101
|
A Comparative Analysis of the Mechanism of Toll-Like Receptor-Disruption by TIR-Containing Protein C from Uropathogenic Escherichia coli. Pathogens 2016; 5:pathogens5010025. [PMID: 26938564 PMCID: PMC4810146 DOI: 10.3390/pathogens5010025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/17/2022] Open
Abstract
The TIR-containing protein C (TcpC) of uropathogenic Escherichia coli strains is a powerful virulence factor by impairing the signaling cascade of Toll-like receptors (TLRs). Several other bacterial pathogens like Salmonella, Yersinia, Staphylococcus aureus but also non-pathogens express similar proteins. We discuss here the pathogenic potential of TcpC and its interaction with TLRs and TLR-adapter proteins on the molecular level and compare its activity with the activity of other bacterial TIR-containing proteins. Finally, we analyze and compare the structure of bacterial TIR-domains with the TIR-domains of TLRs and TLR-adapters.
Collapse
|
102
|
Christie N, Tobias PA, Naidoo S, Külheim C. The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots. FRONTIERS IN PLANT SCIENCE 2016; 6:1238. [PMID: 26793216 PMCID: PMC4709456 DOI: 10.3389/fpls.2015.01238] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/20/2015] [Indexed: 05/03/2023]
Abstract
Eucalyptus grandis is a commercially important hardwood species and is known to be susceptible to a number of pests and pathogens. Determining mechanisms of defense is therefore a research priority. The published genome for E. grandis has aided the identification of one important class of resistance (R) genes that incorporate nucleotide binding sites and leucine-rich repeat domains (NBS-LRR). Using an iterative search process we identified NBS-LRR gene models within the E. grandis genome. We characterized the gene models and identified their genomic arrangement. The gene expression patterns were examined in E. grandis clones, challenged with a fungal pathogen (Chrysoporthe austroafricana) and insect pest (Leptocybe invasa). One thousand two hundred and fifteen putative NBS-LRR coding sequences were located which aligned into two large classes, Toll or interleukin-1 receptor (TIR) and coiled-coil (CC) based on NB-ARC domains. NBS-LRR gene-rich regions were identified with 76% organized in clusters of three or more genes. A further 272 putative incomplete resistance genes were also identified. We determined that E. grandis has a higher ratio of TIR to CC classed genes compared to other woody plant species as well as a smaller percentage of single NBS-LRR genes. Transcriptome profiles indicated expression hotspots, within physical clusters, including expression of many incomplete genes. The clustering of putative NBS-LRR genes correlates with differential expression responses in resistant and susceptible plants indicating functional relevance for the physical arrangement of this gene family. This analysis of the repertoire and expression of E. grandis putative NBS-LRR genes provides an important resource for the identification of novel and functional R-genes; a key objective for strategies to enhance resilience.
Collapse
Affiliation(s)
- Nanette Christie
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Peri A. Tobias
- Department of Plant and Food Sciences, Faculty of Agriculture and Environment, University of SydneyNSW, Australia
| | - Sanushka Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Carsten Külheim
- Research School of Biology, College of Medicine, Biology and Environment, Australian National UniversityCanberra, ACT, Australia
| |
Collapse
|
103
|
Williams SJ, Yin L, Foley G, Casey LW, Outram MA, Ericsson DJ, Lu J, Boden M, Dry IB, Kobe B. Structure and Function of the TIR Domain from the Grape NLR Protein RPV1. FRONTIERS IN PLANT SCIENCE 2016; 7:1850. [PMID: 28008335 PMCID: PMC5143477 DOI: 10.3389/fpls.2016.01850] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/23/2016] [Indexed: 05/22/2023]
Abstract
The N-terminal Toll/interleukin-1 receptor/resistance protein (TIR) domain has been shown to be both necessary and sufficient for defense signaling in the model plants flax and Arabidopsis. In examples from these organisms, TIR domain self-association is required for signaling function, albeit through distinct interfaces. Here, we investigate these properties in the TIR domain containing resistance protein RPV1 from the wild grapevine Muscadinia rotundifolia. The RPV1 TIR domain, without additional flanking sequence present, is autoactive when transiently expressed in tobacco, demonstrating that the TIR domain alone is capable of cell-death signaling. We determined the crystal structure of the RPV1 TIR domain at 2.3 Å resolution. In the crystals, the RPV1 TIR domain forms a dimer, mediated predominantly through residues in the αA and αE helices ("AE" interface). This interface is shared with the interface discovered in the dimeric complex of the TIR domains from the Arabidopsis RPS4/RRS1 resistance protein pair. We show that surface-exposed residues in the AE interface that mediate the dimer interaction in the crystals are highly conserved among plant TIR domain-containing proteins. While we were unable to demonstrate self-association of the RPV1 TIR domain in solution or using yeast 2-hybrid, mutations of surface-exposed residues in the AE interface prevent the cell-death autoactive phenotype. In addition, mutation of residues known to be important in the cell-death signaling function of the flax L6 TIR domain were also shown to be required for RPV1 TIR domain mediated cell-death. Our data demonstrate that multiple TIR domain surfaces control the cell-death function of the RPV1 TIR domain and we suggest that the conserved AE interface may have a general function in TIR-NLR signaling.
Collapse
Affiliation(s)
- Simon J. Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, BrisbaneQLD, Australia
- Research School of Biology, The Australian National University, CanberraACT, Australia
- *Correspondence: Simon J. Williams, Bostjan Kobe, Ian B. Dry,
| | - Ling Yin
- Guangxi Crop Genetic Improvement and Biotechnology Key Lab, Guangxi Academy of Agricultural SciencesNanning, China
- Commonwealth Scientific and Industrial Research Organisation, UrrbraeSA, Australia
- College of Food Science and Nutritional Engineering, China Agricultural UniversityBeijing, China
| | - Gabriel Foley
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, BrisbaneQLD, Australia
| | - Lachlan W. Casey
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, BrisbaneQLD, Australia
| | - Megan A. Outram
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, BrisbaneQLD, Australia
| | | | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural UniversityBeijing, China
- Department of Plant Science, Shanghai Jiao Tong UniversityShanghai, China
| | - Mikael Boden
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, BrisbaneQLD, Australia
| | - Ian B. Dry
- Guangxi Crop Genetic Improvement and Biotechnology Key Lab, Guangxi Academy of Agricultural SciencesNanning, China
- Commonwealth Scientific and Industrial Research Organisation, UrrbraeSA, Australia
- *Correspondence: Simon J. Williams, Bostjan Kobe, Ian B. Dry,
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, BrisbaneQLD, Australia
- *Correspondence: Simon J. Williams, Bostjan Kobe, Ian B. Dry,
| |
Collapse
|
104
|
Carlsson E, Ding JL, Byrne B. SARM modulates MyD88-mediated TLR activation through BB-loop dependent TIR-TIR interactions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:244-53. [PMID: 26592460 DOI: 10.1016/j.bbamcr.2015.11.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/16/2015] [Accepted: 11/20/2015] [Indexed: 12/21/2022]
Abstract
Toll-like receptors (TLRs) recognise invading pathogens and initiate an innate immune response by recruiting intracellular adaptor proteins via heterotypic Toll/interleukin-1 receptor (TIR) domain interactions. Of the five TIR domain-containing adaptor proteins identified, Sterile α- and armadillo-motif-containing protein (SARM) is functionally unique; suppressing immune signalling instead of promoting it. Here we demonstrate that the recombinantly expressed and purified SARM TIR domain interacts with both the major human TLR adaptors, MyD88 and TRIF. A single glycine residue located in the BB-loop of the SARM TIR domain, G601, was identified as essential for interaction. A short peptide derived from this motif was also found to interact with MyD88 in vitro. SARM expression in HEK293 cells was found to significantly suppress lipopolysaccharide (LPS)-mediated upregulation of inflammatory cytokines, IL-8 and TNF-α, an effect lost in the G601A mutant. The same result was observed with cytokine activation initiated by MyD88 expression and stimulation of TLR2 with lipoteichoic acid (LTA), suggesting that SARM is capable of suppressing both TRIF- and MyD88- dependent TLR signalling. Our findings indicate that SARM acts on a broader set of target proteins than previously thought, and that the BB-loop motif is functionally important, giving further insight into the endogenous mechanisms used to suppress inflammation in immune cells.
Collapse
Affiliation(s)
- Emil Carlsson
- Department of Life Sciences, Imperial College London, SW7 2AZ, UK; Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore.
| | - Jeak Ling Ding
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore.
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, SW7 2AZ, UK.
| |
Collapse
|
105
|
Radons J, Falk W, Dove S. Identification of critical regions within the TIR domain of IL-1 receptor type I. Int J Biochem Cell Biol 2015; 68:15-20. [PMID: 26279140 DOI: 10.1016/j.biocel.2015.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/05/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
Interleukin-1 receptor type I (IL-1RI) belongs to a superfamily of proteins characterized by an intracellular Toll/IL-1 receptor (TIR) domain. This domain harbors three conserved regions called boxes 1-3 that play crucial roles in mediating IL-1 responses. Boxes 1 and 2 are considered to be involved in binding of adapter molecules. Amino acids possibly crucial for IL-1RI signaling were predicted via homology models of the IL-1RI TIR domain based on the crystal structure of IL-1RAPL. The role of ten of these residues was investigated by site-directed mutagenesis and a functional luciferase assay reflecting NF-κB activity in transiently transfected Jurkat cells. In particular, the mutants E437K/D438K, E472A/E473A and S465A/S470A/S471A/E472A/E473A showed decreased and the mutant E437A/D438A increased IL-1 responsiveness compared to the mouse IL-1RI wild type. In conclusion, the αC' helix (Q469-E473 in mouse IL-1RI) is probably involved in heterotypic interactions of IL-1RI with IL-1RAcP or MyD88.
Collapse
Affiliation(s)
- Jürgen Radons
- Department of Internal Medicine I, University Clinic Regensburg, D-93042 Regensburg, Germany.
| | - Werner Falk
- Department of Internal Medicine I, University Clinic Regensburg, D-93042 Regensburg, Germany
| | - Stefan Dove
- Institute of Pharmacy, University of Regensburg, D-93040 Regensburg, Germany
| |
Collapse
|
106
|
Kobe B, Ve T, Williams SJ. Fusion-protein-assisted protein crystallization. Acta Crystallogr F Struct Biol Commun 2015; 71:861-9. [PMID: 26144231 PMCID: PMC4498707 DOI: 10.1107/s2053230x15011061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/07/2015] [Indexed: 01/29/2023] Open
Abstract
Fusion proteins can be used directly in protein crystallization to assist crystallization in at least two different ways. In one approach, the `heterologous fusion-protein approach', the fusion partner can provide additional surface area to promote crystal contact formation. In another approach, the `fusion of interacting proteins approach', protein assemblies can be stabilized by covalently linking the interacting partners. The linker connecting the proteins plays different roles in the two applications: in the first approach a rigid linker is required to reduce conformational heterogeneity; in the second, conversely, a flexible linker is required that allows the native interaction between the fused proteins. The two approaches can also be combined. The recent applications of fusion-protein technology in protein crystallization from the work of our own and other laboratories are briefly reviewed.
Collapse
Affiliation(s)
- Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia
| |
Collapse
|
107
|
Williams SJ, Ve T, Kobe B. A linker strategy for the production and crystallization of Toll/interleukin-1 receptor/resistance protein domain complexes. Protein Eng Des Sel 2015; 28:137-45. [PMID: 25777769 DOI: 10.1093/protein/gzv013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/11/2015] [Indexed: 02/02/2023] Open
Abstract
Structural characterization of protein-protein complexes is required to fully understand biological processes. However, such studies can be difficult, particularly when the interactions are transient. In some cases, the covalent linking of weakly interacting binding partners has been shown to facilitate structural studies. Here, we used this approach to investigate, by X-ray crystallography, the interactions between TIR (Toll/interleukin-1 receptor/resistance protein) domains from proteins involved in plant and animal innate immunity. Combinations of TIR domains known to interact were covalently attached using short glycine- and serine-rich linkers. This approach enabled the production of a number of TIR-TIR domain complexes in soluble form, facilitating crystallization studies. Crystallization of two of the tested combinations was achieved. Furthermore, production in soluble form was achieved for another two combinations, where this was not possible for individual proteins. Our results demonstrate that the linker strategy can aid in the structural studies of TIR domains. Similarly, this approach has potential for improving protein production and facilitating structural studies of other protein-protein interaction domains.
Collapse
Affiliation(s)
- Simon J Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| |
Collapse
|