Publications

Publications @PubMed

Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products. Bayless AM, Chen S, Ogden SC, Xu X, Sidda JD, Manik MK, Li S, Kobe B, Ve T, Song L, Grant M, Wan L, Nishimura MT. Science Advances. 2023 Mar 15;9(11):eade8487. doi: 10.1126/sciadv.ade8487

Broader functions of TIR domains in Arabidopsis immunity. Jacob P, Hige J, Song L, Bayless A, Russ D, Bonardi V, El Kasmi F, Wünsch L, Yang Y, Fitzpatrick CR, McKinney BJ, Nishimura MT, Grant MR, Dangl JL. Proc Natl Acad Sci USA. 2023 Mar 14;120(11):e2220921120. doi: 10.1073/pnas.2220921120.

NADases as weapons for both plant pathogens and their hosts. Ogden SC, Nishimura MT. Proc Natl Acad Sci USA. 2023 Mar 7;120(10):e2300970120. doi: 10.1073/pnas.2300970120. 

The nucleotide revolution: immunity at the intersection of TIR-domains, nucleotides, and Ca2. Eastman S, Bayless A, Guo M. Mol Plant Microbe Interact. 2022 Jul 26. doi: 10.1094/MPMI-06-22-0132-CR.

Shared TIR enzymatic functions regulate cell death and immunity across the tree of life. Essuman K, Milbrandt J, Dangl JL, Nishimura MT. Science. 2022 Jul 29;377(6605)

Arabidopsis ADR1 helper NLR immune receptors localize and function at the plasma membrane in a phospholipid dependent manner. Saile SC, Ackermann FM, Sunil S, Keicher J, Bayless A, Bonardi V, Wan L, Doumane M, Stöbbe E, Jaillais Y, Caillaud MC, Dangl JL, Nishimura MT, Oecking C, El Kasmi F. New Phytol. 2021 Dec;232(6):2440-2456.

Bayless AM, Nishimura MT. Reinventing the wheel with a synthetic plant inflammasome. PNAS. 2020, Aug 25; 117(34):20357-20359.

Bayless AM, Nishimura MT. Enzymatic functions for Toll/Interleukin-1 receptor domain proteins in the plant immune system. Frontiers in Genetics. 2020, Jun 02;

Wan L, Essuman K, Anderson RG, Sasaki Y, Monteiro F, Chung EH, Osborne Nishimura E, DiAntonio A, Milbrandt J, Dangl JL, Nishimura MT. TIR domains of plant immune receptors are NAD+-cleaving enzymes that promote cell death. Science. 2019, 365(6455):799-803.

Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, Jones J, Dangl JL, Weigel D, & Bemm F. A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell. 2019, 178(5), 1260–1272.

Monteiro F, Nishimura MT. Structural, functional and genomic diversity of plant NLR proteins: an evolved resource for rational engineering of plant immunity. Annual Review of Phytopathology 2018 Aug 25;56:243-267.

Park M, Krause C, Karnahl M, Reichardt I, El Kasmi F, Mayer U, Stierhof YD, Hiller U, Strompen G, Bayer M, Kientz M, Sato MH, Nishimura MT, Dangl JL, Sanderfoot AA, Jurgens G. Concerted action of evolutionarily ancient and novel SNARE complexes in flowering-plant cytokinesis. Developmental Cell. 2018, 44(4):500-511.

Chen H, Chen J, Li M, Chang M, Xu K, Shang Z, Zhao Y, Palmer I, Zhang Y, McGill J, Alfano JM, Nishimura MT, Liu F, Fu ZQ. A bacterial type III effector targets the master regulator of salicylic acid signalling, NPR1, to subvert plant immunity. Cell Host and Microbe. 2017, 22(6):777-788.

Nishimura MT*, Anderson RG*, Cherkis KA*, Law TF, Liu QL, Machius M, Nimchuk ZL, Yang L, Chung E-H, El Kasmi F, Hyunh M, Osborne-Nishimura E, Sondek JE, Dangl JL. TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis. Proceedings of the National Academy of Sciences. 2017, 114(10):E2053-E2062.

El Kasmi F, Nishimura MT. Structural insights into plant NLR immune receptor function. Proceedings of the National Academy of Sciences. 2016, 113(45), 12619-12621.

Peterson BA, Haak DC, Nishimura MT, Teixeira PJPL, James SR, Dangl JL, Nimchuk ZL. Genome-wide assessment of efficiency and specificity in CRISPR/Cas9 mediated multiple site targeting in Arabidopsis. PLoS One. 2016, 11(9):e0162169.

Zhao T, Rui L, Li J, Nishimura MT, Vogel JP, Liu N, Liu S, Zhao Y, Dangl JL, Tang D. A truncated NLR protein, TIR-NBS2, is required for activated defense responses in the exo70B1 mutant. PLoS Genetics. 2015, 11(1):e1004945.

Nishimura MT, Monteiro F, Dangl JL. Treasure your exceptions: unusual domains in immune receptors reveal host virulence targets. Cell. 2015, 161(5): 957-960.

Hockett KL*, Nishimura MT*, Karlsrud E, Dougherty K, Baltrus DA. Pseudomonas syringae CC1557: a highly virulent strain with an unusually small type III effector repertoire that includes a novel effector. Molecular Plant Microbe Interactions. 2014, 27: 923-32.

Mucyn TS, Yourstone S, Lind AL, Biswas S, Nishimura MT, Baltrus DA, Cumbie JS, Chang JH, Jones CD, Dangl JL, Grant SR. Variable suites of non-effector genes are co-regulated in the type III secretion virulence regulon across the Pseudomonas syringae phylogeny. PLoS Pathogens. 2014, 10: e1003807.

Nishimura MT, Dangl JL. Paired plant immune receptors. Science. 2014, 344: 267-8.

Baltrus DA, Nishimura MT, Dougherty KM, Biswas S, Muhktar S, Vicente JG, Holub EB, Dangl J. The molecular basis of host specialization in bean pathovars of Pseudomonas syringae. Molecular Plant Microbe Interactions. 2012, 25: 877-88.

Bonardi V, Cherkis K, Nishimura MT, Dangl JL. A new eye on NLR proteins: focused on clarity or diffused by complexity? Current Opinion in Immunology. 2012, 24: 41-50.

Wang Y, Nishimura MT, Zhao T, Tang D. ATG2, an autophagy-related protein, negatively affects powdery mildew resistance and mildew-induced cell death in Arabidopsis. The Plant Journal. 2011, 68: 74-87.

Mukhtar MS, Carvunis AR, Dreze M, Epple P, Steinbrenner J, Moore J, Tasan M, Galli M, Hao T, Nishimura MT, Pevzner SJ, Donovan SE, Ghamsari L, Santhanam B, Romero V, Poulin MM, Gebreab F, Gutierrez BJ, Tam S, Monachello D, Boxem M, Harbort CJ, McDonald N, Gai L, Chen H, He Y; European Union Effectoromics Consortium, Vandenhaute J, Roth FP, Hill DE, Ecker JR, Vidal M, Beynon J, Braun P, Dangl JL. Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science. 2011, 333: 596-601.

Baltrus DA*, Nishimura MT*, Romanchuk A, Chang JH, Mukhtar MS, Cherkis K, Roach J, Grant SR, Jones CD, Dangl JL. Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates. PLoS Pathogens. 2011, 7: e1002132.

Nishimura MT, Dangl JL. Arabidopsis and the plant immune system. The Plant Journal. 2010, 61:1053-66.

Mukhtar MS, Nishimura MT, Dangl J. NPR1 in plant defense: it’s not over ’til it’s turned over. Cell. 2009, 137: 804-

Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Research. 2009, 19: 294-305.

Vorwerk S, Schiff C, Santamaria M, Koh S, Nishimura M, Vogel J, Somerville C, Somerville S. EDR2 negatively regulates salicylic acid-based defenses and cell death during powdery mildew infections of Arabidopsis thaliana. BMC Plant Biology. 2007, 7:35.

Nishimura MT*, Stein M*, Hou BH, Vogel JP, Edwards H, Somerville SC. Loss of a callose synthase results in salicylic acid-dependent disease resistance. Science. 2003, 301: 969-72.   *these authors contributed equally.

Nishimura M, Somerville S. Plant biology. Resisting attack. Science. 2002, 295: 2032-3.

Somerville, S.C., Nishimura, M., Hughes, D., Wilson, I., and Vogel, J. 1998. Alternate methods of gene discovery — the candidate gene approach and DNA microarrays. Pages 297-309 in: Cellular Integration of Signaling Pathways in Plant Development. NATO ASI Series, Vol. H104 (F. Lo Schiavo, R.L. Last, G. Morelli, and N.V. Raikhel, eds.). Springer-Verlag, Berlin.

Botella MA, Coleman MJ, Hughes DE, Nishimura MT, Jones JD, Somerville SC. Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes. The Plant Journal. 1997, 12:1197-211.