Recognition of the Helical Cytokine Fold

Tissue-protective cytokines: structure and evolution

Cytokines are important mediators of host defense and immunity, and were first identified for their role in immunity to infections. It was then found that some of them are pathogenic mediators in inflammatory diseases and much of the emphasis is now on pro-inflammatory cytokines, also in consideration of the fact that TNF inhibitors became effective drugs in chronic inflammatory diseases. The recent studies on the tissue-protective activities of erythropoietin (EPO) led to the term "tissue-protective cytokine." We discuss here how tissue-protective actions might be common to other cytokines, particularly those of the 4-alpha helical structural superfamily.

The K1K2 region of Lys-gingipain of Porphyromonas gingivalis blocks induction of HLA expression by gamma interferon

In the context of periodontal disease, cysteine proteinases or gingipains from Porphyromonas gingivalis have been implicated in the hydrolysis of cytokines, including gamma interferon (IFN-γ). This cytokine plays a crucial role in host defenses, in part, by regulating expression of major histocompatibility complex molecules. Our recent analysis has identified three structurally defined modules, K1, K2, and K3, of the hemagglutinin region of the lysine gingipain Kgp. These three structurally homologous domains have a common β-sandwich topology that is similar to that found in a superfamily of adhesins and carbohydrate binding domains. The three Kgp hemagglutinin modules are distinguished by variation in some of the loops projecting from the β-sandwich core. Recombinant products corresponding to both single and multidomain regions as well as native Kgp bound IFN-γ with similar affinities. Among the adhesin domain constructs, only the K1K2 polypeptide inhibited the upregulation of HLA-1 expression in a human erythroleukemia (K562) line induced by both recombinant and native IFN-γ. The K1K2 polypeptide also inhibited HLA-DR expression induced by IFN-γ in human umbilical vein endothelial cells. These effects were competitively inhibited by coincubation with sodium or potassium chloride solution. The N-terminal residues of IFN-γ were implicated in mediating the effect of K1K2, while antibody binding to loop 1 of K2 blocked the action of K1K2. The findings indicate the potential significance of structurally defined Kgp adhesin modules in the inactivation of IFN-γ but also the potential of K1K2 in locating the target for the catalytic domain of Kgp.

[Genome-wide prediction of interferon family members of tree shrew and their molecular characteristics analysis]

Interferons (IFNs) represent proteins with antiviral activities that are secreted from cells in response to a variety of stimuli. In addition to antiviral, antibacterial and anti-parasitic host-defense functions they are now also recognized as crucial regulators of cell proliferation, differentiation, survival and death as well as activators of specialized cell functions particularly in the immune system and play important roles in infectious and inflammatory diseases, autoimmunity and cancer. Tree shrews (Tupaia belangeri) were found to be susceptible to several human viruses and therefore are widely regarded as good models for analyzing mechanism of human diseases. In this report, we have forecasted the interferon family members of tree shrew from its genome mainly using the methods like Blast (whole genome shotgun sequence) and gene prediction. Our data show that tree shrew interferon system includes: type I IFN: α (five subtypes), β, ω, κ, epsilon, δ; type II IFN: γ; type III IFN: λ1, λ2/3. Furthermore, the predicted structures of α and λ have similar character with those of other mammals. However, there are some differences in cysteine position and N-glycosylation numbers between human and Tree shrew IFNs. These results provide fundamental basis for further molecular cloning and function analysis of tree shrew IFNs in future.

Drosophila Helical factor is an inducible protein acting as an immune-regulated cytokine in S2 cells

The innate immunity of Drosophila melanogaster is based on cellular and humoral components. Drosophila Helical factor (Hf), is a molecule previously discovered using an in silico approach and whose expression is controlled by the immune deficiency (Imd) pathway. Here we present evidence demonstrating that Hf is an inducible protein constitutively produced by the S2 hemocyte-derived cell line. Hf expression is stimulated by bacterial extracts that specifically trigger the Imd pathway. In absence of any bacterial challenge, the recombinant form of Hf can influence the expression of the antimicrobial peptides (AMPs) defensin but not drosomycin. These data suggest that in vitro Hf is an inducible and immune-regulated factor, with functions comparable to those of secreted vertebrate cytokines.

The role of genomic data in the discovery, annotation and evolutionary interpretation of the interferon-lambda family

BACKGROUND

Type-I interferons, type-II interferons, and the IL-10 family are helical cytokines with similar three-dimensional folds. However, their homologous relationship is difficult to detect on the basis of sequence alone. We have previously described the discovery of the human type-III interferons (IFN lambda-1, -2, -3 or IL-29, IL-28A, IL-28B), which required a combination of manual and computational techniques applied to predicted protein sequences.

PRINCIPAL FINDINGS

Here we describe how the use of gene structure analysis and comparative genomics enabled a more extensive understanding of these genes early in the discovery process. More recently, additional mammalian genome sequences have shown that there are between one and potentially nine copies of interferon lambda genes in each genome, and that several species have single exon versions of the interferon lambda gene.

SIGNIFICANCE

The variable number of single exon type-I interferons in mammals, along with recently identified genes in zebrafish homologous to interferons allows a story of interferon evolution to be proposed. This model suggests that the gene duplications and single exon retrotransposons of mammalian type-III interferons are positively selected for within a genome. These characteristics are also shared with the fish interferons and could be responsible for the generation of the IL10 family and also the single exon type-I interferons.

Gene finding for the helical cytokines

MOTIVATION

Gene finding remains an open problem well after the sequencing of the human genome. The low gene sensitivity of current methods is a problem for divergent protein families, because fairly accurate exon assemblies are required before sensitive fold recognition algorithms can be applied. This paper presents a new genomic threading algorithm which integrates the gene finding and fold recognition steps into a single process. The method is applicable to evolutionarily divergent protein families that have retained some trace of their common ancestry, number and phase of introns, sizes of exons and placement of structural elements on specific exons. Such conserved structural signals may be visible despite dramatic evolution of protein sequence.

RESULTS

The method is evaluated on the family of helical cytokines by cross-validation sensitivity analysis. The method has also been applied to all intergenic regions of the human genome, and an expression and cloning approach has been coupled with the predictions of the method. Two genes discovered by this method are discussed.

SUPPLEMENTARY INFORMATION

All data used and the results obtained in the cross-validation analysis are available at http://www.soi.city.ac.uk/~conklin/papers/GT/