Defense against infections logo

Van der

Last update 27-4-2008

The Innate Immune System


  1. Introduction
  2. The innate immune system may predate adaptive immune system
  3. Discrimination between self and non-self; e.g. pathogen recognition by phasgocytes
  4. Binding of pathogens in innate immunity
  5. The invariant molecular structures of microorganisms that play a role in innate immune recognition
  6. Ligands (receptor sites) developed by the host organism
  7. PRRs
  8. The innate signaling by PAMPs
  9. Complement links innate immunity and the memory B cell response
  10. Defensins
  11. References

Innate immunity

This concerns a defense system that:

  1. Recognizes microorganisms
  2. Can bind them to phagocytes
  3. Can kill them clear microorganisms by phagocytosis, killing and digestion.

Innate immune recognition distinguishes self from non-self perfectly (a condition not always met by the adaptive immune response).

The innate immune system uses receptors which are ancient in their lineage.

Killing of microorganisms can be accomplished outside the host cells by defensins but also intra-cellularly as will be outlined comprehensively later in point 5.
Defensins thus form an essential part of innate defense.
The past decennium brought several discoveries that focused attention on antimicrobial peptides on epithelial surfaces. Highlights included new insights into the relative selectivity of antimicrobial peptides for microbial membranes, their primary site of action.
The vertebrate arsenal includes inorganic disinfectants, such as hydrogen peroxide, hypochlorite and nitric oxide, made by 'professional phagocytes'. It also contains an array of constitutive or inducible antimicrobial proteins and peptides. Similar peptides produced by plants, protozoans and invertebrates.

Definitions and terminology

Pathogen recognition is mediated by the nonclonal innate recognition system. In evolution this part of (innate) defense may have developed prior to adaptive immunity.
Pathogen recognition is based on the recognition of pathogen associated molecular patterns (PAMPs) by pathogen recognition receptors (PRRs) on epthelial and immune cells. PRRs appear perfectly able to discriminate between "self" from "non-self" structures (pathogen-associated structures). PRRs may signal the presence of a pathogen which then can be interpreted as such by the adaptive immune system.

1. Introduction

The innate immune system is the immediate available part of the defense to invading (penetrating the mucosal layer) and reaching remote sites (translocating) microorganisms. Innate immunity, in other words, is the immediate ability of a host organism to prevent or control an infectious challenge.
When vertebrates evolved as a separate subphylum, these responses retained their original function, but over time acquired 'new properties' as well. Responses induced by pathogen recognizing receptors upon recognition of pathogens consist of host defense mechanisms which are found in all organisms [1-3]. Meant are responses such as phagocytosis, the production of antibacterial peptides and other microbicidal and antiviral mechanisms.

2. The innate immune system may predate adaptive immune system

From the perspective of a microbe, the tissues of living multicellular organisms are rich sources of nutrients.
To avoid being parasitized and digested, multicellular organisms conduct continuous antimicrobial warfare by production of endogenous antibiotic substances wherever their tissues interface with the external environment.
Challenged by the remarkable plasticity of microbes, vertebrates have evolved multiple and varied molecular defenses which will be briefly reviewed:

3. Discrimination between self and non-self; e.g. pathogen recognition by phagocytes

The physiologic defense may have evolved since the first monocellular cells developed under strong selective pressure imposed by microorganisms. As a result, higher organisms have developed the ability to recognize invading microbes and regard them as different from self [3].
For the development of a recognition repertoire in phagocytes, a certain upper limit on the number of recognition molecules which could be encoded in the genomes of the hosts is a serious restriction factor. Relatively few germline encoded molecules can recognize a vast number of diverse molecular structures associated with pathogens.

Note: The 'early' (multi)cellular host organisms have developed a set of nonclonal receptors which can recognize pathogens. These receptors have a broad specificity, since they can recognize a number of different ligands, as long as the ligands share a common molecular pattern [4].

4. Binding of pathogens in innate immunity

Requirements for potential targets by innate immune recognition:

  1. Molecular patterns recognized by the innate immune system must be shared by large groups of pathogens, and thus must represent general patterns rather then specific structures.
  2. These molecular patterns must be conserved products of microbial metabolism, which are not subject to antigenic variability. Although the immune system selects against these patterns, pathogens cannot 'change' them because they are essential for the survival or pathogenicity of the microorganisms. Any attempts to change them, will be lethal to the microbe or render it nonpathogenic.
  3. The overall effect of immune recognition and the destruction of the target requires that the recognized structures be absolutely distinct from self-antigens. The major consequence of this requirement is the ability of the innate immune system to discriminate between self and non-self [3].

5. The invariant molecular structures of microorganisms that play a role in innate immune recognition

The invariant molecular structures in pathogens that meet the above requirements represent the main targets of innate immune recognition, named : Pathogen-Associated Molecular Patterns (PAMP). [5]

The features, characteristic of PAMPs, can be demonstrated by several well known examples of microbial modulators/stimulators of innate immune responses; i.e.:

  1. The general structure of lipopolysaccharides and teichoic acids are shared by all gram-negative, respectively gram-positive bacteria
  2. The unmethylated CpG motif is characteristic of bacterial DNA; but not mammalian DNA
  3. Double stranded RNA represents the signature of RNA viruses
  4. mannans are conserved components of yeast cell walls

Most importantly, none of these structures is made by the host organism and all of them are shared by large groups of pathogens and are absolutely essential for their physiology.

6. Ligands (receptor sites) developed by the host organism

PAMPS may have a number of pattern-recognition receptors (PRRs) [5].
The main distinction of PRRs from clonally-distributed receptors of T and B lymphocytes is, that their specificities are germline coded, which means, that they were formed in evolution due to selection by pathogens at the population level. The ligand molecules are often refered to as the TOLL-receptor family. [5]

7. PRRs

PRRs are strategically expressed on cells that are the first to encounter pathogens during infection, such as surface epithelia, and also on all types of effector cells of the innate immune system.
Recognition of pathogens on the basis of ''pathogen-associated molecular patterns" (PAMPs) by PRRs results in the activation of various types of innate immune responses and often represents a direct induction of effector functions. There are several "families" of molecules that contribute to these recognition processes.

  1. a. Families of proteins with the characteristics of PRRs
    Different to the antigen receptors of adaptive immunity, which are encoded exclusively by rearranging of the immunoglobulin (Ig) superfamily, innate immune recognition is not mediated by members of a single protein family.
    In fact, members of several protein families have been adapted to function as PRRs. Other members of these families are used in different molecular recognition processes by the neuro-endocrine system.
    Currently, seven protein families that area believed to play a central role in forming PRRs can be distinguished.
  2. Induction of co-stimulatory molecules
    It has been well documented that a second so-called co-stimulatory signal is required for lymphocyte stimulation [5]. Because activation of lymphocytes is only appropriate when they are specific to pathogen-derived antigens, it is likely that the function of the co-stimulatory activity is to signal the presence of a pathogen. This requires that the expression of co-stimulatory activity be controlled by pathogen recognition [7], although other signals (e.g. those caused by trauma or surgery) may be able to induce co-stimulation expression as well.

8. The innate signalling by PAMPs

The endogenous signals induced by PAMPs can be grouped into the following three categories:

  1. Signals which directly mediate the inflammatory response. This includes IL-1, tumor necrosis factor (TNF)-alpha, (IL-6, type 1 interferons (IFNs), and various other cytokines.
  2. Signals which function as co-stimulators of T cell activation; so far only two molecules - B7.1 and B7.2 - belong to this category with certainty. Other molecules, such as intercellular adhesion molecules (ICAM)-1, that contribute to various aspects of T cell stimulation, do not share all the critical attributes of co-stimulatory activity, and are not considered to be co-stimulators.
  3. Signals which control the induction of effector functions; these include IL-4, IL-5, IL-10, IL-12, transforming growth factor (TNF)-beta and IFN-gamma.

9. Complement links innate immunity and the memory B cell response

In mice, B-1 cells and dentritic cells express specific receptors (CD35 [6] and CD21 [7-9]) which bind cleavage products from complement factor C3. CD35 has six additional amino-terminal short consensus repeats which contain the C3b binding site in addition to CD21.
On human B cells, CD21 forms a complex with CD19 and Tapa-1 (target for antiproliferative antibody-1/CD81) termed the B cell coreceptor [10-14]. Coligation of the CD21/CD19/Tapa-1 coreceptor with the B cell receptor for antigen (BCR) lowers the amount of antigen required for B cell activation in vitro by 10-100 fold [15,16.]

The functional importance of the co-receptor is illustrated by mice deficient in CD21 [15-17] have an impaired humoral response to T-cell dependent antigens. Mice deficient in C3 (or C4 required for C3 activation) have an impaired memory response to T-cell dependent antigens [18]. Thus, deficiency in either the C3d ligand or its receptor (CD21) results in an impaired humoral response. Such C3 or C4 deficient mice are highly susceptible to lipopolyscacchrides (LPS); LPS clearance is therefore mediated by the classicle pathway which leads to the conclusion that 'natural' IgM is involved in the protection to LPS [19].

Expression of CD21 (or CD35) on B cells is critical for at least two distinct stages in activation within the secondary lymphoid compartment, these being follicular retention and germinal center survival.
Naive B cells, which encounter T-cell dependent antigens within the splenic white pulp, migrate into the periarteriolar lymphoid sheath zone, where in the presence of T-helper cells they proliferate and either initiate foci of antibody forming cells or re-enter the B-cell follicle and initiate a so-called germinal center reaction [20].
Survival in germinal centers requires at least two signals: T-cell help (via CD40 ligand) and antigen contact [21,22].

10. α, β Defensins

Defensins are broad-spectrum antimicrobial peptides with three intra-molecular cystein disulfide bonds. The vertebrate defensin family contains two branches, designated alfa defensins and beta defensins. Although similar in shape to α-defensins, β-defensins are slightly larger and differ in the placement and connectivity of their six conserved cysteine residues.
Humans produce six different α-defensins, and two beta-defensins.
Four human α-defensins (HD) are found in the primary (azurophil) granules of neutrophils [22 ] and are expressed as well by the mucosal lining and inparticular human small intestinal Paneth cells.

Paneth cells are specialized, granule-laden, secretory epithelial cells located at the bottom of crypts in the small intestine [23]. They release lysozyme, secretory phospholipase A2 and enteric alpha-defensins after bacterial or cholinergic stimuli [24 ]. Because experimental access to human Paneth cells is limited, rodents provide useful models [24,25]. The secretion of defensins into the capillary-like crypt lumen should generate high local concentrations of defensins. As Paneth cells are located just below the zone of mitotic cells, whose progeny replace continuously shed epithelial lining cells, it is likely that HD-5 and HD-6 either have low intrinsic cytotoxicity or that crypt secretions contain other factors that mitigate their cytotoxic effects.
Certain murine defensins form chloride channels in model epithelial monolayers [26]. If this effect also occurs in vivo, it might increase water influx and distribute enteric defensins throughout and beyond the crypt lumen. The recently accomplished production of recombinant HD-5 and of polyclonal antibodies reactive with native HD-5 peptides [27,28] should facilitate future studies of human intestinal defensins.

The discovery that human beta-defensins HBD-1 and HBD-2 are produced in various epithelia is noteworthy. Structurally and perhaps functionally, these peptides resemble bovine epithelial β-defensins [29,30].
Unlike the α-defensins, β-defensins of neutrophils [22,30] or Paneth cells [23,10], epithelial beta-defensins are not stored in cytoplasmic granules so that their local concentration may rely primarily by their synthesis and secretion rates.
Production of the bovine tracheal beta-defensins tracheal antimicrobial peptide [29, 30] and the human beta-defensin HBD-2 [29] are stimulated by bacteria, bacterial products, and TNF-alpha.

Prior to the development of somatic mechanisms of generating a specific recognition repertoire diversity -the hallmark of adaptive immunity- there was a certain upper limit to the number of recognition molecules which could be encoded in the genomes of the host organisms. In contrast, for innate immunity, relatively few germline encoded molecules had to be able to recognize a vast number of diverse molecular structures associated with pathogens.

The innate immune system has a low specificity. Innate immunity is believed to have predated the adaptive (highly specific) immune, response on several grounds:

  1. The problem with recognizing pathogens is due to their strong variability and molecular heterogeneity.
  2. This variability is further aggravated by their adaptivity, i.e. high mutational rate of microorganisms.


  1. Medzhitov R, Janeway ChA. An ancient system of host defense. Curr Opin Immunol 1998, !0:12-15.
  2. Janeway CA. Approaching the asymptote? Evolution and revolution in immunology. Cold Spring Harb Symp Quant Biol 1989, 54:1-13
  3. Janeway CA. The immune system evolved to discriminate infectious nonself from noninfectious self. Immunol Today 1992, 13:11-16.
  4. Medzhitow R, Janeway CA. On the of immune recognition. Res Immunol 1996, 47:208-214.
  5. Kopp EB, Medzhitov R. The Toll-receptor family and control of innate immunity. Curr Opin Immunol 1999, 11:13-18.
  6. Ahearn J, Fischer M, Croix D, Goerg S, Ma M, Xia J, Zhou X, Howard R, Rothstein T, Carroll M: Disruption of the Cr2 locus results in a reduction in B-1a cells and in an impaired B cell response to T-dependent antigen. Immunity 1996, 4:251-262.
  7. Ridge JP, Matzinger P."> Neonatal tolerance revisited: turning on newborn T cells with dendritic cells. Science 1996 :1723-1726.
  8. Kinoshita T, Lavoie S, Nussenzweig V: Regulatory proteins for the activated third and fourth components of complement (C3b and C4b) in mice. II Identification and properties of complement receptor 1 (CR1). J Immunol 1985, 134:2564-2570.
  9. Fingeroth JD, Benedict MA, Levy DN, Strominger JL: Identification of murine complement receptor type 2. Proc Natl Acad Sci USA 1989, 86:242-246.
  10. Kurtz CB, O’Toole E, Christensen SM, Weis JH: The murine complement receptor gene family. IV. Alternative splicing of Cr2 gene transcripts predicts two distinct gene products that share homologous domains with both human CR2 and CR1. J Immunol 1990, 144:3581-3591.
  11. Molina H, Kinoshita T, Inoue K, Carel J-C, Holers VM: A molecular and immunochemical characterization of mouse CR2. J Immunol 1990, 145:2974-2983.
  12. Carter RH, Tuveson DA, Park DJ, Rhee SG, Fearon DT: The CD19 complex of B lymphocytes. Activation of phospholipase C by a protein tyrosine-kinase-dependent pathway that can be enhanced by the membrane IgM complex. J Immunol 1991, 147:3663-3671.
  13. Bradbury LE, Kansas GS, Levy S, Evans RL, Tedder TT: The CD19/CD21 signal transducing complex of human B lymphocytes includes the target of antiproliferative antibody-1 and Leu-13 molecules. J Immunol 1992, 149:2841-2850.
  14. Kansas GS, Tedder TF: Transmembrane signals generated through MHC class II, CD19, CD20, CD39 and CD40 antigens induce LFA-1 dependent adhesion in human B cells through a tyrosine kinase-dependent pathway. J Immunol 1991, 147:4094-4102.
  15. Carter RH, Fearon DT: CD19: Lowering the threshold for antigen receptor stimulation of B lymphocytes. Science 1992, 256:105-107.
  16. Tedder TF, Zhou LJ, Engel P: The CD19/CD21 signal transduction complex of B lymphocytes. Immunol Today 1994, 15:437-441.
  17. Croix D, Ahearn J, Rosengard A, Han S, Kelsoe G, Ma M, Carroll M: Antibody response to a T-dependent antigen requires B cell expression of complement receptors. J Exp Med 1996, 183:1857-1864.
  18. Molina H, Holers V, Li B, Fung Y, Mariathasan S, Goellner J, Strauss-Schoenberger J, Karr R, Chaplin D: Markedly impaired humoral immune response in mice deficient in complement receptors 1 and 2. Proc Natl Acad Sci USA 1996, 93:3357-3361.
  19. Weisser D, Williams JP, Moove FD, Kobzik L, Ma M, Hechtman HB, Carroll MC. Reperfusion injury of ischemic skeletal muscle is mediated by natural antibody and complement. J Exp Med 1996, 183:2343-2348.
  20. Reid RR, Prodeus A, Khan W, Hsu T, Rosen FS, Carroll MC. Endotoxin shock in antibody deficient mice: unraveling the role of natural antibody and complement in the clearance of lipopolysaccharide. J Immunol 1997, 159:970-975.
  21. Kelsoe G: In situ studies of the germinal center reaction. Adv Immunol 1995, 60:267-288.
  22. Kelsoe G: The germinal center reaction. Immunol Today 1995, 16:324-326.
  23. MacLennan I: Germinal Centers. Annu Rev Immunol 1994, 12:117-139.
  24. Ganz T, Lehrer RI: Antimicrobial peptides of leukocytes. Curr Opin Hematol 1997, 4:53-58.
  25. Ouellette AJ, Selsted ME: Paneth cell defensins: endogenous peptide components of intestinal host defense. FASEB J, 1996,10:1280-1289.
  26. Qu XD, Lloyd KC, Walsh JH, Lehrer RI: Secretion of type II phospholipase A2 and cryptdin by rat small intestinal Paneth cells. Infect Immun 1996, 64:5161-5165.
  27. Darmoul D, Ouellette AJ: Positional specificity of defensin gene expression reveals Paneth cell heterogeneity in mouse small intestine. Am J Physiol 1996, 271:G68-74.
  28. Lencer WI, Cheung G, Strohmeier GR, Currie MG, Ouellette AJ, Selsted ME, Madara JL: Induction of epithelial chloride secretion by channel-forming cryptdins 2 and 3. Proc Natl Acad Sci USA 1997, 94:8585-8589.
  29. Porter EM, Liu L, Oren A, Anton PA, Ganz T: Localization of human intestinal defensin 5 in Paneth cell granules. Infect Immunity 1997, 65:2389-2395.
  30. Porter EM, Van Dam E, Valore EV, Ganz T: Broad-spectrum antimicrobial activity of human intestinal defensin 5. Infect Immunity 1997, 65:2396-2401.
  31. Harder J, Bartels J, Christophers E, Schroeder J-M: A peptide antibiotic from human skin. Nature 1997, 387:861-862.
  32. Diamond G, Russell JP, Bevins CL: Inducible expression of an antibiotic peptide gene in lipopolysaccharide-challenged tracheal epithelial cells. Proc Natl Acad Sci USA 1996, 93:5156-5160.