The innat immune system dtects the presence of foreign organisms and initiates a coordinated response to eliminate infectious threats. Among the microbial products sensed by innate immune effectors, efficient recognition of nucleic acids (DNA and RNA) is critical. However, the detection of nucleic acids also presents a risk for self-recognition and self-activation in response to host nucleic acids which is associated with many autoimmune diseases. Inappropriate detection of self-molecuels is prevented through subcellular compartmentalization of receptors, degradation of self nucleic acids by endogenous nucleases, and specialization of innate receptors that detect conserved microbial featrues absent form the host. Typcial microbial freatures recognized by the innate immune system include distinct products of post-transcriptional processing, such as nucleotide chemical modificaitons and specific 5′ or 3′ moeiteis. In addition, microbial genomes display specific nueleic acid patters as at a different requency compared to human genome. Fore rexample, differential CpG and UpA usage patters create a metric that computationally aggregates the genomes of some viruses, including positive, negative and double-stranded RNA viruses., DNA viruses and even tumors. CpG methylation of DNA, a feature vastly more prevalent in mammals than baceteria, promotes cytosine deamination, leading to accelerated bytosine to thymine mutation. Thus, GpG methylation is thought to acount for underrepresentation of CpG motifess in mammalian genomes. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65). 

A popular approach for studying the interaction of the immune system with viral sequence patterns is the large scale synonymous recording of viral genomes. Taking advantge of the genetic ode’s degeneracy, this strategy consists of replaicng whole portions of viral genomes with sequences either enriched for or depleted of the pattern of itnerest, wout altering the prtoein coding sequence. Pioneering syutdies introduced rare condons in the cpasid-coding reigon of poliovirus genome and observed that it led to viruses with altered replication fitness, lowered virulence and infectivity. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65)

The structure of nucleic acids depends on base-paring interactions, and thus is inherently linked to sequence. For instance, GC rich RNA tend ot fold into mroe stable structures than AU righ RNAs, simply becasue a GC pair has three hydrogen bonds whereas an AU pair only has two. Thus, GC rich sequences may form robust secondary structures wehreas AU rich fragments should have higher flexibility. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65)

Molecular stability is another property linked to nucleic acid sequence. Unique sequence elemnets found at hte 3′ end of cellular mRNAs can mediate theri degradation, such as AU rich elements (AREs), that are characterized by a tandem repeat AUUUA sequence or a simple U rich region. AREs are observed in the sequence of many mRNAs related to the immune response and binds specific prtoeins, such as AU-binding factor I (AUFI), which reocgnies AREs and targets mRNA for rapid degradation. Interestinly, AUF1 can also directly target regions of viral RNA and inhibit viral replication, as observed during enterovirus and human rhinovirus infection. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65)

The receptors involved in cellular innate recognition of essential structural molecules of microbes depends on germ line encoded moleuctures wehreas AU rich fragments should have higher flexibility. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65)cules often called pattern recognition receptors (PRRs) that do not undergo somatic mutation like the receptors of the adaptive immune system. These PRRs include membrane bound receptors, such as the Type A, B and C scavenger receptors, integrins and the Toll Like Receptors, C type lectin receptors as well as intracellular receptors like the recently identified nucleotide binding oligomerication domain (NOD) proteins.

PRRs are expressed on cells of the innate immune system including macrophages, polymorphonuclear leukocytes, DCs and NK cells but also many other cell types including eptiehlia cells and adipocytes.

The response of cells to recognition of microbial products via innate recognition receptors ranges from phagocytosis and related intracellular processes essential for handling ingested microbes to release of a broad range of mediators. These mediators are all involved in the efferent arm of the innate immune response. Important mediators are cytokines, chemokines, antimicrobial peptides, lysozyme, BPI, lactoferrin, proteases, lipases, glycosidases, superoxides, nitric oxide and many others.

Extracellular or Membrane PRRs

Scavenger receptors: recognize endotoxin, lipoteichic acid and bacterial wall.

Toll like receptors 1-9: see outline

Intracellular PRRs

NLRs (Nod Like Receptors):

The best-characterized members of the NOD-LRR family are NOD1 and NOD2, which recognize distinct elements of bacterial cell wall peptidoglycan in the cytosol to mount or modulate a proinlfammatory immune response or to promote apoptosis. NOD1/NOD2 are the NBS-LRR proteins involved in intracellular recognition of microbes through specific products derived from peptidoglycans. The NBS-LRR proteins are characterized by 3 structural domains: a C-terminal LRR domain able to sense a microbial motif; an intermediary NBS essential for the ogligomerization of the molecule that is necessary for the signal transduction induced by different N-terminal effeector motifs such as a pyrin domain; and a caspase activating and recruitment domain (CARD) or a baculovirus inhibitor of apoptosis protein repeat domain.

Nod1/Nod2 can sense intracellular bacteria; mice deficient in either show increased sensitivity to infection. Nod1 senses a peptidoglycan motif containing a diaminopimelate containing N-acetylglucosamine-N-acetylmuramic acid tripeptide found mainly in Gram-negative bacterial.

After oligomerization, RIP2 is recruited to Nod through homophilic CARD-CARD interactions. RIP2 is an adaptor protein sharing homology with IRAK and Rip group proteins. Interaction between Nod1 or Nod2 and RIP2 leads to the activation of the NF-kB pathway through the recruitment of the IkB kinase (IKK) complex to the central domain of RIP2.

–NOD1: is an intracellular PRR which detects bacterial when they enter the cytoplasm. For example, onceShagella flexneri or H. pylori, or P. aeruginosa gets into the cytoplasm it activate NOD1 which leads to activation of NF-kB. The motif that is recognized is peptidoglycan from the bacterial cell wall.

–NOD2: As with NOD1, NOD2 recognizes peptidoglycan from the bacterial cell wall. Nod2 senses another peptidoglycan motif, muramyl dipeptide found in both Gram-positive and Gram-negative bacterial. Muramyl dipeptie (MDP) is the minimal PGN motif common to both Gram-positive and Gram-negative bacteria.

–Naip5

In mouse macrophages, the NOD-LRR protein Naip5 (Birc1e) restricts intracellular replication of the opportunistic human pathogen Legionella pneumophila. Naip5 is compirsed of 3 modules: NH2-terminal baculoviral inhibitor of apoptosis repeats, a central NOD domain, and COOH-terminal LRRs. By analogy to other NOD-LRR proteins, the LRR region is thought to recognize microbial products, triggering oligomerization via the NOD domain and activation of a cellular response that is governed by various NH2-terminal effector-binding domains. Whereas virtually all mice are reistant to L. pneumophila the A/J strain encodes a naip5 allele that confers susceptibility to infection.

Other PRRs

Pentraxins:

RIG-I-like Receptors:

–RIG1: The best studied cytosolic RNA sensors are retinoic acid indicible gene I (RIG-I) and melanoma differentiation factor 5 (MDA5). RIG-I primarily relies on structural features like 5′ triphosphate extremities and dsRNA fragments to detect viral RNA. RIG-I has been shown to recognize specific sequences of viral genomes, such as poly-U/UC motifes found in the 3′ untranslated region of hepatitis C virus and in the N gene of Hantaan virus. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65)

–MDA5: binds dsRNA independently of its terminal moieties and, according to structural studies, without any direct sequence specificity. Indeed, MDA5 interacts primarily with a phosphate backbone and 2′ hydroxyl gorups of ribose in dsRNA, using it as a platform to stack along dsRNA in a head-to-tail arrangement. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65)

Interferon-induced proteins with tetratricopeptide repeats 2 (IFIT2): can direclty bind viral RNAs and exert antiviral functions such as inhibition of viral translation and activation of anti-viral signaling pathways. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65)

DEAD Box Helicase 17 (DDX17): is a multifunctional helicase that binds stem-loop structures of viral RNA in the cytosol of infected cells. In the nucleus, DDX17 binds both CA and CT repeat elemtns found in mature cellular mRNAs and the (GTA)CATCC(CTA) motif found in miRNAs. Thus, DDX17 uses both primary sequence and secondary structure for optimal binding to ligands. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65)

Cyclic GMP-AMP synthase (cGAS): senses cytosolic dsDNA predominantly by binding to its sugar phosphate backbone, suggesting sequence independent innate sensing. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65)

Sox2: is a transcirption factor that has alo been shown to act as a cytosolic dsDNA receptor. To detect microbial DNA, Sox2 binds to sequence motifs in bacterial genomes such as L. monocytogenes. Interestingly, these sequences are similar to the endogenous DNA motifs Sox2 binds when acting as a transcription factor. (Greenbaum, “Sequence-specific sensing of nucleic acids” Trends Immunol 2017, 38(1); 53-65)

Indirect Recognition of viral infection

TLR and c-type lectin receptors recognize PAMP in the extracellular space, but many pathogens reach the cell cytoplams so that host have had to evolve mechanisms to detect pathogens intracellularly. For virus infections, a good example of this is the detection of dsRNA in the cytoplasm by protein kinase R (PKR) activation.

It is also important that the immune system is primed to respond to a nearby infection without coming into direct contact with a virus. Bystander DC can respond to signals originating from other DC or stromal cells that come into contact with PAMP. Some of the inflammatory mediators responisble for this paracrine activaiton are type I IFN and TNFalpha. As viral infection of DC impairs their direct stimulatory capacity in many instances, the implied reliance on cross presentation by uninfected bystander DC becomes all the more important.