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Innate Immunity

The ability of a multicellular organism to defend itself against invasion by pathogens (bacteria, fungi, viruses, etc.) depends on its ability to mount immune responses. All metazoans (probably) have inborn defense mechanisms that constitute innate immunity. Vertebrates have not only innate immunity but also are able to mount defense mechanisms that constitute adaptive immunity. This table gives some of the distinguishing features of each type of immunity.

Innate Immunity	Adaptive Immunity
Pathogen recognized by receptors encoded in the germline	Pathogen recognized by receptors generated randomly
Receptors have broad specificity, i.e., recognize many related molecular structures called PAMPs (pathogen-associated molecular patterns)	Receptors have very narrow specificity; i.e., recognize a particular epitope
PAMPs are essential polysaccharides and polynucleotides that differ little from one pathogen to another but are not found in the host.	Most epitopes are derived from polypeptides (proteins) and reflect the individuality of the pathogen.
Receptors are PRRs (pattern recognition receptors)	Receptors are B-cell (BCR) and T-cell (TCR) receptors for antigen
Immediate response	Slow (3–5 days) response (because of the need for clones of responding cells to develop — Link)
No memory of prior exposure	Memory of prior exposure [Link]
Occurs in all metazoans?	Occurs in jawed vertebrates only
Discussed on this page	Discussed at these links: The cells of the system. Types of antigen receptors. How BCR and TCR diversity is generated. How clones of specific B and T cells are selected for development.

In addition to their innate pathogen-recognition systems, vertebrates (including ourselves) and invertebrates (e.g., Drosophila) secrete antimicrobial peptides that protect them from invasion by bacteria and other pathogens. These are discussed below.

Pathogen-Associated Molecular Patterns (PAMPs)

Pathogens, especially prokaryotes, have molecular structures that

are not shared with their host;
are shared by many related pathogens;
are relatively invariant; that is, do not evolve rapidly (in contrast, for example, to such pathogen molecules as the hemagglutinin and neuraminidase of influenza viruses).

Examples:

the flagellin of bacterial flagella;
the peptidoglycan of gram-positive bacteria;
the lipopolysaccharide (LPS, also called endotoxin) of gram-negative bacteria;
double-stranded RNA. (Some viruses of both plants and animals have a genome of dsRNA. And many other viruses of both plants and animals have an RNA genome that in the host cell is briefly converted into dsRNA [link to examples]).
unmethylated DNA (many of the CpG islands in eukaryotes have methyl groups attached).

Pattern Recognition Receptors (PRRs)

There are three groups:

secreted molecules that circulate in blood and lymph;
surface receptors on phagocytic cells like macrophages that bind the pathogen for engulfment;
cell-surface receptors that bind the pathogen initiating a signal leading to the release of effector molecules (cytokines).

1. Secreted PRRs

Example: a circulating protein that binds to the mannose (a monosaccharide) residues found on the surface of many pathogens. This interaction triggers the cleavage of the complement components

C4 and C2 leading to the cleavage of
C3 and the remaining steps of complement fixation.

The result is the opsonization of the pathogen and its speedy phagocytosis.

2. Phagocytosis Receptors

Macrophages have cell-surface receptors that recognize certain PAMPs, e.g., those containing mannose. When a pathogen covered with polysaccharide with mannose at its tips binds to these, it is engulfed into a phagosome.

3. Toll-Like Receptors (TLRs)

Macrophages, dendritic cells, and epithelial cells have a set of transmembrane receptors that recognize different types of PAMPs. These are called Toll-like receptors (TLRs) because of their homology to receptors first discovered and named in Drosophila.

In macrophages and dendritic cells, the pathogen is exposed to the TLRs when it is inside the phagosome. Which TLR(s) it binds to will determine what the response will be. In this way, the TLRs identify the nature of the pathogen and turn on an effector response appropriate for dealing with it. These signaling cascades lead to the expression of various cytokine genes.

Mammals have 10 different TLRs each of which specializes — often with the aid of accessory molecules — in a subset of PAMPs.

Examples:

TLR-2.
Binds to the peptidoglycan of gram-positive bacteria like Streptococci and Staphylococci.
TLR-3.
Binds to double-stranded RNA
TLR-4.
Binds to the lipopolysaccharide (endotoxin) in the outer membrane of gram-negative bacteria like Salmonella and E. coli O157:H7
TLR-5.
Binds to the flagellin of motile bacteria like Listeria.
TLR-6.
Forms a heterodimer with TLR-2 which responds to peptidoglycan and certain lipids.
TLR-7.
Binds to the single-stranded RNA (ssRNA) genomes of such viruses as influenza, measles, and mumps.
TLR-8.
Also binds to ssRNA.
TLR-9.
Binds to the unmethylated CpG of the DNA of the pathogen. (CpG islands in the host tend to have methyl groups attached.)
TLR-11.
In mice, it binds proteins expressed by several infectious protozoans (Apicomplexa).

In all these cases, binding of the pathogen to the TLR initiates a signaling pathway leading to the activation of NF-κB. [Link to discussion]

This transcription factor turns on many cytokine genes such as those for

tumor necrosis factor-alpha (TNF-α);
Interleukin-1 (IL-1);
chemokines, which attract white blood cells to the site.

All of these effector molecules lead to inflammation at the site.

And even before these late events occur, the binding of

gram-positive bacteria to TLR-2 and
gram-negative bacteria to TLR-4

enhances phagocytosis and the fusion of the phagosomes with lysosomes.

The innate immune system and commensal bacteria

The human large intestine (colon) contains an enormous (~10¹⁴) population of microorganisms. (Our bodies consist of only ~10¹³ cells!) Most of the species live there perfectly harmlessly; that is, they are commensals. Some are actually beneficial, e.g.,

by synthesizing vitamins
by digesting polysaccharides for which we have no enzymes
by stimulating the development of the adaptive immune system, including Th1 helper cells (which then inhibit Th2 helper cells which may provide protection against allergies like asthma) [Link]

Despite the name ("pathogen-associated"), PAMPs are found on all these nonpathogenic bacteria as well.

It turns out that not only do these bacteria not trigger inflammation, but their presence is needed (at least in mice) to maintain a healthy colon.

Mice that are raised in a germfree environment [Link] or are treated with antibiotics to clean all the bacteria out of their colon are unhealthy and have G.I. tracts that are hypersensitive to injury. However, if they are given
- LPS (from gram-negative bacteria) or
- lipoteichoic acid (from the peptidoglycan of gram-positive bacteria)
in their drinking water, their colons resist injury.
However, "knockout" mice that
- lack TLR-2 or TLR-4 or
- cannot signal through their TLRs [Link]
are not protected by such treatment.

These results

suggest that a continuous low level of activity of the innate immune system is essential to health — even in the absence of pathogens;
explain why deliberating feeding harmless bacteria ("probiotics") has proved beneficial to some human patients with a diseased colon;
provide another reason for avoiding the indiscriminate use of antibiotics (which kill harmless bacteria as easily as pathogenic ones).

Innate Immunity can trigger Adaptive Immunity

This can occur in several ways:

1.

Macrophages and dendritic cells are phagocytes and are also responsible for "presenting" antigens to T cells to initiate both cell-mediated and antibody-mediated adaptive immune responses.

Digested fragments of the engulfed pathogen are returned to the cell surface nestled in the cavity of class II histocompatibility molecules. [Link to a detailed description.]
Gene transcription turned on by the interaction of PAMPs and TLRs causes transmembrane molecules called B7 to appear at the cell surface.
T cells have a receptor for B7 called CD28.
Simultaneous binding of
- CD28 to B7 and
- the antigen/class II complex to TCRs specific for it [View]
activates the T cell.
This leads to repeated mitotic divisions producing clones of CD4⁺ T cells that can
- carry out cell-mediated immune responses and/or
- stimulate B cells to secrete antibodies of the appropriate specificity. [Discussion]

2.

The interaction of PAMPs and TLRs on the surface of dendritic cells causes them to secrete cytokines, including interleukin 6 (IL-6), which interfere with the ability of regulatory T cells to suppress the responses of effector T cells to antigen. A double-negative is a positive.

Link to discussion of regulatory T cells (Tr cells).

3.

B cells are also antigen-presenting cells. They bind antigen with their BCRs and engulf it into lysosomes. They then transport the digested fragments to the cell surface incorporated in class II histocompatibility molecules just as macrophages and dendritic cells do.

B cells also have TLRs. When a PAMP such as LPS binds the TLR, it enhances the response of the B cell to the antigen.

It has been known for many years that for vaccines to be effective, the preparation must contain not only the antigen but also materials called adjuvants. Several adjuvants contain PAMPs, and their stimulus to the innate immune system enhances the response of the adaptive immune system to the antigen in the vaccine.

4.

Pathogens coated with fragments of the complement protein C3 are not only opsonized for phagocytosis but also bind more strongly to B cells that have bound the pathogen through their BCR. This synergistic effect enables antibody production to occur at doses of antigen far lower than would otherwise be needed.

Some workers feel that, in fact, adaptive immunity is not possible without the assistance of the mechanisms of innate immunity.

Antimicrobial Peptides

Vertebrates (including ourselves), invertebrates (e.g., Drosophila), even plants and fungi secrete antimicrobial peptides that protect them from invasion by bacteria and other pathogens. In fact, probably all multicellular organisms benefit from this form of innate immunity.

For humans, the best-studied antimicrobial peptides are the

defensins and the
cathelicidins

Defensins

All our epithelial surfaces

skin
lining of the GI tract
lining of the genitourinary tracts
lining of the nasal passages and lungs

are protected by defensins.

Some defensins are secreted by the epithelial cells themselves; others are brought to the site by leukocytes, especially neutrophils.
Some are secreted all the time; others only in response to attack by pathogens. (In some cases their genes are turned on by activated TLRs.)
They are synthesized from a larger gene-encoded precursor which is
cut to produce the active peptide.
These range in length from 29 to 42 amino acids.
They contain several invariant cysteines that form disulfide bonds that assist in producing
a secondary structure that consists of a beta sheet.
They attack the outer surface of the cell membrane surrounding the pathogen eventually punching lethal holes in it. (Unlike eukaryotes, the phospholipids in the outer membrane of bacteria carry a surplus of negative charges, and the positive charges on the defensins probably enable them to penetrate the bacterial membranes while sparing host membranes.)

Cathelicidins

The best known human cathelicidin is LL37, a peptide of 37 amino acids secreted by epithelia and neutrophils. Unlike the defensins, its secondary structure is alpha helix.

LL37 and defensins work synergistically; that is, the killing efficiency of LL37 is increased if a defensin is also present.

Humans who suffer from atopic dermatitis (eczema associated with IgE-mediated allergies like asthma and hay fever) are susceptible to skin infections. These occur where there is neither LL37 nor defensin.

Mice whose genes for their homolog of LL37 has been "knocked out" are extremely susceptible to skin infections.

Antimicrobial Peptides and the GI Tract: an example

Food is usually loaded with microbes. But most of these cause no trouble, largely because of the barrier of antimicrobial peptides that exists from mouth to anus.

The epithelium of the mouth and tongue is protected by a layer of antimicrobial peptides as well as those secreted in the saliva.
The stomach is also protected by antimicrobial peptides (cut by pepsin from a larger precursor) as well as by the low pH of gastric juice.
The liquefied contents that leave the stomach are quickly neutralized by the bicarbonate ions in the pancreatic fluid. However, any bacteria that survived the trip through the stomach (e.g., E. coli has a proton pump that enables it to survive the strong acid of the gastric juice) are kept in check by the antimicrobial peptides secreted by the Paneth cells of the small intestine. So, the contents of the small intestine normally contain only a small population of microbes.
Not so for the large intestine (colon). The colon supports an enormous population (>10¹³) of microorganisms, but these seldom invade its lining thanks to
- a protective barrier of antimicrobial peptides as well as
- the protective actions of continuous stimulation of
  - TLR-2s by gram-positive commensals and
  - TLR-4s by gram-negative commensals
The rectum is also protected by an epithelial barrier of antimicrobial peptides.

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23 October 2005