The metabolic interplay between plants and phytopathogens

Metabolites

Volumn 3, Issue 1, 2013, Pages

  Duan, Guangyou ^a   Christian, Nils ^b   Schwachtje, Jens ^a   Walther, Dirk ^a   Ebenhöh, Oliver ^b  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^b UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

Enzymes; Genome; Metabolic impairment; Metabolic networks; Metabolites; Pathogens; Plants; Visualization

Indexed keywords

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; BACTERIAL STEM ROT; BIOMASS PRODUCTION; BIOSYNTHESIS; GENOME; HARVEST; HOST PARASITE INTERACTION; ISOTOPE LABELING; LAURACEAE; METABOLISM; MOULD; MULTIDIMENSIONAL SCALING; NONHUMAN; PLANT DISEASE; PLANT YIELD; PSEUDOMONAS FLUORESCENS; PSEUDOMONAS SYRINGAE; RICE; SCLEROTINIA SCLEROTIORUM; SMUT (PLANT DISEASE); SOYBEAN; STOICHIOMETRY; TOMATO; USTILAGO MAYDIS; XANTHOMONAS ORYZAE;

EID: 85016474185     PISSN: None     EISSN: 22181989     Source Type: Journal    
DOI: 10.3390/metabo3010001     Document Type: Article

References (61)

1. De Vos, M.; Van Oosten, V.R.; Van Poecke, R.M. P.; Van Pelt, J. A; Pozo, M.J.; Mueller, M.J.; Buchala, A.J.; Métraux, J.-P.; Van Loon, L.C.; Dicke, M.; et al. Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack. Mol. Plant Microbe Interact. 2005, 18, 923-937.
2. Jones, J.D. G.; Dangl, J.L. The plant immune system. Nature 2006, 444, 323-329.
3. Ward, J.L.; Forcat, S.; Beckmann, M.; Bennett, M.; Miller, S.J.; Baker, J.M.; Hawkins, N.D.; Vermeer, C.P.; Lu, C.; Lin, W.; et al. The metabolic transition during disease following infection of Arabidopsis thaliana by Pseudomonas syringae pv. tomato. Plant J. 2010, 443-457.
4. Allwood, J.W.; Clarke, A.; Goodacre, R.; Mur, L.A. J. Dual metabolomics: A novel approach to understanding plant-pathogen interactions. Phytochemistry 2010, 71, 590-597.
5. Berger, S.; Sinha, A.K.; Roitsch, T. Plant physiology meets phytopathology: plant primary metabolism and plant-pathogen interactions. J. Exp. Bot. 2007, 58, 4019-4026.
6. Glazebrook, J. Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol 2005, 43, 205-207.
7. Batut, J.; Andersson, S.G. E.; O'Callaghan, D. The evolution of chronic infection strategies in the alpha-proteobacteria. Nat. Rev. Microbiol. 2004, 2, 933-945.
8. Moran, N.A. Microbial minimalism: Genome reduction in bacterial pathogens. Cell 2002, 108, 583-586.
9. Lee, M.-C.; Marx, C.J. Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations. PLoS Genet. 2012, 8, e1002651.
10. Thilmony, R.; Underwood, W.; He, S.Y. Genome-wide transcriptional analysis of the Arabidopsis thaliana interaction with the plant pathogen Pseudomonas syringae pv. tomato DC3000 and the human pathogen Escherichia coli O157:H7. Plant J. 2006, 46, 34-53.
11. Rinaldi, C.; Kohler, A.; Frey, P.; Duchaussoy, F.; Ningre, N.; Couloux, A.; Wincker, P.; Le Thiec, D.; Fluch, S.; Martin, F.; et al. Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina. Plant Physiol. 2007, 144, 347-66.
12. Raghunathan, A.; Reed, J.; Shin, S.; Palsson, B.; Daefler, S. Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst. Biol 2009, 3, 38.
13. Raghunathan, A.; Price, N.D.; Galperin, M.Y.; Makarova, K.S.; Purvine, S.; Picone, A.F.; Cherny, T.; Xie, T.; Reilly, T.J.; Munson, R.; et al. In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. OMICS 2004, 8, 25-41.
14. Pinzón, A.; Rodriguez-R, L.M.; González, A.; Bernal, A.; Restrepo, S. Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. Brief. Bioinformatics 2011, 12, 151-162.
15. Shendure, J.; Mitra, R.D.; Varma, C.; Church, G.M. Advanced sequencing technologies: methods and goals. Nat. Rev. Genet. 2004, 5, 335-344.
16. Kanehisa, M.; Goto, S.; Kawashima, S.; Nakaya, A. The KEGG databases at GenomeNet. Nucleic. Acids Res. 2002, 30, 42-46.
17. Krieger, C.J.; Zhang, P.; Mueller, L. a; Wang, A.; Paley, S.; Arnaud, M.; Pick, J.; Rhee, S.Y.; Karp, P.D. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic. Acids Res. 2004, 32, D438-42.
18. Rico, A.; Preston, G.M. Pseudomonas syringae pv. tomato DC3000 uses constitutive and apoplast-induced nutrient assimilation pathways to catabolize nutrients that are abundant in the tomato apoplast. Mol. Plant Microbe Interact. 2008, 21, 269-282.
19. Handorf, T.; Ebenhöh, O.; Heinrich, R. Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol. 2005, 61, 498-512.
20. Christian, N.; Handorf, T.; Ebenhöh, O. Metabolic synergy: increasing biosynthetic capabilities by network cooperation. Genome Inform 2007, 18, 320-329.
21. Freilich, S.; Kreimer, A.; Meilijson, I.; Gophna, U.; Sharan, R.; Ruppin, E. The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res. 2010, 38, 3857-3868.
22. Borenstein, E.; Feldman, M.W. Topological signatures of species interactions in metabolic networks. J. Comput. Biol. 2009, 16, 191-200.
23. kreimer, A.; Doron, A.; Borenstein, E.; Freilich, S. NetCmpt: A network-based tool for calculating the metabolic competition between bacterial species. Bioinformatics 2012, 28, 2195-2197.
24. Pinon, J.; Frey, P. Interactions between poplar clones and Melampsora populations and their implications for breeding for durable resistance. In Rust Diseases of Willow and Poplar; Pei, M.H.; McCracken, A.R., Eds.; CABI: Wallingford, UK, 2005; pp. 139-154.
25. Salzberg, S.L.; Sommer, D.D.; Schatz, M.C.; Phillippy, A.M.; Rabinowicz, P.D.; Tsuge, S.; Furutani, A.; Ochiai, H.; Delcher, A.L.; Kelley, D.; et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC genomics 2008, 9, 204.
26. Saharan, G.S.; Mehta, N. Sclerotinia Diseases of Crop Plants: Biology, Ecology and Disease Management; Springer-Verlag GmbH: Heidelberg, Germany, 2008.
27. Mueller, O.; Kahmann, R.; Aguilar, G.; Trejo-Aguilar, B.; Wu, A.; de Vries, R.P. The secretome of the maize pathogen Ustilago maydis. Fungal Genet. Biol. 2008, 45 (Suppl. 1), S63-S70.
28. Altschul, S.F.; Madden, T.L.; Schäffer, a a; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389-402.
29. Hammond-Kosack, K.E.; Jones, J.D. G. Plant disease resistance genes. Annu. Rev. Plant Physiol. Plant Mol. Biol. 1997, 48, 575-607.
30. Hacquard, S.; Joly, D.L.; Lin, Y.-C.; Tisserant, E.; Feau, N.; Delaruelle, C.; Legué, V.; Kohler, A.; Tanguay, P.; Petre, B.; et al. A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici-populina (poplar leaf rust). Mol. Plant Microbe Interact. 2012, 25, 279-293.
31. Malenčić, D.; Kiprovski, B.; Popović, M.; Prvulović, D.; Miladinović, J.; Djordjević, V. Changes in antioxidant systems in soybean as affected by Sclerotinia sclerotiorum (Lib.) de Bary. Plant Physiol. Biochem. 2010, 48, 903-908.
32. Amselem, J.; Cuomo, C.A.; van Kan, J.A. L.; Viaud, M.; Benito, E.P.; Couloux, A.; Coutinho, P.M.; de Vries, R.P.; Dyer, P.S.; Fillinger, S.; et al. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet. 2011, 7, e1002230.
33. Initiative, T.A. G. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408, 796-815.
34. Buell, C.R.; Joardar, V.; Lindeberg, M.; Selengut, J.; Paulsen, I.T.; Gwinn, M.L.; Dodson, R.J.; Deboy, R.T.; Durkin, A.S.; Kolonay, J.F.; et al. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 2003, 100, 10181-10186.
35. Yu, J.; Hu, S.; Wang, J.; Wong, G.K.-S.; Li, S.; Liu, B.; Deng, Y.; Dai, L.; Zhou, Y.; Zhang, X.; et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296, 79-92.
36. Ochiai, H.; Inoue, Y.; Takeya, M.; Sasaki, A.; Kaku, H. Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. JARQ. Jpn. Agric. Res. Q. 2005, 39, 275-287.
37. Schnable, P.S.; Ware, D.; Fulton, R.S.; Stein, J.C.; Wei, F.; Pasternak, S.; Liang, C.; Zhang, J.; Fulton, L.; Graves, T.A.; et al. The B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326, 1112-5.
38. Kämper, J.; Kahmann, R.; Bölker, M.; Ma, L.-J.; Brefort, T.; Saville, B.J.; Banuett, F.; Kronstad, J.W.; Gold, S.E.; Müller, O.; et al. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 2006, 444, 97-101.
39. Tuskan, G. a; Difazio, S.; Jansson, S.; Bohlmann, J.; Grigoriev, I.; Hellsten, U.; Putnam, N.; Ralph, S.; Rombauts, S.; Salamov, A.; et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313, 1596-1604.
40. Duplessis, S.; Cuomo, C.A.; Lin, Y.-C.; Aerts, A.; Tisserant, E.; Veneault-Fourrey, C.; Joly, D.L.; Hacquard, S.; Amselem, J.; Cantarel, B.L.; et al. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc. Natl. Acad. Sci. USA 2011, 108, 9166-9171.
41. Schmutz, J.; Cannon, S.B.; Schlueter, J.; Ma, J.; Mitros, T.; Nelson, W.; Hyten, D.L.; Song, Q.; Thelen, J.J.; Cheng, J.; et al. a Genome sequence of the palaeopolyploid soybean. Nature 2010, 463, 178-183.
42. Caspi, R.; Altman, T.; Dale, J.M.; Dreher, K.; Fulcher, C.A.; Gilham, F.; Kaipa, P.; Karthikeyan, A.S.; Kothari, A.; Krummenacker, M.; et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2010, 38, D473-D479.
43. Punta, M.; Coggill, P.C.; Eberhardt, R.Y.; Mistry, J.; Tate, J.; Boursnell, C.; Pang, N.; Forslund, K.; Ceric, G.; Clements, J.; et al. The Pfam protein families database. Nucleic Acids Res. 2011, 1-12.
44. Consortium, T.U. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2011, 1-5.
45. Katoh, K.; Kuma, K.; Toh, H.; Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005, 33, 511-8.
46. Eddy, S.R. Profile hidden Markov models. Bioinformatics 1998, 14, 755-763.
47. Christian, N.; May, P.; Kempa, S.; Handorf, T.; Ebenhöh, O. An integrative approach towards completing genome-scale metabolic networks. Mol Biosyst 2009, 5, 1889-903.
48. Kanehisa, M.; Araki, M.; Goto, S.; Hattori, M.; Hirakawa, M.; Itoh, M.; Katayama, T.; Kawashima, S.; Okuda, S.; Tokimatsu, T.; et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008, 36, D480-4.
49. Handorf, T.; Christian, N.; Ebenhöh, O.; Kahn, D. An environmental perspective on metabolism. J. Theor. Biol. 2008, 252, 530-7.
50. Preston, G.M.; Bertrand, N.; Rainey, P.B. Type III secretion in plant growth-promoting Pseudomonas fluorescens SBW25. Mol. Microbiol. 2001, 41, 999-1014.
51. Sachs, J.L.; Mueller, U.G.; Wilcox, T.P.; Bull, J.J. The Evolution of Cooperation. Q Rev Biol 2004, 79, 135-160.
52. Caspi, R.; Altman, T.; Dreher, K.; Fulcher, C.A.; Subhraveti, P.; Keseler, I.M.; Kothari, A.; Krummenacker, M.; Latendresse, M.; Mueller, L.A.; et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2011, 1-12.
53. Cox, T.F.; M.A.A. Cox Multidimensional Scaling; CRC Press: Boca Raton, FL, USA, 2001.
54. Keseler, I.M.; Collado-Vides, J.; Santos-Zavaleta, A.; Peralta-Gil, M.; Gama-Castro, S.; Muñiz-Rascado, L.; Bonavides-Martinez, C.; Paley, S.; Krummenacker, M.; Altman, T.; et al. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011, 39, D583-D590.
55. May, P.; Christian, J.-O.; Kempa, S.; Walther, D. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics 2009, 10, 209.
56. May, P.; Wienkoop, S.; Kempa, S.; Usadel, B.; Christian, N.; Rupprecht, J.; Weiss, J.; Recuenco-Munoz, L.; Ebenhöh, O.; Weckwerth, W.; et al. Metabolomics-and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics 2008, 179, 157-66.
57. Mueller, L.A.; Zhang, P.; Rhee, S.Y. AraCyc: A Biochemical Pathway Database for Arabidopsis. Plant Physiol. 2003, 132, 453-460.
58. Sloan, D.B.; Moran, N.A. Endosymbiotic bacteria as a source of carotenoids in whiteflies. Biol. Lett. 2012, 8, 986-989.
59. Karp, P.D.; Paley, S.M.; Krummenacker, M.; Latendresse, M.; Dale, J.M.; Lee, T.J.; Kaipa, P.; Gilham, F.; Spaulding, A.; Popescu, L.; et al. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinformatics 2010, 11, 40-79.
60. Matthäus, F.; Salazar, C.; Ebenhöh, O. Biosynthetic potentials of metabolites and their hierarchical organization. PLoS Comput. Biol. 2008, 4, e1000049.
61. Raman, K.; Chandra, N. Flux balance analysis of biological systems: applications and challenges. Brief. Bioinformatics 2009, 10, 435-449.