The crystal structure of a TIR domain from <i>Arabidopsis thaliana</i> reveals a conserved helical region unique to plants

Chan, Syin; Mukasa, Takashi; Santelli, Eugenio; Low, Lieh Yoon; Pascual, Jaime

doi:10.1002/pro.275

Cited by 57 publications

(55 citation statements)

References 24 publications

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“…Plant and animal TIR-domain crystal structures support the existence of a variety of dimer interfaces (12). There are two distinct interfaces from crystal structures of plant TIRs, defined by the homodimeric flax NLR L6 TIR domain and the homo-and heterodimeric Arabidopsis RPS4/RRS1 TIR domains (13)(14)(15)(16). Overexpression of either the L6 or RPS4 TIR domain is sufficient to trigger cell death (13,17).…”

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confidence: 99%

TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death inArabidopsis

Nishimura

Anderson

Cherkis

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

141

131

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Detection of pathogens by plants is mediated by intracellular nucleotide-binding site leucine-rich repeat (NLR) receptor proteins. NLR proteins are defined by their stereotypical multidomain structure: an N-terminal Toll-interleukin receptor (TIR) or coiled-coil (CC) domain, a central nucleotide-binding (NB) domain, and a C-terminal leucine-rich repeat (LRR). The plant innate immune system contains a limited NLR repertoire that functions to recognize all potential pathogens. We isolated Response to the bacterial type III effector protein HopBA1 (RBA1), a gene that encodes a TIR-only protein lacking all other canonical NLR domains. RBA1 is sufficient to trigger cell death in response to HopBA1. We generated a crystal structure for HopBA1 and found that it has similarity to a class of proteins that includes esterases, the hemebinding protein ChaN, and an uncharacterized domain of Pasteurella multocida toxin. Self-association, coimmunoprecipitation with HopBA1, and function of RBA1 require two previously identified TIR-TIR dimerization interfaces. Although previously described as distinct in other TIR proteins, in RBA1 neither of these interfaces is sufficient when the other is disrupted. These data suggest that oligomerization of RBA1 is required for function. Our identification of RBA1 demonstrates that "truncated" NLRs can function as pathogen sensors, expanding our understanding of both receptor architecture and the mechanism of activation in the plant immune system. plant immunity | NLR | Toll-interleukin-1 receptor homology domain | oligomerization | type III secretion

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mentioning

confidence: 99%

TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death inArabidopsis

Nishimura

Anderson

Cherkis

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

141

131

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“…Adaptors include myeloid differentiation factor 88 (MyD88) (12) and MyD88 adaptorlike (Mal) (13,14). In addition, AtTIR (15,16) derived from Arabidopsis thaliana and PdTIR (17) from bacteria have been solved. Each of these TIR domain structures has a ferredoxin fold with five β-strands (βA-βE), five α-helices (αA-αE), and loops connecting β-strands and α-helices (9).…”

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confidence: 99%

Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling

Enokizono

Kumeta

Funami

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Homotypic and heterotypic interactions between Toll/interleukin-1 receptor (TIR) domains in Toll-like receptors (TLRs) and downstream adaptors are essential to evoke innate immune responses. However, such oligomerization properties present intrinsic difficulties in structural studies of TIR domains. Here, using BB-loop mutations that disrupt homotypic interactions, we determined the structures of the monomeric TIR domain-containing adaptor molecule (TICAM)-1 and TICAM-2 TIR domains. Docking of the monomeric structures, together with yeast two hybrid-based mutagenesis assays, reveals that the homotypic interaction between TICAM-2 TIR is indispensable to present a scaffold for recruiting the monomeric moiety of the TICAM-1 TIR dimer. This result proposes a unique idea that oligomerization of upstream TIR domains is crucial for binding of downstream TIR domains. Furthermore, the bivalent nature of each TIR domain dimer can generate a large signaling complex under the activated TLRs, which would recruit downstream signaling molecules efficiently. This model is consistent with previous reports that BB-loop mutants completely abrogate downstream signaling. A large number of TIR domain structures, including receptors and adaptors, have been determined by X-ray crystallography and NMR. The receptors include TLR1 (9), TLR2 (10), and IL-1R accessory protein-like (IL-1RAPL) (11). Adaptors include myeloid differentiation factor 88 (MyD88) (12) and MyD88 adaptorlike (Mal) (13,14). In addition, AtTIR (15, 16) derived from Arabidopsis thaliana and PdTIR (17) from bacteria have been solved. Each of these TIR domain structures has a ferredoxin fold with five β-strands (βA-βE), five α-helices (αA-αE), and loops connecting β-strands and α-helices (9). Although homotypic interactions of the TIR domains have been proposed based on the crystal structures, most proposed models have small interacting surfaces, possibly due to crystal contacts. Recently, however, a crystal structure of the TLR10 TIR domain was reported that forms a homotypic dimer mediated by the loop connecting βB and αB (designated "BB-loop") (18). Interestingly, BB-loop mutations in TLR4 were reported to be dominant-negative and abrogated downstream signaling (19). TICAM-1 and TICAM-2 harboring BB-loop mutations are also dominant-negative and unable to form homotypic interactions (1, 2), reinforcing the importance of BB-loop-mediated homotypic dimer formation in signal propagation.Despite extensive structural studies, it is not known why homotypic interactions are essential for downstream signaling (20-27). To address this issue, it is necessary to discriminate residues required for homotypic and those required for heterotypic interactions. Here, we first determine the structures of the monomeric BB-loop mutants of the TICAM-1 and TICAM-2 TIR domains using NMR. Then, based on the solution structures of the BB-loop mutants, coupled mutagenesis/yeast two-hybrid experiments, and restrained docking calculations, we show that the homotypic interaction of TICAM-2 TIR is es...

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“…The domain boundaries of the expression constructs were selected based on sequence alignments of RPS4, RRS1 and SNC1 with TIR domains of known structure, including those from flax L6 protein (Bernoux et al, 2011) and Arabidopsis NP_177436/At1g72930 (AtTIR; Chan et al, 2010). The sequence identities of RPS4TIR, RRS1TIR and SNC1TIR to L6TIR are 28, 16 and 36%, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…3). AtTIR (Chan et al, 2010) represents the best sequence match for the RRS1 TIR domain to any protein with known structure, with a sequence identity of 21%. In light of the low sequence identity and the deletion within the D helical region, we were unsure whether molecular replacement (MR) would be suitable for structure determination.…”

Section: Resultsmentioning

confidence: 99%

“…Multiple sequence alignment of TIR domains. Amino-acid sequences from the TIR domains of Arabidopsis RPS4 (residues 15-191), Arabidopsis SNC1 (10-180), Arabidopsis RPP1-WsA (50-229), tobacco N (10-191) and Arabidopsis RRS1 (6-153) were aligned with the sequences of TIR domains with known crystal structures, Arabidopsis AtTIR (PDB entry 3jrn; Chan et al, 2010) and flax L6 (PDB entry 3ozi; Bernoux et al, 2011), using MUSCLE (Edgar, 2004). The positions of the secondarystructure elements in L6 are shown at the top.…”

Section: Resultsmentioning

confidence: 99%

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Crystallization and preliminary X-ray diffraction analyses of the TIR domains of three TIR–NB–LRR proteins that are involved in disease resistance inArabidopsis thaliana

et al. 2013

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The Toll/interleukin-1 receptor (TIR) domain is a protein-protein interaction domain that is found in both animal and plant immune receptors. The N-terminal TIR domain from the nucleotide-binding (NB)-leucine-rich repeat (LRR) class of plant disease-resistance (R) proteins has been shown to play an important role in defence signalling. Recently, the crystal structure of the TIR domain from flax R protein L6 was determined and this structure, combined with functional studies, demonstrated that TIR-domain homodimerization is a requirement for function of the R protein L6. To advance the molecular understanding of the function of TIR domains in R-protein signalling, the protein expression, purification, crystallization and X-ray diffraction analyses of the TIR domains of the Arabidopsis thaliana R proteins RPS4 (resistance to Pseudomonas syringae 4) and RRS1 (resistance to Ralstonia solanacearum 1) and the resistance-like protein SNC1 (suppressor of npr1-1, constitutive 1) are reported here. RPS4 and RRS1 function cooperatively as a dual resistanceprotein system that prevents infection by three distinct pathogens. SNC1 is implicated in resistance pathways in Arabidopsis and is believed to be involved in transcriptional regulation through its interaction with the transcriptional corepressor TPR1 (Topless-related 1). The TIR domains of all three proteins have successfully been expressed and purified as soluble proteins in Escherichia coli. Plate-like crystals of the RPS4 TIR domain were obtained using PEG 3350 as a precipitant; they diffracted X-rays to 2.05 Å resolution, had the symmetry of space group P1 and analysis of the Matthews coefficient suggested that there were four molecules per asymmetric unit. Tetragonal crystals of the RRS1 TIR domain were obtained using ammonium sulfate as a precipitant; they diffracted X-rays to 1.75 Å resolution, had the symmetry of space group P4 1 2 1 2 or P4 3 2 1 2 and were most likely to contain one molecule per asymmetric unit. Crystals of the SNC1 TIR domain were obtained using PEG 3350 as a precipitant; they diffracted X-rays to 2.20 Å resolution and had the symmetry of space group P4 1 2 1 2 or P4 3 2 1 2, with two molecules predicted per asymmetric unit. These results provide a good foundation to advance the molecular and structural understanding of the function of the TIR domain in plant innate immunity.

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The crystal structure of a TIR domain from Arabidopsis thaliana reveals a conserved helical region unique to plants

Cited by 57 publications

References 24 publications

TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death inArabidopsis

TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death inArabidopsis

Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling

Crystallization and preliminary X-ray diffraction analyses of the TIR domains of three TIR–NB–LRR proteins that are involved in disease resistance inArabidopsis thaliana

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