Structural Basis of NPR1 in Activating Plant Immunity

Overview

Journal Nature

Specialty Science

Date 2022 May 11

PMID 35545668

Authors

Shivesh Kumar

Raul Zavaliev

Qinglin Wu

Ye Zhou

Jie Cheng

Lucas Dillard

Jordan Powers

John Withers

Jinshi Zhao

Ziqiang Guan

Mario J Borgnia

Alberto Bartesaghi

Xinnian Dong

Pei Zhou

Affiliations

Soon will be listed here.

Abstract

NPR1 is a master regulator of the defence transcriptome induced by the plant immune signal salicylic acid. Despite the important role of NPR1 in plant immunity, understanding of its regulatory mechanisms has been hindered by a lack of structural information. Here we report cryo-electron microscopy and crystal structures of Arabidopsis NPR1 and its complex with the transcription factor TGA3. Cryo-electron microscopy analysis reveals that NPR1 is a bird-shaped homodimer comprising a central Broad-complex, Tramtrack and Bric-à-brac (BTB) domain, a BTB and carboxyterminal Kelch helix bundle, four ankyrin repeats and a disordered salicylic-acid-binding domain. Crystal structure analysis reveals a unique zinc-finger motif in BTB for interacting with ankyrin repeats and mediating NPR1 oligomerization. We found that, after stimulation, salicylic-acid-induced folding and docking of the salicylic-acid-binding domain onto ankyrin repeats is required for the transcriptional cofactor activity of NPR1, providing a structural explanation for a direct role of salicylic acid in regulating NPR1-dependent gene expression. Moreover, our structure of the TGA3-NPR1-TGA3 complex, DNA-binding assay and genetic data show that dimeric NPR1 activates transcription by bridging two fatty-acid-bound TGA3 dimers to form an enhanceosome. The stepwise assembly of the NPR1-TGA complex suggests possible hetero-oligomeric complex formation with other transcription factors, revealing how NPR1 reprograms the defence transcriptome.

Citing Articles

A novel mode of WRKY1 regulating PR1-mediated immune balance to defend against powdery mildew in apple.

Lan L, Cao L, Zhang L, Fu W, Luo C, Wu C Mol Hortic. 2025; 5(1):17.

PMID: 40038814 PMC: 11881497. DOI: 10.1186/s43897-024-00141-z.

ATG6 interacting with NPR1 increases resistance to DC3000/ by increasing its nuclear accumulation and stability.

Zhang B, Huang S, Guo S, Meng Y, Tian Y, Zhou Y Elife. 2025; 13.

PMID: 40036061 PMC: 11879114. DOI: 10.7554/eLife.97206.

Aspirin-responsive gene switch regulating therapeutic protein expression.

Huang J, Teixeira A, Gao T, Xue S, Xie M, Fussenegger M Nat Commun. 2025; 16(1):2028.

PMID: 40016240 PMC: 11868571. DOI: 10.1038/s41467-025-57275-x.

Bibliometric and meta-analysis on the publication status, research trends and impact inducing factors of JA-SA interactions in plants.

Jiao L, Tan R, Chen X, Wang H, Huang D, Mao Y Front Plant Sci. 2024; 15:1487434.

PMID: 39670269 PMC: 11635838. DOI: 10.3389/fpls.2024.1487434.

The transcription factor TGA2 orchestrates salicylic acid signal to regulate cold-induced proline accumulation in Citrus.

Xiao W, Zhang Y, Wang Y, Zeng Y, Shang X, Meng L Plant Cell. 2024; 37(1).

PMID: 39656997 PMC: 11663595. DOI: 10.1093/plcell/koae290.

References

Delaney T, Friedrich L, Ryals J . Arabidopsis signal transduction mutant defective in chemically and biologically induced disease resistance. Proc Natl Acad Sci U S A. 1995; 92(14):6602-6. PMC: 41566. DOI: 10.1073/pnas.92.14.6602. View

Shah J, Tsui F, Klessig D . Characterization of a salicylic acid-insensitive mutant (sai1) of Arabidopsis thaliana, identified in a selective screen utilizing the SA-inducible expression of the tms2 gene. Mol Plant Microbe Interact. 1997; 10(1):69-78. DOI: 10.1094/MPMI.1997.10.1.69. View

Cao H, Bowling S, Gordon A, Dong X . Characterization of an Arabidopsis Mutant That Is Nonresponsive to Inducers of Systemic Acquired Resistance. Plant Cell. 1994; 6(11):1583-1592. PMC: 160545. DOI: 10.1105/tpc.6.11.1583. View

Glazebrook J, Rogers E, Ausubel F . Isolation of Arabidopsis mutants with enhanced disease susceptibility by direct screening. Genetics. 1996; 143(2):973-82. PMC: 1207353. DOI: 10.1093/genetics/143.2.973. View

Ryals J, Weymann K, Lawton K, Friedrich L, Ellis D, Steiner H . The Arabidopsis NIM1 protein shows homology to the mammalian transcription factor inhibitor I kappa B. Plant Cell. 1997; 9(3):425-39. PMC: 156928. DOI: 10.1105/tpc.9.3.425. View

Cao H, Glazebrook J, Clarke J, Volko S, Dong X . The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats. Cell. 1997; 88(1):57-63. DOI: 10.1016/s0092-8674(00)81858-9. View

Backer R, Naidoo S, van den Berg N . The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) and Related Family: Mechanistic Insights in Plant Disease Resistance. Front Plant Sci. 2019; 10:102. PMC: 6381062. DOI: 10.3389/fpls.2019.00102. View

Silva K, Mahna N, Mou Z, Folta K . as a transgenic crop protection strategy in horticultural species. Hortic Res. 2018; 5:15. PMC: 5862871. DOI: 10.1038/s41438-018-0026-1. View

Stogios P, Downs G, Jauhal J, Nandra S, Prive G . Sequence and structural analysis of BTB domain proteins. Genome Biol. 2005; 6(10):R82. PMC: 1257465. DOI: 10.1186/gb-2005-6-10-r82. View

10.

Stogios P, Prive G . The BACK domain in BTB-kelch proteins. Trends Biochem Sci. 2004; 29(12):634-7. DOI: 10.1016/j.tibs.2004.10.003. View

11.

Canning P, Cooper C, Krojer T, Murray J, Pike A, Chaikuad A . Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases. J Biol Chem. 2013; 288(11):7803-7814. PMC: 3597819. DOI: 10.1074/jbc.M112.437996. View

12.

Zhuang M, Calabrese M, Liu J, Waddell M, Nourse A, Hammel M . Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases. Mol Cell. 2009; 36(1):39-50. PMC: 2847577. DOI: 10.1016/j.molcel.2009.09.022. View

13.

Errington W, Khan M, Bueler S, Rubinstein J, Chakrabartty A, Prive G . Adaptor protein self-assembly drives the control of a cullin-RING ubiquitin ligase. Structure. 2012; 20(7):1141-53. DOI: 10.1016/j.str.2012.04.009. View

14.

Gorina S, Pavletich N . Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2. Science. 1996; 274(5289):1001-5. DOI: 10.1126/science.274.5289.1001. View

15.

Li J, Mahajan A, Tsai M . Ankyrin repeat: a unique motif mediating protein-protein interactions. Biochemistry. 2006; 45(51):15168-78. DOI: 10.1021/bi062188q. View

16.

Sedgwick S, Smerdon S . The ankyrin repeat: a diversity of interactions on a common structural framework. Trends Biochem Sci. 1999; 24(8):311-6. DOI: 10.1016/s0968-0004(99)01426-7. View

17.

Wang W, Withers J, Li H, Zwack P, Rusnac D, Shi H . Structural basis of salicylic acid perception by Arabidopsis NPR proteins. Nature. 2020; 586(7828):311-316. PMC: 7554156. DOI: 10.1038/s41586-020-2596-y. View

18.

Mou Z, Fan W, Dong X . Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes. Cell. 2003; 113(7):935-44. DOI: 10.1016/s0092-8674(03)00429-x. View

19.

Canet J, Dobon A, Roig A, Tornero P . Structure-function analysis of npr1 alleles in Arabidopsis reveals a role for its paralogs in the perception of salicylic acid. Plant Cell Environ. 2010; 33(11):1911-22. DOI: 10.1111/j.1365-3040.2010.02194.x. View

20.

Bombarda E, Cherradi H, Morellet N, Roques B, Mely Y . Zn(2+) binding properties of single-point mutants of the C-terminal zinc finger of the HIV-1 nucleocapsid protein: evidence of a critical role of cysteine 49 in Zn(2+) dissociation. Biochemistry. 2002; 41(13):4312-20. DOI: 10.1021/bi015956g. View