You are on page 1of 14

In order to protect against infection, one of the first things the body must do is detect

the presence of microorganisms. The body initially does this by recognizing

molecules unique to groups of related microorganisms and are not associated with
human cells. These unique microbial molecules are called pathogen-associated
molecular patterns or PAMPs. In addition, unique molecules displayed on stressed,
injured, infected, or transformed human cells also be recognized as a part of innate
immunity. These are often referred to as danger-associated molecular patterns or
DAMPs . In all, the innate immune system is thought to recognize approximately 10 3
molecular patterns.

Figure 1: (left) Structure of a Gram-Negative Cell Wall. The Gram-negative cell wall
is composed of a thin, inner layer of peptidoglycan and an outer membrane
consisting of molecules of phospholipids, lipopolysaccharides (LPS), lipoproteins and
surface proteins. The lipopolysaccharide consists of lipid A and O polysaccharide.
(right) The Gram-positive cell wall appears as dense layer typically composed of
numerous rows of peptidoglycan, and molecules of lipoteichoic acid, wall teichoic
acid and surface proteins.
Examples of microbial-associated PAMPs include:

a. lipopolysaccharide (LPS) from the outer membrane of the Gram-negative cell

wall (see Figure 1A);
b. bacterial lipoproteins and lipopeptides (see Figure 1A);
c. porins in the outer membrane of the Gram-negative cell wall (see Figure 1A);
d. peptidoglycan found abundantly in the Gram-positive cell wall and to a lesser
degree in the gram-negative cell wall (see Figure 1B);
e. lipoteichoic acids found in the Gram-positive cell wall (Figure 1B);
f. lipoarabinomannan and mycolic acids found in acid-fast cell walls (Figure 2B)
g. mannose-rich glycans (short carbohydrate chains with the sugar mannose or
fructose as the terminal sugar). These are common in microbial glycoproteins
and glycolipids but rare in those of humans (see Fig. 6).
h. flagellin found in bacterial flagella;
i. bacterial and viral nucleic acid. Bacterial and viral genomes contain a high
frequency of unmethylated cytosine-guanine dinucleotide or CpG sequences
(a cytosine lacking a methyl or CH3 group and located adjacent to a guanine).
Mammalian DNA has a low frequency of CpG sequences and most are
methylated which may mask recognition by pattern-recognition receptors .
Also, human DNA and RNA does not normally enter cellular endosomes
where the pattern-recognition receptors for microbial DNA and RNA are
j. N-formylmethionine , an amino acid common to bacterial proteins;
k. double-stranded viral RNA unique to many viruses in some stage of their
l. single-stranded viral RNA from many` viruses having an RNA genome;
m. lipoteichoic acids, glycolipids, and zymosan from yeast cell walls; and
n. phosphorylcholine and other lipids common to microbial membranes.

Gary Kaiser

Pathogen-Associated Molecular Patterns

(PAMPs) and Danger-Associated Molecular
Patterns (DAMPs)
1. Last updated
12:43, 10 Apr 2017

PAMPs are conserved molecular structures produced by microorganisms and recognized as

foreign by the receptors of the innate immune system.

Pathogen-associated molecular patterns (PAMPs) and receptors (PRRs)

Author: V. Dimov, M.D., Allergist/Immunologist and Assistant Professor at University of Chicago

Reviewer: S. Randhawa, M.D., Allergist/Immunologist and Assistant Professor at LSU (Shreveport)

Department of Allergy and Immunology

Pathogen-associated molecular patterns (PAMPs)

Microbial products which stimulate innate immunity are called pathogen-associated molecular
patterns (PAMPs). Pathogen-associated molecular patterns (PAMPs) are on bacteria - they bind to
receptors called pattern recognition receptors.

Innate immunity reacts to these common bacterial structures - PAMPs, pathogen-associated

molecular patterns. PAMPs are produced only by the bacterial invader and not by the host. If it were
the other way around, innate immunity would get "confused" and attack the host instantly and
immediately as it is typical of its nature.

PAMPs include:

- lipopolysaccharides (LPS) on Gram-negative bacteria

- lipoteichoic acid on Gram-positive bacteria
- peptidoglycans
- mannan
- bacterial RNA and DNA
- glucan

Receptors that bind these PAMPs are called pattern recognition receptors (PRRs). PAMPs
are unique to microbes. Mammalian cells do not have PAMPs and this one of the reasons
why there is no autoimmune disease caused by innate immunity.

For example, human cells do not have mannose - bacteria do. Receptors recognize mannose
on bacteria - and this starts the mannose-lectin complement pathway.

Mannose is one of the PAMPs. TLRs are pattern recognition receptors.

Example of a match: ligand-receptor: mannose (bacteria)-mannose-binding lectin (MBL)

(soluble recognition molecule in humans)

Mannose-binding lectin (MBL) starts the third complement pathway. MBL is plasma protein
that functions as an opsonin.

APC (macrophages) have PAMPs-recognition receptors, called pattern-recognition

receptors in short.

PAMPs are the molecular patterns that are displayed on various pathogens. Immune cells
recognize these patterns and initiate the innate immune response.

• PAMPs include combinations of sugars, certain proteins, particular lipid-bearing molecules

and some nucleic acid motifs
Educational Website by Board-certified Allergist at Cleveland Clinic

Pathogen Recognition Receptors, TLRs. This video is from: Janeway's Immunobiology, 7th
Edition Murphy, Travers, & Walport. Source: Garland Science.
The Function of Toll-Like Receptors
Zlatko Dembic.

Go to:


The Toll family of receptors comprises numerous related proteins implicated in the
development and defense of plants and animals. Toll was first discovered in Drosophila
melanogaster as a gene that controlled the dorsal-ventral axis of the developing embryo.
Elements of its molecular structure; the extracellular leucine-rich repeat domain (LRR), short
cysteine rich patches, a transmembrane portion, and an intracellular domain homologous to
that of the human interleukin-1 receptor (IL-1R) are discussed in detail in other chapters.
Here we are principally concerned with the role of the Toll like receptors (TLRs) and their
signaling pathways in the immune system.

TLRs are found in Arabidopsis as intracellular proteins, whereas the Toll proteins of
Drosophila, Tol in Caenorhabditis elegans, and the mammalian TLRs are all transmembrane
proteins. The human TLRs comprise a family of ten related proteins (Fig. 1). Across
mammalian species the number of TLRs differs, as does their expression in different cell
types and their transcriptional regulation in activated cells. Ligands (some synthetic) for all
but the tenth TLR have been identified, and their number is rapidly growing, due in no small
part to the frenetic research activity in this area.

Figure 1

Human TLRs.

TLR ligands are varied, comprising bacterial cell wall components, bacterial genomic DNA,
fungal, parasitic and viral products and synthetic analogs of natural products. Interestingly,
TLRs can also bind autologous (self ) molecules such as heat shock proteins (HSPs),
intercellular matrix products, and mammalian genomic DNA. In general terms, the ligands
for mammalian TLRs are either products of microbial origin that have an unusual molecular
motif (pattern) or can be derived from the host species itself. A closer look reveals that host-
derived ligands are usually shielded or concealed from the immune system and their
emergence, for example after tissue trauma, signals that intervention by the immune system is

The presence of LRR modules in plant and animal proteins suggests an evolutionarily
conserved role as a molecular pattern recognition receptor. Additionally, the developmental
functions of TLRs in the fruit fly and nematode point to another role for TLRs in higher
vertebrates, which could be to sense tissue integrity. This role could have arisen after the
developmental functions that we ordinarily attribute to TLRs. Additionally; we can envisage
other functions for TLRs if we consider that their activation can give rise to ten potentially
divergent signals. These signals, modulated by their intensity, the cell type (including
differentiation stage) of their derivation, and cellular microenvironment, may synergize or
compete with one another to generate distinct TLR signals. Thus, the action of B and T cells
could depend on the type of TLR signal generated by antigen presenting cells.

TLRs help the immune system to fight the dangerous, protect the useful and neglect the vast
majority of harmless microorganisms that colonize our bodies. These three functions could be
generalized in a statement not dissimilar to “immunity maintains the integrity of tissues”.
This statement can be taken as a start point for the “Integrity Hypothesis”, which proposes
three functions for TLRs. The first is to detect unusual molecular patterns. The second is to
sense the extent of tissue damage, and the third is to determine the class of immune response.
Specialized cells of central immunity such as dendritic cells and T and B cells are principle
players in integrating these TLR signals into a specific immune response.

Clearly a better understanding of the function of TLRs in higher vertebrates is crucial for
biomedical research as it will allow us to improve health care by refining the therapeutic
regimes with which we treat disease
Toll-Like Receptors (TLRs) play a critical role in the early innate immune response to
invading pathogens by sensing microorganism and are involved in sensing endogenous
danger signals.

TLRs are evolutionarily conserved receptors are homologues of the Drosophila Toll protein,
discovered to be important for defense against microbial infection [1]. TLRs recognize highly
conserved structural motifs known as pathogen-associated microbial patterns (PAMPs),
which are exclusively expressed by microbial pathogens,
or danger-associated molecular patterns (DAMPs) that are endogenous molecules released
from necrotic or dying cells.

PAMPs include various bacterial cell wall components such as lipopolysaccharide (LPS),
peptidoglycan (PGN) and lipopeptides, as well as flagellin, bacterial DNA and viral double-
stranded RNA. DAMPs include intracellular proteins such as heat shock proteins as well as
protein fragments from the extracellular matrix.

Stimulation of TLRs by the corresponding PAMPs or DAMPs initiates signaling cascades

leading to the activation of transcription factors, such as AP-1, NF-κB and interferon
regulatory factors (IRFs). Signaling by TLRs result in a variety of cellular responses
including the production of interferons (IFNs), pro-inflammatory cytokines and effector
cytokines that direct the adaptive immune response.

The TLR Family

TLRs are type I transmembrane proteins characterized by an extracellular domain containing

leucine-rich repeats (LRRs) and a cytoplasmic tail that contains a conserved region called the
Toll/IL-1 receptor (TIR) domain. The structure of the extracellular domain of TLR3 was
revealed by crystallography studies as a large horseshoe-shape [2].

TLRs are predominantly expressed in tissues involved in immune function, such as spleen
and peripheral blood leukocytes, as well as those exposed to the external environment such as
lung and the gastrointestinal tract.
Their expression profiles vary among tissues and cell types. TLRs are located on the plasma
membrane with the exception of TLR3, TLR7, TLR9 which are localized in the endosomal
compartment [3].
Ten human and twelve murine TLRs have been characterized, TLR1 to TLR10 in humans,
and TLR1 to TLR9, TLR11, TLR12 and TLR13 in mice, the homolog of TLR10 being a

TLR2 is essential for the recognition of a variety of PAMPs from Gram-positive bacteria,
including bacterial lipoproteins, lipomannans and lipoteichoic acids. TLR3 is implicated in
virus-derived double-stranded RNA. TLR4 is predominantly activated by lipopolysaccharide.
TLR5 detects bacterial flagellin and TLR9 is required for response to unmethylated CpG
DNA. Finally, TLR7 and TLR8 recognize small synthetic antiviral molecules [4], and
single-stranded RNA was reported to be their natural ligand [5]. TLR11(12) has been
reported to recognize uropathogenic E.coli [6] and a profilin-like protein from Toxoplasma
gondii [7].

The repertoire of specificities of the TLRs is apparently extended by the ability of TLRs to
heterodimerize with one another. For example, dimers of TLR2 and TLR6 are required for
responses to diacylated lipoproteins while TLR2 and TLR1 interact to recognize triacylated
lipoproteins [8]. Specificities of the TLRs are also influenced by various adapter and
accessory molecules, such as MD-2 and CD14 that form a complex with TLR4 in response to
LPS [9].

TLR Signaling

TLR signaling consists of at least two distinct pathways: a MyD88-dependent pathway that
leads to the production of inflammatory cytokines, and a MyD88-independent pathway
associated with the stimulation of IFN-β and the maturation of dendritic cells.

The MyD88-dependent pathway is common to all TLRs, except TLR3 [10]. Upon activation
by PAMPs or DAMPs, TLRs hetero- or homodimerize inducing the recruitment of adaptor
proteins via the cytoplasmic TIR domain.
Adaptor proteins include the TIR-domain containing proteins, MyD88, TIRAP (TIR-
associated protein), Mal (MyD88 adaptor-like protein), TRIF (TIR domain-containing
adaptor protein-inducing IFN-β) and TRAM (TRIF-related adaptor molecule).
Recruitment of MyD88 for instance, in turn recruits IRAK1 and IRAK4. IRAK4
subsequently activates IRAK1 by phosphorylation. Both IRAK1 and IRAK4 leave the
MyD88-TLR complex and associate temporarily with TRAF6 leading to its ubiquitination.
Bcl10 and MALT1 form oligomers that bind to TRAF6 promoting TRAF6 self-ubiquitination
Recently, IRAK2 was shown to play a central role in TRAF6 ubiquitination [12]. Following
ubiquitination, TRAF6 forms a complex with TAB2/TAB3/TAK1 inducing TAK1 activation
[13]. TAK1 then couples to the IKK complex, which includes the scaffold protein NEMO,
leading to the phosphorylation of IκB and the subsequent nuclear localization of NF-κB.
Activation of NF-κB triggers the the production of pro-inflammatory cytokines such as TNF-
α, IL-1 and IL-12.

Individual TLRs induce different signaling reponses by usage of the different adaptor
TLR4 and TLR2 signaling requires the adaptor TIRAP/Mal, which is involved in the
MyD88-dependent pathway [14]. TLR3 triggers the production of IFN-β in response to
double-stranded RNA, in a MyD88-independent manner, through the adaptor TRIF/TICAM-
1 [15]. TRAM/TICAM-2 is another adaptor molecule involved in the MyD88-independent
pathway [5] which function is restricted to the TLR4 pathway [16].

TLR3, TLR7, TLR8 and TLR9 recognize viral nucleic acids and induce type I IFNs. The
signaling mechanisms leading to the induction of type I IFNs differ depending on the TLR
activated. They involve the interferon regulatory
factors, IRFs, a family of transcription factors known to play a critical role in antiviral
defense, cell growth and immune regulation. Three IRFs (IRF3, IRF5 and IRF7) function as
direct transducers of virus-mediated TLR signaling. TLR3 and TLR4 activate IRF3 and IRF7
[17], while TLR7 and TLR8 activate IRF5 and IRF7 [18]. Furthermore, type I IFN
production stimulated by TLR9 ligand CpG-A has been shown to be mediated by PI(3)K and
mTOR [19].

TLR-Targeted Therapeutics

Significant progress has been made over the past years in the understanding of TLR function
[20]. TLRs are essential receptors in host defense against pathogens by activating the innate
immune system, a prerequisite to the induction of adaptive immune responses.

Although TLR-mediated signaling is paramount in eradicating microbial infections and

promoting tissue repair, the regulation must be tight. TLRs are implicated in a number of
inflammatory and immune disorders and play a role in cancer [21].
Many single nucleotide polymorphisms have been identified in various TLR genes and are
associated with particular diseases. Several therapeutic agents targeting the TLRs are now
under pre-clinical and clinical
evaluation [22].

However, the complexity lies in that TLRs act as double-edged swords either promoting or
inhibiting disease progression. Furthermore, therapeutic agents targeting the TLRs must be
able to antagonize the harmful effects resulting without affecting host defense functions.
Nonetheless, the potential of harnessing and directing the innate immune system with drugs
targeting TLRs, to prevent or treat human inflammatory and autoimmune diseases as well as
cancer, appears to be promising.

Immune Cell Signal

TLR PAMPs DAMPs Production
Expression Adaptor

Triacylated lipoproteins
TLR1+ Cell surface (Pam3CSK4) (TLR2 DAMPs listed
MyD88, IC
TLR2 Mo, MΦ, DC, B Peptidoglycans, below)
Heat Shock Proteins
(HSP 60, 70, Gp96)
Cell surface High mobility group TIRAP,
Diacylated lipoproteins
TLR2+ Mo, MΦ, MC, proteins (HMGB1) MyD88, IC
TLR6 B Proteoglycans Mal
(Versican, Hyaluronic
Acid fragments)

Endosomes dsRNA (poly (I:C)) mRNA IC,

B, T, NK, DC tRNA, siRNA tRNA type1 IFN

Heat Shock Proteins

(HSP22, 60, 70,72,
High mobility group
Cell surface/ TRAM,
proteins (HMGB1)
endosomes Lipopolysaccharides TRIF
Proteoglycans IC,
(Versican, Heparin type1 IFN
MC, Paclitaxel MyD88
IE Mal
Hyaluronic Acid

Cell surface
TLR5 Mo, MΦ, DC, Flagellin MyD88 IC

Endosomes IC,
TLR7 (R848) ssRNA MyD88
Mo, MΦ, DC. B type1 IFN
Guanosine analogs

Endosomes ssRNA,
TLR8 Mo, MΦ, DC, Imidazoquinolines ssRNA MyD88
type1 IFN
MC (R848)

CpG DNA Chromatin IgG IC,
TLR9 Mo, MΦ, DC, MyD88
CpG ODNs complex type1 IFN

TLR10 Endosomes profilin-like proteins MyD88 IC

Mo, MΦ, DC

Mo: monocytes, MΦ: marcophages, DC: dendritic cells, MC: Mast cells, B: B cells, T: T
cells, IE: Intestinal epithelium, IC: Inflammatory cytokines