title: Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1.
abstract: The tomato mosaic virus (ToMV) resistance gene Tm-1 encodes a protein that shows no sequence homology to functionally characterized proteins. Tm-1 binds ToMV replication proteins and thereby inhibits replication complex formation. ToMV mutants that overcome this resistance have amino acid substitutions in the helicase domain of the replication proteins (ToMV-Hel). A small region of Tm-1 in the genome of the wild tomato Solanum habrochaites has been under positive selection during its antagonistic coevolution with ToMV. Here we report crystal structures for the N-terminal inhibitory domains of Tm-1 and a natural Tm-1 variant with an I91-to-T substitution that has a greater ability to inhibit ToMV RNA replication and their complexes with ToMV-Hel. Each complex contains a Tm-1 dimer and two ToMV-Hel monomers with the interfaces between Tm-1 and ToMV-Hel bridged by ATP. Residues in ToMV-Hel and Tm-1 involved in antagonistic coevolution are found at the interface. The structural differences between ToMV-Hel in its free form and in complex with Tm-1 suggest that Tm-1 affects nucleoside triphosphatase activity of ToMV-Hel, and this effect was confirmed experimentally. Molecular dynamics simulations of complexes formed by Tm-1 with ToMV-Hel variants showed how the amino acid changes in ToMV-Hel impair the interaction with Tm-1 to overcome the resistance. With these findings, together with the biochemical properties of the interactions between ToMV-Hel and Tm-1 variants and effects of the mutations in the polymorphic residues of Tm-1, an atomic view of a step-by-step coevolutionary arms race between a plant resistance protein and a viral protein emerges.
authors.affiliation: Plant-Microbe Interactions Research Unit and.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Ishibashi
authors.affiliation: Department of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 020-0023, Japan; and.
authors.forename: Yuichiro
authors.initials: Y
authors.lastname: Kezuka
authors.affiliation: Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
authors.forename: Chihoko
authors.initials: C
authors.lastname: Kobayashi
authors.affiliation: Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
authors.forename: Masahiko
authors.initials: M
authors.lastname: Kato
authors.affiliation: Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Inoue
authors.affiliation: Department of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 020-0023, Japan; and.
authors.forename: Takamasa
authors.identifier: http://orcid.org/0000-0002-5353-0289
authors.initials: T
authors.lastname: Nonaka
authors.affiliation: Plant-Microbe Interactions Research Unit and.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Ishikawa
authors.affiliation: Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan matsumura@chem.eng.osaka-u.ac.jp ekatoh@nias.affrc.go.jp.
authors.forename: Hiroyoshi
authors.initials: H
authors.lastname: Matsumura
authors.affiliation: Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan; matsumura@chem.eng.osaka-u.ac.jp ekatoh@nias.affrc.go.jp.
authors.forename: Etsuko
authors.initials: E
authors.lastname: Katoh
mesh_terms: D000483:Alleles; D005814:Genes, Viral; D057131:Immune Evasion / Q000235:genetics*; D018551:Solanum lycopersicum / Q000821:virology*; D056004:Molecular Dynamics Simulation; D009029:Mosaic Viruses / Q000235:genetics / Q000276:immunology* / Q000502:physiology; D014779:Virus Replication
keywords: protein complex; virus resistance
references.citation: Nat Immunol. 2012 Feb 16;13(3):214-22
references.pmid: 22344284
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W545-9
references.pmid: 20457744
references.citation: Bioinformatics. 2003 Jan 22;19(2):311-2
references.pmid: 12538265
references.citation: Virology. 2010 Jul 5;402(2):292-302
references.pmid: 20413140
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9
references.pmid: 21109532
references.citation: Nat Struct Mol Biol. 2009 Jan;16(1):63-70
references.pmid: 19043413
references.citation: Methods Enzymol. 2012;511:131-47
references.pmid: 22713318
references.citation: Nature. 2009 Jan 22;457(7228):485-9
references.pmid: 19043403
references.citation: EMBO J. 1988 Jun;7(6):1575-81
references.pmid: 16453849
references.citation: J Virol. 2013 Jul;87(14):7933-9
references.pmid: 23658455
references.citation: Protein Expr Purif. 2012 Jan;81(1):89-95
references.pmid: 21964444
references.citation: PLoS Pathog. 2012;8(10):e1002975
references.pmid: 23093939
references.citation: PLoS Comput Biol. 2009 Mar;5(3):e1000316
references.pmid: 19282967
references.citation: J Mol Biol. 1998 Jul 3;280(1):1-9
references.pmid: 9653027
references.citation: Biochemistry. 2002 May 28;41(21):6573-82
references.pmid: 12022860
references.citation: Plant Cell. 2013 May;25(5):1489-505
references.pmid: 23709626
references.citation: Nat Rev Immunol. 2012 Oct;12(10):687-95
references.pmid: 22976433
references.citation: Mol Microbiol. 1999 Dec;34(5):867-77
references.pmid: 10594814
references.citation: Angew Chem Int Ed Engl. 2012 Feb 27;51(9):2012-8
references.pmid: 22308055
references.citation: Proteins. 1998 Feb 1;30(2):144-54
references.pmid: 9489922
references.citation: Annu Rev Genet. 2012;46:677-700
references.pmid: 23145935
references.citation: Protein Expr Purif. 2013 May;89(1):1-6
references.pmid: 23415925
references.citation: J Virol. 2012 Jul;86(14):7565-76
references.pmid: 22573863
references.citation: Curr Top Microbiol Immunol. 2013;371:123-51
references.pmid: 23686234
references.citation: Arch Virol. 2007;152(5):903-14
references.pmid: 17238011
references.citation: Science. 1995 Jan 20;267(5196):383-6
references.pmid: 7529940
references.citation: Curr Opin Virol. 2012 Dec;2(6):699-704
references.pmid: 23063494
references.citation: Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13833-8
references.pmid: 17699618