1462 Biochemical Society Transactions (2003) Volume 31, part 6 Signalling networks, inflammation and innate immunity S.K. Dower 1 and E.E. Qwarnstrom Academic Unit of Cell Biology, Section of Functional Genomics, Division of Genomic Medicine, University of Sheffield, Royal Hallamshire Hospital, Glossop Road, Sheffield S10 2JF, U.K. Abstract We have been analysing the signalling systems that couple to receptors of the TIR (Toll/interleukin-1 receptor) family, which signal through a common cytoplasm region; the TIR domain. These systems are of both practical and fundamental biological significance, being central to the pathogenesis of chronic inflammatory diseases such as atherosclerosis, to host defence throughout the biological world, and are ancient in the context of life on earth, having originated more than 1 billion years ago: prior to the divergence of plants and animals. TIR domain receptors couple to at least two sets of well-characterized pathways: those leading to the activation of inhibitory κ B kinase complexes/nuclear factor κ B, and those leading to the activation of mitogen-activated protein kinase/AP-1/ATF-2 etc. We have been investigating these systems using a combination of expression screening methods to identify new components, and real-time green fluorescent protein-based techniques to observe execution of signalling programmes in real time. Our data reveal that there is a very large level of cell-to-cell variation in signal programme execution even in clonal populations and that at least one mechanism for dealing with this heterogeneity is the assembly of signal transduction components into large multiprotein complexes. Introduction Defence against pathogens and repair of damage caused by injury and infection are indispensable to the survival of all multicellular organisms. In both plants and animals, the basis of this defence is the innate immune system and a broader array of systems generally termed ‘inflammatory’, although this fails to stress their physiological and beneficial role in integrating and underpinning responses to environmental ‘damage’, whether created by bacteria and viruses, toxic chemicals, burns or mechanical trauma. Higher animals, where a circulating blood system allows the rapid interrog- ation of foreign matter (usually proteins) by a vast array of clones of cells each bearing a specific receptor, possess in addition an adaptive immune system, and can hence generate specific immune responses. In this brief review we will discuss innate immunity and inflammation, focusing on one subset of the components and the signalling networks it controls, and on the approaches our groups are taking to analysis of signal flow through networks underlying the control of gene regulation during host response to injury and infection and in chronic inflammation. Comparison of protein sequences of known components, in plants, mammals, arthropods and micro- Key words: green fluorescent protein, immunity, inflammation, networks, signal transduction. Abbreviations used: TIR, Toll/interleukin-1 receptor; NF-κB, nuclear factor κB; IL, interleukin; IL- 1R, IL-1 receptor; I-κB, inhibitory κB; IKK, inhibitory κB kinase; MAPK, mitogen-activated protein kinase; EGFP, enhanced green fluorescent protein; DD, death domain; ERK, extracellular-signal- regulated kinase; JNK, c-Jun N-terminal kinase; FRET, fluorescence resonance energy transfer; AcP, accessory protein; ODE, ordinary differential equation; IRAK-1, IL-1-receptor-associated kinase; TAK-1, transforming growth factor β-associated kinase; TAB, TAK–binding protein; MKK, MAPK kinase; MKKK, MKK kinase. 1 To whom correspondence should be addressed (e-mail s.dower@sheffield.ac.uk). organisms, shows innate immune/inflammatory systems to be ancient – probably predating eukaryotes [1]. Thus, they mediate the responses of all cells to potentially deleterious features in the environment. From a practical point of view, breakdown in appropriate regulation of immunity and inflammation underlies a wide range of common diseases, for example cardiovascular disease, arthritis, chronic interstitial nephritis and inflammatory bowel disease. The primary biological function of host defence systems is to preserve health until the next generation has been produced and matured. Much of the evolutionary selection pressure arises from co-evolution of host and pathogens, a classic predator– prey relationship, given that survival of pathogens requires survival of the host species [2]. The result of host–pathogen and indirectly therefore host–host competition is that host defence systems have expanded and diversified more rapidly than almost any other in higher organisms; this rate of evolution is reflected in rapid interspecies sequence diver- gence and a high degree of intraspecies polymorphism [3]. Rapid and continuing evolution, in combination with the idea that high pre- and co-reproductive activity, which is selected for, may lead to post reproductive malfunction, which is not selected against, provides a plausible explanation for a high failure rate and prevalence of inflammatory diseases in later life. Inflammatory diseases, therefore, are a result of a biological control network that has become misprogrammed. Simplistically therefore, we know that a state exists which can be maintained stably for decades and which is ‘healthy’, and the aim is to switch the system back by appropriate intervention. To do this we need to understand the signal transduction networks that underlie innate immunity and C  2003 Biochemical Society