fact, it is only recently that some branching enzymes have been purified and characterized Table 2. They can be divided into two groups according to the nature of the amino acid incorporated: 1 Glycine and l -amino acids are activated as aminoacyl-tRNAs and transferred to the precursors by a family of nonribosomal peptide bond-forming enzymes called Fem transferases Mainardi et al.

The precursor substrate of the branching enzymes varies among species: lipid II for S. An interesting case deserves to be mentioned. The nature of the enzyme catalyzing the unusual transpeptidation reaction between d -Ala acyl donor and the N-terminal l -Ala acyl acceptor is unknown.

This gives rise to the appearance of 3—3 cross-links, which were originally discovered in Mycobacteria Wietzerbin et al. Their formation is catalyzed by penicillin-insensitive l , d -transpeptidases Mainardi et al. As for the main peptide chain, the interpeptide bridge can be further modified after its assembly. In Thermus thermophilus , where the amino acid at position 3 is l -Orn and the bridge consists of a diglycyl residue between positions 3 and 4, a significant proportion of glycyl residues not engaged in the bridge with the donor peptide stem are acylated with phenylacetic acid Quintela et al.

Besides the diversity in the nature of cross-linkage, there is a considerable variation in the degree of cross-linkage, which varies from ca. Translated in terms of muropeptide content, these figures mean that in E.

Considering that the variations in peptidoglycan structure have taxonomic implications, Schleifer and Kandler established a tri-digital system of classification of peptidoglycans. The first digit, a Roman capital letter, represents the mode of cross-linkage A and B for the 3—4 and 2—4 cross-linkages, respectively. The second digit, a number, refers to the type of interpeptide bridge, or lack of it, involved in the cross-linkage. The third digit, a Greek letter, indicates the amino acid found at position 3 of the peptide stem.

As a consequence, the examples of peptidoglycan depicted in Fig. The fine structure of the bacterial sacculi is reflected in the detailed muropeptide composition of peptidoglycan as determined by means of high-resolution techniques. Information on the abundance and peculiarities of families of muropeptides with specific structural functions is crucial to understand the architecture and physiology of the sacculus itself. Systematic studies in the model bacterium E.

Aging brings with it a progressive variation of the indicated parameters in a process that apparently requires about one mass doubling time to complete. Peptidoglycan fine structure is also subjected to global variations when the state of growth changes Pisabarro et al.

The transition of E. Of course, the inverse transition also takes place when cells resume active growth from a resting condition. Although data are quite limited, recovery of the muropeptide composition characteristic for actively growing cells might involve active modification of total peptidoglycan in addition to the expected variation due to mixing of old resting phase and new growth phase peptidoglycans de la Rosa, ; Pisabarro et al.

A rather surprising ability of E. Studies conducted under conditions limiting supply of precursors showed that E. Cells with reduced peptidoglycan content were nevertheless more sensitive to penicillin and other damaging agents. A comprehensive survey of peptidoglycan fine structure in different bacterial species is simply nonexistent at present. Only a few Gram-positive bacteria have lent themselves to analysis by HPLC and in most cases their composition could be only partially solved Garcia-Bustos et al.

A large variability in fine structure is evident, as expected from their heterogeneity in chemical composition and cross-linking. Even among the more homogeneous Gram-negative organisms, large differences in fine structure have been clearly shown in spite of the limited number of well-studied organisms Folkening et al. Therefore, it seems that there is no optimal or standard value for parameters as cross-linkage or glycan strand length, but rather each species selects the values or range of values appropriate for its particular life conditions.

Variations in peptidoglycan fine structure have also been associated with bacterial pathogenesis in a number of cases. The nature of the profits bacteria derived from these adaptations is still unknown, but is likely relevant for their survival. When present at a high concentration in the growth medium, analogues of peptidoglycan amino acids can be incorporated into the macromolecule and modify its composition. The most-known example is that of glycine, which can replace alanine at position 1, 4 or 5 in several bacterial species Hammes et al.

The fact that several A 2 pm analogues are able to complement A 2 pm auxotrophy in E. Interestingly, the presence of hydroxylysine, which is often considered to be a natural constituent of the peptidoglycan of certain species, is in most cases the result of particular growth conditions, namely lysine deprivation and hydroxylysine supplementation see e. Peptidoglycan composition varies in mutants or genetically engineered cells with respect to wild type. This is well documented in E.

A dapF mutant lacking A 2 pm epimerase was shown to contain a huge pool of ll -A 2 pm that was incorporated into peptidoglycan Mengin-Lecreulx et al.