Tracing the ancient origins of plant innate immunity

Golstein, 2003, Cell-death alternative model organisms: why and which?, Nat. Rev. Mol. Cell Biol., 4, 798, 10.1038/nrm1224 Cornillon, 1994, Programmed cell death in Dictyostelium, J. Cell Sci., 107, 2691, 10.1242/jcs.107.10.2691 Zipfel, 2005, Plants and animals: a different taste for microbes?, Curr. Opin. Plant Biol., 8, 353, 10.1016/j.pbi.2005.05.004 Mackey, 2006, MAMPs and MIMPs: proposed classifications for inducers of innate immunity, Mol. Microbiol., 61, 1365, 10.1111/j.1365-2958.2006.05311.x Bianchi, 2007, DAMPs, PAMPs and alarmins: all we need to know about danger, J. Leukoc. Biol., 81, 1, 10.1189/jlb.0306164 Ausubel, 2005, Are innate immune signalling pathways in plants and animals conserved? Nat, Immunol., 10, 973 Rolff, 2007, Why did the acquired immune system of vertebrates evolve?, Dev. Comp. Immunol., 31, 476, 10.1016/j.dci.2006.08.009 van der Biezen, 1998, Plant disease resistance proteins and the gene-for-gene concept, Trends Biochem. Sci., 23, 454, 10.1016/S0968-0004(98)01311-5 Jones, 2006, The plant immune system, Nature, 444, 323, 10.1038/nature05286 McDonald, 2002, Pathogen population genetics, evolutionary potential, and durable resistance, Annu. Rev. Phytopathol., 40, 349, 10.1146/annurev.phyto.40.120501.101443 Kover, 2001, The genetic architecture of disease resistance in plants and the maintenance of recombination by parasites, Mol. Ecol., 10, 1, 10.1046/j.1365-294X.2001.01124.x Koonin, 2002, Origin and evolution of eukaryotic apoptosis: the bacterial connection, Cell Death Differ., 9, 394, 10.1038/sj.cdd.4400991 Magor, 2001, Evolution of effectors and receptors of innate immunity, Dev. Comp. Immunol., 25, 651, 10.1016/S0145-305X(01)00029-5 Dacks, 2001, Reconstructing/deconstructing the earliest eukaryotes: how comparative genomics can help, Cell, 107, 419, 10.1016/S0092-8674(01)00584-0 Blair, 2005, Evolutionary sequence analysis of complete eukaryote genomes, BMC Bioinformatics, 6, 53, 10.1186/1471-2105-6-53 Ciccarelli, 2006, Toward automatic reconstruction of highly resolved tree of life, Science, 311, 1283, 10.1126/science.1123061 Hunter, 2005, Common defences – comparisons between plant and animal immunity can benefit both research communities, EMBO J., 6, 504, 10.1038/sj.embor.7400439 Tuskan, 2006, The genome of black cottonwood, Populus trichocarpa (Torr. & Gray), Science, 313, 1596, 10.1126/science.1128691 Meyers, 2002, TIR-X and TIR-NB proteins: two new families related to disease resistance TIR-NB-LRR proteins encoded in Arabidopsis and other plant genomes, Plant J., 32, 77, 10.1046/j.1365-313X.2002.01404.x Dangl, 2006, Two modes of pathogen recognition by plants, Proc. Natl. Acad. Sci. U. S. A., 103, 8575, 10.1073/pnas.0603183103 Hofius, 2007, Inducible cell death in plant immunity, Semin. Cancer Biol., 17, 166, 10.1016/j.semcancer.2006.12.001 Glazebrook, 2005, Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens, Annu. Rev. Phytopathol., 43, 205, 10.1146/annurev.phyto.43.040204.135923 Staal, 2006, Transgressive segregation reveals two Arabidopsis TIR-NB-LRR resistance genes effective against Leptosphaeria maculans, causal agent of blackleg disease, Plant J., 46, 218, 10.1111/j.1365-313X.2006.02688.x Tian, 2004, The absence of TIR-type resistance gene analogues in the sugar beet (Beta vulgaris L.) genome, J. Mol. Evol., 58, 40, 10.1007/s00239-003-2524-4 Meyers, 1999, Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily, Plant J., 20, 317, 10.1046/j.1365-313X.1999.t01-1-00606.x Liu, 2003, Isolation, genetic variation and expression of TIR-NBS-LRR resistance gene analogs from western white pine (Pinus monticola Dougl. Ex. D. Don.), Mol. Genet. Genomics, 270, 432, 10.1007/s00438-003-0940-1 Akita, 2000, A novel gene family in moss (Physcomitrella patens) shows sequence homology and a phylogenetic relationship with the TIR-NBS class of plant disease resistance genes, J. Mol. Evol., 55, 595, 10.1007/s00239-002-2355-8 Cannon, 2002, Diversity, distribution and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies, J. Mol. Evol., 54, 548, 10.1007/s00239-001-0057-2 van der Biezen, 1998, The NB-ARC domain: a novel signalling motif shared by plant resistance gene products and regulators of cell death in animals, Curr. Biol., 8, R226, 10.1016/S0960-9822(98)70145-9 Leipe, 2004, STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phylogenetic patterns and evolution by horizontal gene transfer, J. Mol. Biol., 343, 1, 10.1016/j.jmb.2004.08.023 Inohara, 2003, NODs: intracellular proteins involved in inflammation and apoptosis, Nat. Rev. Immunol., 3, 371, 10.1038/nri1086 Petrilli, 2005, The inflammasome, Curr. Biol., 15, R581, 10.1016/j.cub.2005.07.049 Mestre, 2005, Elicitor-mediated oligomerization of the tobacco N disease resistance protein, Plant Cell, 18, 491, 10.1105/tpc.105.037234 Hibino, 2006, The immune gene repertoire encoded in the purple sea urchin genome, Dev. Biol., 300, 349, 10.1016/j.ydbio.2006.08.065 Fedorova, 2005, Comparative analysis of programmed cell death pathways in filamentous fungi, BMC Genomics, 6, 177, 10.1186/1471-2164-6-177 Beutler, 2002, Evolution of the TIR, tolls and TLRs: functional inferences from computational biology, Curr. Top. Microbiol. Immunol., 270, 1 Wiens, 2007, Toll-like receptors are part of the innate immune defense system of sponges (Demospongiae: Porifera), Mol. Biol. Evol., 24, 792, 10.1093/molbev/msl208 Faigon-Soverna, 2006, A constitutive shade-avoidance mutant implicates TIR-NBS-LRR proteins in Arabidopsis photomorphogenic development, Plant Cell, 18, 2919, 10.1105/tpc.105.038810 Liew, 2005, Negative regulation of Toll-like receptor-mediated immune responses, Nat. Rev. Immunol., 5, 446, 10.1038/nri1630 O’Neill, 2006, How Toll-like receptors signal: what we know and what we don’t know, Curr. Opin. Immunol., 18, 3, 10.1016/j.coi.2005.11.012 Michael Weaver, 2006, The Arabidopsis thaliana TIR-NB-LRR R-protein, RPP1A; protein localization and constitutive activation of defence by truncated alleles in tobacco and Arabidopsis, Plant J., 47, 829, 10.1111/j.1365-313X.2006.02834.x Marcotte, 1999, Detecting protein function and protein–protein interactions from genome sequences, Science, 285, 751, 10.1126/science.285.5428.751 Dardick, 2006, Plant and animal pathogen recognition receptors signal through non-RD kinases, PLoS Pathog., 2, 14, 10.1371/journal.ppat.0020002 Fritz, 2005, Synergistic stimulation of human monocytes and dendritic cells by Toll-like receptor 4 and NOD1- and NOD2-activating agonists, Eur. J. Immunol., 35, 2459, 10.1002/eji.200526286 Gabriëls, 2006, cDNA-AFLP combined with functional analysis reveals novel genes involved in the hypersensitive response, Mol. Plant Microbe Interact., 19, 567, 10.1094/MPMI-19-0567 de la Fuente van Bentem, 2005, Heat shock protein 90 and its co-chaperone protein phosphatase 5 interact with distinct regions of the tomato I-2 disease resistance protein, Plant J., 43, 284, 10.1111/j.1365-313X.2005.02450.x Hahn, 2005, Regulation of Nod1 by Hsp90 chaperone complex, FEBS Lett., 579, 4513, 10.1016/j.febslet.2005.07.024 Mayor, 2007, A crucial function of SGT1 and HSP90 in inflammasome activity links mammalian and plant innate immune responses, Nat. Immunol., 8, 497, 10.1038/ni1459 da Silva Correia, 2007, SGT1 is essential for Nod1 activation, Proc. Natl. Acad. Sci. U. S. A., 104, 6764, 10.1073/pnas.0610926104 Lahaye, 2002, The Arabidopsis RRS1-R disease resistance gene – uncovering the plant's nucleus as the new battlefield of plant defense?, Trends Plant Sci., 7, 425, 10.1016/S1360-1385(02)02334-8 Shen, 2007, Nuclear activity of MLA immune receptors links isolate-specific and basal disease resistance responses, Science, 315, 1098, 10.1126/science.1136372 Uren, 2000, Identification of paracaspases and metacaspases: Two ancient families of caspase-like proteins, one of which plays a key role in MALT lymphoma, Mol. Cell, 6, 961, 10.1016/S1097-2765(00)00094-0 Siegel, 2006, Caspases at the crossroads of immune-cell life and death, Nat. Rev. Immunol., 6, 308, 10.1038/nri1809 Vercammen, 2004, Type II metacaspases Atmc4 and Atmc9 of Arabidopsis thaliana cleave substrates after arginine and lysine, J. Biol. Chem., 279, 45329, 10.1074/jbc.M406329200 Bozhkov, 2005, Cysteine protease mcII-Pa executes programmed cell death during plant embryogenesis, Proc. Natl. Acad. Sci. U. S. A., 102, 14463, 10.1073/pnas.0506948102 Hatsugai, 2004, A plant vacuolar protease, VPE, mediates virus-induced hypersensitive cell death, Science, 305, 855, 10.1126/science.1099859 Rojo, 2004, VPEγ exhibits a caspase-like activity that contributes to defense against pathogens, Curr. Biol., 14, 1897, 10.1016/j.cub.2004.09.056 Hoeberichts, 2003, A tomato metacaspase is upregulated during programmed cell death in Botrytis cinerea-infected leaves, Planta, 217, 517, 10.1007/s00425-003-1049-9 Watanabe, 2005, Two Arabidopsis metacaspases AtMCP1b and AtMCP2b are arginine/lysine-specific cysteine proteases and activate apoptosis-like cell death in yeast, J. Biol. Chem., 280, 14691, 10.1074/jbc.M413527200 Madeo, 2002, A caspase-related protease regulates apoptosis in yeast, Mol. Cell, 9, 911, 10.1016/S1097-2765(02)00501-4 Suarez, 2004, Metacaspase-dependent programmed cell death is essential for plant embryogenesis, Curr. Biol., 14, R339, 10.1016/j.cub.2004.04.019 Bozhkov, 2007, Autophagy and cell death proteases in plants: two wheels of a funeral cart, J. Exp. Bot., 3, 136 Belenghi, 2007, Metacaspase activity of Arabidopsis thaliana is regulated by S-nitrosylation of a critical cysteine residue, J. Biol. Chem., 282, 1352, 10.1074/jbc.M608931200 Feechan, 2005, A central role for S-nitrosothiols in plant disease resistance, Proc. Natl. Acad. Sci. U. S. A., 102, 8054, 10.1073/pnas.0501456102 Zeidler, 2004, Innate immunity in Arabidopsis thaliana: lipopolysaccharides activate nitric oxide synthase (NOS) and induce defense genes, Proc. Natl. Acad. Sci. U. S. A., 101, 15811, 10.1073/pnas.0404536101 Zhivotovsky, 2002, From the nematode and mammals back to the pine tree: on the diversity and evolution of programmed cell death, Cell Death Differ., 9, 867, 10.1038/sj.cdd.4401084 Liu, 2005, Autophagy regulates programmed cell death during the plant innate immune response, Cell, 121, 567, 10.1016/j.cell.2005.03.007 Roisin-Bouffay, 2004, Developmental cell death in Dictyostelium does not require paracaspase, J. Biol. Chem., 19, 11489, 10.1074/jbc.M312741200 Kawasaki, 2005, A duplicated pair of Arabidopsis RING-finger E3 ligases contribute to the RPM1- and RPS2-mediated hypersensitive response, Plant J., 44, 258, 10.1111/j.1365-313X.2005.02525.x Thomma, 2002, Plant defensins, Planta, 216, 193, 10.1007/s00425-002-0902-6 Pfisterer, 1996, CRISP-3, a protein with homology to plant defense proteins is expressed in mouse B cells under the control of Oct2, Mol. Cell. Biol., 16, 6160, 10.1128/MCB.16.11.6160 van Eijk, 2005, Characterization of human phagocyte-derived chitotriosidase, a component of innate immunity, Int. Immunol., 17, 1505, 10.1093/intimm/dxh328 Rahme, 2000, Plants and animals share functionally common bacterial virulence factors, Proc. Natl. Acad. Sci. U. S. A., 97, 8815, 10.1073/pnas.97.16.8815 He, 2004, The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes, Proc. Natl. Acad. Sci. U. S. A., 101, 2530, 10.1073/pnas.0304622101 Jha, 2005, Enterococcus faecalis mammalian virulence-related factors exhibit potent pathogenicity in the Arabidopsis thaliana plant model, Infect. Immun., 73, 464, 10.1128/IAI.73.1.464-475.2005 Finlay, 2006, Anti-immunology: evasion of the host immune system by bacterial and viral pathogens, Cell, 124, 767, 10.1016/j.cell.2006.01.034 Chisholm, 2006, Host–microbe interactions: shaping the evolution of the plant immune response, Cell, 124, 803, 10.1016/j.cell.2006.02.008 Lindmark, 2001, Enteric bacteria counteract lipopolysaccharide induction of antimicrobial peptide genes, J. Immunol., 167, 6920, 10.4049/jimmunol.167.12.6920 Shao, 2002, A Yersinia effector and a Pseudomonas avirulence protein define a family of cysteine proteases functioning in bacterial pathogenesis, Cell, 109, 575, 10.1016/S0092-8674(02)00766-3 Bhattacharjee, 2006, The malaria host-targeting signal is conserved in the Irish potato famine pathogen, PLoS Pathog., 2, 453, 10.1371/journal.ppat.0020050 Winnenburg, 2006, PHI-base: a new database for pathogen host interactions, Nucleic Acids Res., 34, D459, 10.1093/nar/gkj047 Beutler, 2004, Genetic analysis of innate immunity: TIR adapter proteins in innate and adaptive immune responses, Microbes Infect., 6, 1374, 10.1016/j.micinf.2004.08.017 Gomez-Gomez, 2000, FLS2: an LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis, Mol. Cell, 5, 1003, 10.1016/S1097-2765(00)80265-8 Swofford, D.L. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), version 4, Sinauer Associates Yoon, 2004, A molecular timeline for the origin of photosynthetic eukaryotes, Mol. Biol. Evol., 21, 809, 10.1093/molbev/msh075 Azevedo, 2006, Role of SGT1 in resistance protein accumulation in plant immunity, EMBO J., 25, 2007, 10.1038/sj.emboj.7601084