Proteomic approaches to study plant-pathogen interactions

Phytochemistry

Volumn 71, Issue 4, 2010, Pages 351-362

  Quirino, B F ^a,b   Candido, E S ^a   Campos, P F ^a   Franco, O L ^a   Kruger R H ^c  

^a UNIVERSIDADE CATÓLICA DE BRASÍLIA   (Brazil)

^b Embrapa Agroenergia ^*  (Brazil)

^c UNIVERSITY OF BRASILIA   (Brazil)

Author keywords

Pathogen; Pathosystem; Plant; Proteome; Proteomics

Indexed keywords

GENETICS; GENOMICS; HOST PATHOGEN INTERACTION; METABOLISM; PLANT; PROTEOMICS; REVIEW;

GENOMICS; HOST-PATHOGEN INTERACTIONS; PLANTS; PROTEOMICS;

EID: 76249129588     PISSN: 00319422     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.phytochem.2009.11.005     Document Type: Review

References (116)

1. Andrade A.E., Silva L.P., Pereira J.L., Noronha E.F., Reis Jr. F.B., Bloch Jr. C., dos Santos M.F., Domont G.B., Franco O.L., and Mehta A. In vivo proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the host plant Brassica oleracea. FEMS Microbiol. Lett. 281 (2008) 167-174
2. Arai Y., Hayashi M., and Nishimura M. Proteomic analysis of highly purified peroxisomes from etiolated soybean cotyledons. Plant Cell Physiol. 49 (2008) 526-539
3. Asai T., Tena G., Plotnikova J., Willmann M.R., Chiu W.L., Gomez-Gomez L., Boller T., Ausubel F.M., and Sheen J. MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 415 (2002) 977-983
4. Bell K.S., Sebaihia M., Pritchard L., Holden M.T., Hyman L.J., Holeva M.C., Thomson N.R., Bentley S.D., Churcher L.J., Mungall K., Atkin R., Bason N., Brooks K., Chillingworth T., Clark K., Doggett J., Fraser A., Hance Z., Hauser H., Jagels K., Moule S., Norbertczak H., Ormond D., Price C., Quail M.A., Sanders M., Walker D., Whitehead S., Salmond G.P., Birch P.R., Parkhill J., and Toth I.K. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc. Natl. Acad. Sci. USA 101 (2004) 11105-11110
5. Bentley S.D., Corton C., Brown S.E., Barron A., Clark L., Doggett J., Harris B., Ormond D., Quail M.A., May G., Francis D., Knudson D., Parkhill J., and Ishimaru C.A. Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation. J. Bacteriol. 190 (2008) 2150-2160
6. Bindschedler L.V., Palmblad M., and Cramer R. Hydroponic isotope labelling of entire plants (HILEP) for quantitative plant proteomics; an oxidative stress case study. Phytochemistry 69 (2008) 1962-1972
7. Brizard J.P., Carapito C., Delalande F., Van Dorsselaer A., and Brugidou C. Proteome analysis of plant-virus interactome: comprehensive data for virus multiplication inside their hosts. Mol. Cell. Proteomics 5 (2006) 2279-2297
8. Brugiere S., Kowalski S., Ferro M., Seigneurin-Berny D., Miras S., Salvi D., Ravanel S., d'Herin P., Garin J., Bourguignon J., Joyard J., and Rolland N. The hydrophobic proteome of mitochondrial membranes from Arabidopsis cell suspensions. Phytochemistry 65 (2004) 1693-1707
9. Brunner A.M., Busov V.B., and Strauss S.H. Poplar genome sequence: functional genomics in an ecologically dominant plant species. Trends Plant Sci. 9 (2004) 49-56
10. 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., Madupu R., Daugherty S., Brinkac L., Beanan M.J., Haft D.H., Nelson W.C., Davidsen T., Zafar N., Zhou L., Liu J., Yuan Q., Khouri H., Fedorova N., Tran B., Russell D., Berry K., Utterback T., Van Aken S.E., Feldblyum T.V., D'Ascenzo M., Deng W.L., Ramos A.R., Alfano J.R., Cartinhour S., Chatterjee A.K., Delaney T.P., Lazarowitz S.G., Martin G.B., Schneider D.J., Tang X., Bender C.L., White O., Fraser C.M., and Collmer A. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 100 (2003) 10181-10186
11. Carpentier S.C., Witters E., Laukens K., Deckers P., Swennen R., and Panis B. Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two-dimensional gel electrophoresis analysis. Proteomics 5 (2005) 2497-2507
12. Carpentier S.C., Panis B., Vertommen A., Swennen R., Sergeant K., Renaut J., Laukens K., Witters E., Samyn B., and Devreese B. Proteome analysis of non-model plants: a challenging but powerful approach. Mass. Spectrom. Rev. 27 (2008) 354-377
13. Chen C.H. Review of a current role of mass spectrometry for proteome research. Anal. Chim. Acta 624 (2008) 16-36
14. Chen S., and Harmon A.C. Advances in plant proteomics. Proteomics 6 (2006) 5504-5516
15. Chen F., Yuan Y., Li Q., and He Z. Proteomic analysis of rice plasma membrane reveals proteins involved in early defense response to bacterial blight. Proteomics 7 (2007) 1529-1539
16. Chivasa S., Ndimba B.K., Simon W.J., Robertson D., Yu X.L., Knox J.P., Bolwell P., and Slabas A.R. Proteomic analysis of the Arabidopsis thaliana cell wall. Electrophoresis 23 (2002) 1754-1765
17. Chivasa S., Simon W.J., Yu X.L., Yalpani N., and Slabas A.R. Pathogen elicitor-induced changes in the maize extracellular matrix proteome. Proteomics 5 (2005) 4894-4904
18. Clauser K.R., Baker P., and Burlingame A.L. Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71 (1999) 2871-2882
19. Coaker G., and Francis D. Mapping, genetic effects, and epistatic interaction of two bacterial canker resistance QTLs from Lycopersicon hirsutum. Theor. Appl. Genet. 108 (2004) 1047-1055
20. Coaker G.L., Willard B., Kinter M., Stockinger E.J., and Francis D.M. Proteomic analysis of resistance mediated by Rcm 2.0 and Rcm 5.1, two loci controlling resistance to bacterial canker of tomato. Mol. Plant Microbe Interact. 17 (2004) 1019-1028
21. Cooper B., Eckert D., Andon N.L., Yates J.R., and Haynes P.A. Investigative proteomics: identification of an unknown plant virus from infected plants using mass spectrometry. J. Am. Soc. Mass Spectrom. 14 (2003) 736-741
22. da Silva A.C., Ferro J.A., Reinach F.C., Farah C.S., Furlan L.R., Quaggio R.B., Monteiro-Vitorello C.B., Van Sluys M.A., Almeida N.F., Alves L.M., do Amaral A.M., Bertolini M.C., Camargo L.E., Camarotte G., Cannavan F., Cardozo J., Chambergo F., Ciapina L.P., Cicarelli R.M., Coutinho L.L., Cursino-Santos J.R., El-Dorry H., Faria J.B., Ferreira A.J., Ferreira R.C., Ferro M.I., Formighieri E.F., Franco M.C., Greggio C.C., Gruber A., Katsuyama A.M., Kishi L.T., Leite R.P., Lemos E.G., Lemos M.V., Locali E.C., Machado M.A., Madeira A.M., Martinez-Rossi N.M., Martins E.C., Meidanis J., Menck C.F., Miyaki C.Y., Moon D.H., Moreira L.M., Novo M.T., Okura V.K., Oliveira M.C., Oliveira V.R., Pereira H.A., Rossi A., Sena J.A., Silva C., de Souza R.F., Spinola L.A., Takita M.A., Tamura R.E., Teixeira E.C., Tezza R.I., Trindade dos Santos M., Truffi D., Tsai S.M., White F.F., Setubal J.C., and Kitajima J.P. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417 (2002) 459-463
23. Dani V.S.W., Duranti M., and Croy R.R. Changes in the tobacco leaf apoplast proteome in response to salt stress. Proteomics 5 (2005) 737-745
24. Dean R.A., Talbot N.J., Ebbole D.J., Farman M.L., Mitchell T.K., Orbach M.J., Thon M., Kulkarni R., Xu J.R., Pan H., Read N.D., Lee Y.H., Carbone I., Brown D., Oh Y.Y., Donofrio N., Jeong J.S., Soanes D.M., Djonovic S., Kolomiets E., Rehmeyer C., Li W., Harding M., Kim S., Lebrun M.H., Bohnert H., Coughlan S., Butler J., Calvo S., Ma L.J., Nicol R., Purcell S., Nusbaum C., Galagan J.E., and Birren B.W. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434 (2005) 980-986
25. Devos S., Laukens K., Deckers P., Van Der Straeten D., Beeckman T., Inze D., Van Onckelen H., Witters E., and Prinsen E. A hormone and proteome approach to picturing the initial metabolic events during Plasmodiophora brassicae infection on Arabidopsis. Mol. Plant Microbe Interact. 19 (2006) 1431-1443
26. Dóczi R., Brader G., Pettkó-Szandtner A., Rajh I., Djamei A., Pitzschke A., Teige M., and Hirt H. The Arabidopsis mitogen-activated protein kinase kinase MKK3 is upstream of group C mitogen-activated protein kinases and participates in pathogen signaling. Plant Cell 19 (2007) 3266-3279
27. Doddapaneni H., Lin H., Walker M.A., Yao J., and Civerolo E.L. VitisExpDB: a database resource for grape functional genomics. BMC Plant Biol. 8 (2008) 23
28. Dunkley T.P.J., Watson R., Griffin J.L., Dupree P., and Lilley K.S. Localization of organelle proteins by isotope tagging (LOPIT). Mol. Cell. Proteomics 3 (2004) 1128-1134
29. Feil H., Feil W.S., Chain P., Larimer F., DiBartolo G., Copeland A., Lykidis A., Trong S., Nolan M., Goltsman E., Thiel J., Malfatti S., Loper J.E., Lapidus A., Detter J.C., Land M., Richardson P.M., Kyrpides N.C., Ivanova N., and Lindow S.E. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 102 (2005) 11064-11069
30. Gartemann K.H., Abt B., Bekel T., Burger A., Engemann J., Flugel M., Gaigalat L., Goesmann A., Grafen I., Kalinowski J., Kaup O., Kirchner O., Krause L., Linke B., McHardy A., Meyer F., Pohle S., Ruckert C., Schneiker S., Zellermann E.M., Puhler A., Eichenlaub R., Kaiser O., and Bartels D. The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity. J. Bacteriol. 190 (2008) 2138-2149
31. Gleason M.L., Gitaitis R.D., and Ricker M.D. Recent progress in understanding and controlling bacterial cancer in eastern North America. Plant Disease 77 (1993) 1069-1076
32. Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B., Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K., Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M., Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C., Gurson J., Lomo C., Sear C., Strub G., Cielo C., and Slater S. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294 (2001) 2323-2328
33. Gurlebeck D., Thieme F., and Bonas U. Type III effector proteins from the plant pathogen Xanthomonas and their role in the interaction with the host plant. J. Plant Physiol. 163 (2006) 233-255
34. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 (1999) 994-999
35. Hartman N.T., Sicilia F., Lilley K.S., and Dupree P. Proteomic complex detection using sedimentation. Anal. Chem. 79 (2007) 2078-2083
36. Hayward A.C. The hosts of Pseudomonas solanacearum. In: Hartman G.L. (Ed). Bacterial Wilt: The Disease and Its Causative Agent, Pseudomonas solanacearum (1994), CAB International, Wallingford 9-24
37. Hsing Y.I., Chern C.G., Fan M.J., Lu P.C., Chen K.T., Lo S.F., Sun P.K., Ho S.L., Lee K.W., Wang Y.C., Huang W.L., Ko S.S., Chen S., Chen J.L., Chung C.I., Lin Y.C., Hour A.L., Wang Y.W., Chang Y.C., Tsai M.W., Lin Y.S., Chen Y.C., Yen H.M., Li C.P., Wey C.K., Tseng C.S., Lai M.H., Huang S.C., Chen L.J., and Yu S.M. A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol. Biol. 63 (2007) 351-364
38. Initiative T.A.G. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (2000) 796-815
39. Jacobs D.I., van Rijssen M.S., van der Heijden R., and Verpoorte R. Sequential solubilization of proteins precipitated with trichloroacetic acid in acetone from Catharanthus roseus yields 52% more spots after two-dimensional electrophoresis. Proteomics 1 (2001) 1345-1350
40. Jaillon O., Aury J.M., Noel B., Policriti A., Clepet C., Casagrande A., Choisne N., Aubourg S., Vitulo N., Jubin C., Vezzi A., Legeai F., Hugueney P., Dasilva C., Horner D., Mica E., Jublot D., Poulain J., Bruyere C., Billault A., Segurens B., Gouyvenoux M., Ugarte E., Cattonaro F., Anthouard V., Vico V., Del Fabbro C., Alaux M., Di Gaspero G., Dumas V., Felice N., Paillard S., Juman I., Moroldo M., Scalabrin S., Canaguier A., Le Clainche I., Malacrida G., Durand E., Pesole G., Laucou V., Chatelet P., Merdinoglu D., Delledonne M., Pezzotti M., Lecharny A., Scarpelli C., Artiguenave F., Pe M.E., Valle G., Morgante M., Caboche M., Adam-Blondon A.F., Weissenbach J., Quetier F., and Wincker P. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449 (2007) 463-467
41. Jaquinod M., Villiers F., Kieffer-Jaquinod S., Hugouvieux V., Bruley C., Garin J., and Bourguignon J. A proteomics dissection of Arabidopsis thaliana vacuoles isolated from cell culture. Mol. Cell. Proteomics 6 (2007) 394-412
42. Joardar V., Lindeberg M., Jackson R.W., Selengut J., Dodson R., Brinkac L.M., Daugherty S.C., Deboy R., Durkin A.S., Giglio M.G., Madupu R., Nelson W.C., Rosovitz M.J., Sullivan S., Crabtree J., Creasy T., Davidsen T., Haft D.H., Zafar N., Zhou L., Halpin R., Holley T., Khouri H., Feldblyum T., White O., Fraser C.M., Chatterjee A.K., Cartinhour S., Schneider D.J., Mansfield J., Collmer A., and Buell C.R. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J. Bacteriol. 187 (2005) 6488-6498
43. Jones A.M., Thomas V., Truman B., Lilley K., Mansfield J., and Grant M. Specific changes in the Arabidopsis proteome in response to bacterial challenge: differentiating basal and R-gene mediated resistance. Phytochemistry 65 (2004) 1805-1816
44. Jones A.M., Bennett M.H., Mansfield J.W., and Grant M. Analysis of the defence phosphoproteome of Arabidopsis thaliana using differential mass tagging. Proteomics 6 (2006) 4155-4165
45. Jung Y.H., Rakwal R., Agrawal G.K., Shibato J., Kim J.A., Lee M.O., Choi P.K., Jung S.H., Kim S.H., Koh H.J., Yonekura M., Iwahashi H., and Jwa N.S. Differential expression of defense/stress-related marker proteins in leaves of a unique rice blast lesion mimic mutant (blm). J. Proteome Res. 5 (2006) 2586-2598
46. Kawasaki T., Nam J., Boyes D.C., Holt III B.F., Hubert D.A., Wiig A., and Dangl J.L. A duplicated pair of Arabidopsis RING-finger E3 ligases contribute to the RPM1- and RPS2-mediated hypersensitive response. Plant J. 44 (2005) 258-270
47. Kazemi-Pour N., Condemine G., and Hugouvieux-Cotte-Pattat N. The secretome of the plant pathogenic bacterium Erwinia chrysanthemi. Proteomics 4 (2004) 3177-3186
48. Kim S.T., Cho K.S., Yu S., Kim S.G., Hong J.C., Han C.D., Bae D.W., Nam M.H., and Kang K.Y. Proteomic analysis of differentially expressed proteins induced by rice blast fungus and elicitor in suspension-cultured rice cells. Proteomics 3 (2003) 2368-2378
49. Kim H.S., Desveaux D., Singer A.U., Patel P., Sondek J., and Dangl J.L. The Pseudomonas syringae effector AvrRpt2 cleaves its C-terminally acylated target, RIN4, from Arabidopsis membranes to block RPM1 activation. Proc. Natl. Acad. Sci. USA 102 (2005) 6496-6501
50. Kim S.T., Kim S.G., Kang Y.H., Wang Y., Kim J.Y., Yi N., Kim J.K., Rakwal R., Koh H.J., and Ky K. Proteomics analysis of rice lesion mimic mutant (spl1) reveals tightly localized probenazole-induced protein (PBZ1) in cells undergoing programmed cell death. J. Proteome Res. 7 (2008) 1750-1760
51. Koller A., Washburn M.P., Lange B.M., Andon N.L., Deciu C., Haynes P.A., Hays L., Ulaszek R., Wei J., Wolters D., and Yates J.R. Proteomic survey of metabolic pathways in rice. Proc. Natl. Acad. Sci. USA 99 (2002) 11969-11974
52. Lee B.M., Park Y.J., Park D.S., Kang H.W., Kim J.G., Song E.S., Park I.C., Yoon U.H., Hahn J.H., Koo B.S., Lee G.B., Kim H., Park H.S., Yoon K.O., Kim J.H., Jung C.H., Koh N.H., Seo J.S., and Go S.J. The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucl. Acid. Res. 33 (2005) 577-586
53. Lopez M.F., Berggren K., Chernokalskaya E., Lazarev A., Robinson M., and Patton W.F. A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling. Electrophoresis 20 (2000) 3673-3683
54. Mackey D., Holt III B.F., Wiig A., and Dangl J.L. RIN4 interacts with Pseudomonas syringae type III effector molecules and is required for RPM1-mediated resistance. Cell 108 (2002) 743-754
55. Majeran W., Cai Y., Sun Q., and van Wijk K.J. Functional differentiation of bundle sheath and mesophyll maize chloroplasts determined by comparative proteomics. Plant Cell 17 (2005) 3111-3140
56. Majoul T., Bancel E., Triboï E., Ben Hamida J., and Branlard G. Proteomic analysis of the effect of heat stress on hexaploid wheat grain: characterization of heat-responsive proteins from non-prolamins fraction. Proteomics 4 (2004) 505-513
57. Maltman D.J., Gadd S.M., Simon W.J., and Slabas A.R. Differential proteomic analysis of the endoplasmic reticulum from developing and germinating seeds of castor (Ricinus communis) identifies seed protein precursors as significant components of the endoplasmic reticulum. Proteomics 7 (2007) 1513-1528
58. Manzano C., Abraham Z., Lopez-Torrejon G., and Del Pozo J.C. Identification of ubiquitinated proteins in Arabidopsis. Plant Mol. Biol. 68 (2008) 145-158
59. Marchand C., Le Marechal P., Meyer Y., and Decottignies P. Comparative proteomic approaches for the isolation of proteins interacting with thioredoxin. Proteomics 6 (2006) 6528-6537
60. Marra R., Ambrosino P., Carbone V., Vinale F., Woo S.L., Ruocco M., Ciliento R., Lanzuise S., Ferraioli S., Soriente I., Gigante S., Turra D., Fogliano V., Scala F., and Lorito M. Study of the three-way interaction between Trichoderma atroviride, plant and fungal pathogens by using a proteomic approach. Curr. Genet. 50 (2006) 307-321
61. Masaki S., Yamada T., Hirasawa T., Todaka D., and Kanekatsu M. Proteomic analysis of RNA-binding proteins in dry seeds of rice after fractionation by ssDNA affinity column chromatography. Biotechnol. Lett. 30 (2008) 955-960
62. Mehta A., and Rosato Y.B. Differentially expressed proteins in the interaction of Xanthomonas axonopodis pv. citri with leaf extract of the host plant. Proteomics 1 (2001) 1111-1118
63. Mehta A., Brasileiro A.C., Souza D.S., Romano E., Campos M.A., Grossi-de-Sa M.F., Silva M.S., Franco O.L., Fragoso R.R., Bevitori R., and Rocha T.L. plant-pathogen interactions: what is proteomics telling us?. FEBS J. 275 (2008) 3731-3746
64. Michelmore R. Molecular approaches to manipulation of disease resistance genes. Annu. Rev. Phytopathol. 33 (1995) 393-427
65. Ming R., Hou S., Feng Y., Yu Q., Dionne-Laporte A., Saw J.H., Senin P., Wang W., Ly B.V., Lewis K.L., Salzberg S.L., Feng L., Jones M.R., Skelton R.L., Murray J.E., Chen C., Qian W., Shen J., Du P., Eustice M., Tong E., Tang H., Lyons E., Paull R.E., Michael T.P., Wall K., Rice D.W., Albert H., Wang M.L., Zhu Y.J., Schatz M., Nagarajan N., Acob R.A., Guan P., Blas A., Wai C.M., Ackerman C.M., Ren Y., Liu C., Wang J., Na J.K., Shakirov E.V., Haas B., Thimmapuram J., Nelson D., Wang X., Bowers J.E., Gschwend A.R., Delcher A.L., Singh R., Suzuki J.Y., Tripathi S., Neupane K., Wei H., Irikura B., Paidi M., Jiang N., Zhang W., Presting G., Windsor A., Navajas-Perez R., Torres M.J., Feltus F.A., Porter B., Li Y., Burroughs A.M., Luo M.C., Liu L., Christopher D.A., Mount S.M., Moore P.H., Sugimura T., Jiang J., Schuler M.A., Friedman V., Mitchell-Olds T., Shippen D.E., dePamphilis C.W., Palmer J.D., Freeling M., Paterson A.H., Gonsalves D., Wang L., and Alam M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452 (2008) 991-996
66. Monteiro-Vitorello CB C.L., Van Sluys M.A., Kitajima J.P., Truffi D., do Amaral A.M., Harakava R., de Oliveira J.C., Wood D., de Oliveira M.C., Miyaki C., Takita M.A., da Silva A.C., Furlan L.R., Carraro D.M., Camarotte G., Almeida Jr. N.F., Carrer H., Coutinho L.L., El-Dorry H.A., Ferro M.I., Gagliardi P.R., Giglioti E., Goldman M.H., Goldman G.H., Kimura E.T., Ferro E.S., Kuramae E.E., Lemos E.G., Lemos M.V., Mauro S.M., Machado M.A., Marino C.L., Menck C.F., Nunes L.R., Oliveira R.C., Pereira G.G., Siqueira W., de Souza A.A., Tsai S.M., Zanca A.S., Simpson A.J., Brumbley S.M., and Setúbal J.C. The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli. Mol. Plant Microbe Interact. 17 (2004) 827-836
67. Nagabhushan N., Gulyas A., and Zalik S. Comparison of plant cytoplasmic ribosomal proteins by two-dimensional polyacrylamide gel electrophoresis. Plant Physiol. 53 (1974) 516-518
68. Ochiai H., Inoue Y., Takeya M., Sasaki A., and Kaku H. Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. Jpn. Agr. Res. Q. 39 (2005) 275-287
69. Oh I.S., Park A.R., Bae M.S., Kwon S.J., Kim Y.S., Lee J.E., Kang N.Y., Lee S., Cheong H., and Park O.K. Secretome analysis reveals an Arabidopsis lipase involved in defense against Alternaria brassicicola. Plant Cell 17 (2005) 2832-2847
70. Ong S., Foster L.J., and Mann M. Mass spectrometric-based approaches in quantitative proteomics. Methods 29 (2003) 124-130
71. Orrick L.R., Olson M.O.J., and Busch H. Comparison of nucleolar proteins of normal rat liver and Novikoff hepatoma ascites cells by two-dimensional polyacrylamide gel electrophoresis. Proc. Natl. Acad. Sci. USA 70 (1973) 1316-1320
72. Pandey A., Chakraborty S., Datta A., and Chakraborty N. Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.). Mol. Cell. Proteomics 7 (2008) 88-107
73. Park J.W., Lee S.G., Song J.Y., Joo J.S., Chung M.J., Kim S.C., Youn H.S., Kang H.L., Baik S.C., Lee W.K., Cho M.J., and Rhee K.H. Proteomic analysis of Helicobacter pylori cellular proteins fractionated by ammonium sulfate precipitation. Electrophoresis 29 (2008) 2891-2903
74. Patton W.F. Detection technologies in proteome analysis. J. Chromatogr. B - Anal. Technol. Biomed. Life Sci. 771 (2002) 3-31
75. Peck S.C., Nuhse T.S., Hess D., Iglesias A., Meins F., and Boller T. Directed proteomics identifies a plant-specific protein rapidly phosphorylated in response to bacterial and fungal elicitors. Plant Cell 13 (2001) 1467-1475
76. Project, International Rice Genome Sequencing. The map-based sequence of the rice genome. Nature 436 (2005) 793-800
77. Qian W., Jia Y., Ren S.X., He Y.Q., Feng J.X., Lu L.F., Sun Q., Ying G., Tang D.J., Tang H., Wu W., Hao P., Wang L., Jiang B.L., Zeng S., Gu W.Y., Lu G., Rong L., Tian Y., Yao Z., Fu G., Chen B., Fang R., Qiang B., Chen Z., Zhao G.P., Tang J.L., and He C. Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris. Genome Res. 15 (2005) 757-767
78. Quirino B.F., and Bent A.F. Deciphering host resistance and pathogen virulence: the Arabidopsis/Pseudomonas interaction as a model. Mol. Plant Pathol. 4 (2003) 517-530
79. Quirino B.F., Genger R., Ham J.H., Zabala G., and Bent A.F. Identification and functional analysis of Arabidopsis proteins that interact with resistance gene product RPS2 in yeast. Physiol. Mol. Plant Pathol. 65 (2004) 257-267
80. Rajjou L., Belghazi M., Huguet R., Robin C., Moreau A., Job C., and Job D. Proteomic investigation of the effect of salicylic acid on Arabidopsis seed germination and establishment of early defense mechanisms. Plant Physiol. 141 (2006) 910-923
81. Rampitsch C., Bykova N.V., McCallum B., Beimcik E., and Ens W. Analysis of the wheat and Puccinia triticina (leaf rust) proteomes during a susceptible host-pathogen interaction. Proteomics 6 (2006) 1897-1907
82. Reinhardt J.A., Baltrus D.A., Nishimura M.T., Jeck W.R., Jones C.D., and Dangl J.L. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res. 19 (2009) 294-305
83. Rep M., Dekker H.L., Vossen J.H., de Boer A.D., Houterman P.M., Speijer D., Back J.W., de Koster C.G., and Cornelissen B.J. Mass spectrometric identification of isoforms of PR proteins in xylem sap of fungus-infected tomato. Plant Physiol. 130 (2002) 904-917
84. Reumann S., Babujee L., Ma C., Wienkoop S., Siemsen T., Antonicelli G.E., Rasche N., Luder F., Weckwerth W., and Jahn O. Proteome analysis of Arabidopsis leaf peroxisomes reveals novel targeting peptides, metabolic pathways, and defense mechanisms. Plant Cell 19 (2007) 3170-3193
85. Roberto S.R., Coutinho A., De Lima J.E.O., Miranda V.S., and Carlos E.F. Transmissão de Xyllela fastidiosa pelas cigarrinhas Dilobopterus costalimai, Acrogonia terminalis e Oncometopia facialis em citros. Fitopatol. Bras. 21 (1996) 517-518
86. Romeis T. Protein kinases in the plant defence response. Curr. Opin. Plant Biol. 4 (2001) 407-414
87. Romeis T., Ludwig A.A., Martin R., and Jones J.D. Calcium-dependent protein kinases play an essential role in a plant defence response. EMBO J. 20 (2001) 5556-5567
88. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., Khainovski N., Pillai S., Dey S., Daniels S., Purkayastha S., Juhasz P., Martin S., Bartlet-Jones M., He F., Jacobson A., and Pappin D.J. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3 (2004) 1154-1169
89. Rossignol M., Peltier J.B., Mock H.P., Matros A., Maldonado A.M., and Jorrin J.V. Plant proteome analysis: a 2004-2006 update. Proteomics 6 (2006) 5529-5548
90. Salanoubat M., Genin S., Artiguenave F., Gouzy J., Mangenot S., Arlat M., Billault A., Brottier P., Camus J.C., Cattolico L., Chandler M., Choisne N., Claudel-Renard C., Cunnac S., Demange N., Gaspin C., Lavie M., Moisan A., Robert C., Saurin W., Schiex T., Siguier P., Thebault P., Whalen M., Wincker P., Levy M., Weissenbach J., and Boucher C.A. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415 (2002) 497-502
91. 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., Madupu R., Puiu D., Radune D., Shumway M., Trapnell C., Aparna G., Jha G., Pandey A., Patil P.B., Ishihara H., Meyer D.F., Szurek B., Verdier V., Koebnik R., Dow J.M., Ryan R.P., Hirata H., Tsuyumu S., Won Lee S., Ronald P.C., Sonti R.V., Van Sluys M.A., Leach J.E., White F.F., and Bogdanove A.J. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genom. 9 (2008) 204
92. Schmidt U.G., Endler A., Schelbert S., Brunner A., Schnell M., Neuhaus H.E., Marty-Mazars D., Marty F., Baginsky S., and Martinoia E. Novel tonoplast transporters identified using a proteomic approach with vacuoles isolated from cauliflower buds. Plant Physiol. 145 (2007) 216-229
93. Simpson A.J., Reinach F.C., Arruda P., Abreu F.A., Acencio M., Alvarenga R., Alves L.M., Araya J.E., Baia G.S., Baptista C.S., Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R., Bueno M.R., Camargo A.A., Camargo L.E., Carraro D.M., Carrer H., Colauto N.B., Colombo C., Costa F.F., Costa M.C., Costa-Neto C.M., Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H., Facincani A.P., Ferreira A.J., Ferreira V.C., Ferro J.A., Fraga J.S., Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H., Goldman M.H., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D., Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E., Laigret F., Lambais M.R., Leite L.C., Lemos E.G., Lemos M.V., Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M., Madeira H.M., Marino C.L., Marques M.V., Martins E.A., Martins E.M., Matsukuma A.Y., Menck C.F., Miracca E.C., Miyaki C.Y., Monteriro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L., Netto L.E., Nhani Jr. A., Nobrega F.G., Nunes L.R., Oliveira M.A., de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R., Pereira G.A., Pereira Jr. H.A., Pesquero J.B., Quaggio R.B., Roberto P.G., Rodrigues V., de M.R.A.J., de Rosa Jr. V.E., de Sa R.G., Santelli R.V., Sawasaki H.E., da Silva A.C., da Silva A.M., da Silva F.R., da Silva Jr. W.A., da Silveira J.F., Silvestri M.L., Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D., Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S., Vettore A.L., Zago M.A., Zatz M., Meidanis J., and Setubal J.C. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature 406 (2000) 151-159
94. Siuzdak G. Mass Spectrometry for Biotechnology (1996), Academic Press, San Diego
95. Slater S.C., Goldman B.S., Goodner B., Setubal J.C., Farrand S.K., Nester E.W., Burr T.J., Banta L., Dickerman A.W., Paulsen I., Otten L., Suen G., Welch R., Almeida N.F., Arnold F., Burton O.T., Du Z., Ewing A., Godsy E., Heisel S., Houmiel K.L., Jhaveri J., Lu J., Miller N.M., Norton S., Chen Q., Phoolcharoen W., Ohlin V., Ondrusek D., Pride N., Stricklin S.L., Sun J., Wheeler C., Wilson L., Zhu H., and Wood D.W. Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J. Bacteriol. 191 8 (2009) 2501-2511
96. In: Sparkman O.D. (Ed). Mass Spectrometry Desk Reference (2000), Global View Publications, Pittsburgh
97. Stokstad E. Poplar tree sequence yields genome double take. Science 5793 (2006) 1556
98. Sussman M.R., Amasino R.M., Young J.C., Krysan P.J., and Austin-Phillips S. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiol. 124 (2000) 1465-1467
99. Tahara S.T., Mehta A., and Rosato Y.B. Proteins induced by Xanthomonas axonopodis pv. Passiflorae with leaf extract of the host plant (Passiflorae edulis). Proteomics 3 (2003) 95-102
100. Takemoto D., and Jones D.A. Membrane release and destabilization of Arabidopsis RIN4 following cleavage by Pseudomonas syringae AvrRpt2. Mol. Plant Microbe Interact. 18 (2005) 1258-1268
101. Thieme F., Koebnik R., Bekel T., Berger C., Boch J., Buttner D., Caldana C., Gaigalat L., Goesmann A., Kay S., Kirchner O., Lanz C., Linke B., McHardy A.C., Meyer F., Mittenhuber G., Nies D.H., Niesbach-Klosgen U., Patschkowski T., Ruckert C., Rupp O., Schneiker S., Schuster S.C., Vorholter F.J., Weber E., Puhler A., Bonas U., Bartels D., and Kaiser O. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. Vesicatoria revealed by the complete genome sequence. J. Bacteriol. 187 (2005) 7254-7266
102. Tsunezuka H., Fujiwara M., Kawasaki T., and Shimamoto K. Proteome analysis of programmed cell death and defense signaling using the rice lesion mimic mutant cdr2. Mol. Plant Microbe Interact. 18 (2005) 52-59
103. Tuskan G.A., Difazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., Schein J., Sterck L., Aerts A., Bhalerao R.R., Bhalerao R.P., Blaudez D., Boerjan W., Brun A., Brunner A., Busov V., Campbell M., Carlson J., Chalot M., Chapman J., Chen G.L., Cooper D., Coutinho P.M., Couturier J., Covert S., Cronk Q., Cunningham R., Davis J., Degroeve S., Dejardin A., Depamphilis C., Detter J., Dirks B., Dubchak I., Duplessis S., Ehlting J., Ellis B., Gendler K., Goodstein D., Gribskov M., Grimwood J., Groover A., Gunter L., Hamberger B., Heinze B., Helariutta Y., Henrissat B., Holligan D., Holt R., Huang W., Islam-Faridi N., Jones S., Jones-Rhoades M., Jorgensen R., Joshi C., Kangasjarvi J., Karlsson J., Kelleher C., Kirkpatrick R., Kirst M., Kohler A., Kalluri U., Larimer F., Leebens-Mack J., Leple J.C., Locascio P., Lou Y., Lucas S., Martin F., Montanini B., Napoli C., Nelson D.R., Nelson C., Nieminen K., Nilsson O., Pereda V., Peter G., Philippe R., Pilate G., Poliakov A., Razumovskaya J., Richardson P., Rinaldi C., Ritland K., Rouze P., Ryaboy D., Schmutz J., Schrader J., Segerman B., Shin H., Siddiqui A., Sterky F., Terry A., Tsai C.J., Uberbacher E., Unneberg P., Vahala J., Wall K., Wessler S., Yang G., Yin T., Douglas C., Marra M., Sandberg G., Van de Peer Y., and Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313 (2006) 1596-1604
104. Tyler B.M., Tripathy S., Zhang X., Dehal P., Jiang R.H., Aerts A., Arredondo F.D., Baxter L., Bensasson D., Beynon J.L., Chapman J., Damasceno C.M., Dorrance A.E., Dou D., Dickerman A.W., Dubchak I.L., Garbelotto M., Gijzen M., Gordon S.G., Govers F., Grunwald N.J., Huang W., Ivors K.L., Jones R.W., Kamoun S., Krampis K., Lamour K.H., Lee M.K., McDonald W.H., Medina M., Meijer H.J., Nordberg E.K., Maclean D.J., Ospina-Giraldo M.D., Morris P.F., Phuntumart V., Putnam N.H., Rash S., Rose J.K., Sakihama Y., Salamov A.A., Savidor A., Scheuring C.F., Smith B.M., Sobral B.W., Terry A., Torto-Alalibo T.A., Win J., Xu Z., Zhang H., Grigoriev I.V., Rokhsar D.S., and Boore J.L. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313 (2006) 1261-1266
105. Van Sluys M.A., de Oliveira M.C., Monteiro-Vitorello C.B., Miyaki C.Y., Furlan L.R., Camargo L.E., da Silva A.C., Moon D.H., Takita M.A., Lemos E.G., Machado M.A., Ferro M.I., da Silva F.R., Goldman M.H., Goldman G.H., Lemos M.V., El-Dorry H., Tsai S.M., Carrer H., Carraro D.M., de Oliveira R.C., Nunes L.R., Siqueira W.J., Coutinho L.L., Kimura E.T., Ferro E.S., Harakava R., Kuramae E.E., Marino C.L., Giglioti E., Abreu I.L., Alves L.M., do Amaral A.M., Baia G.S., Blanco S.R., Brito M.S., Cannavan F.S., Celestino A.V., da Cunha A.F., Fenille R.C., Ferro J.A., Formighieri E.F., Kishi L.T., Leoni S.G., Oliveira A.R., Rosa Jr. V.E., Sassaki F.T., Sena J.A., de Souza A.A., Truffi D., Tsukumo F., Yanai G.M., Zaros L.G., Civerolo E.L., Simpson A.J., Almeida Jr. N.F., Setubal J.C., and Kitajima J.P. Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J. Bacteriol. 185 (2003) 1018-1026
106. Velasco R., Zharkikh A., Troggio M., Cartwright D.A., Cestaro A., Pruss D., Pindo M., Fitzgerald L.M., Vezzulli S., Reid J., Malacarne G., Iliev D., Coppola G., Wardell B., Micheletti D., Macalma T., Facci M., Mitchell J.T., Perazzolli M., Eldredge G., Gatto P., Oyzerski R., Moretto M., Gutin N., Stefanini M., Chen Y., Segala C., Davenport C., Dematte L., Mraz A., Battilana J., Stormo K., Costa F., Tao Q., Si-Ammour A., Harkins T., Lackey A., Perbost C., Taillon B., Stella A., Solovyev V., Fawcett J.A., Sterck L., Vandepoele K., Grando S.M., Toppo S., Moser C., Lanchbury J., Bogden R., Skolnick M., Sgaramella V., Bhatnagar S.K., Fontana P., Gutin A., Van de Peer Y., Salamini F., and Viola R. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2 (2007) e1326
107. Vorholter F.J., Schneiker S., Goesmann A., Krause L., Bekel T., Kaiser O., Linke B., Patschkowski T., Ruckert C., Schmid J., Sidhu V.K., Sieber V., Tauch A., Watt S.A., Weisshaar B., Becker A., Niehaus K., and Puhler A. The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis. J. Biotechnol. 134 (2008) 33-45
108. Washburn M.P., Wolters D., and Yates III J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19 (2001) 242-247
109. Watt S.A., Wilke A., Patschkowski T., and Niehaus K. Comprehensive analysis of the extracellular proteins from Xanthomonas campestris pv. campestris B100. Proteomics 5 (2005) 153-167
110. Wong J.H., Cai N., Balmer Y., Tanaka C.K., Vensel W.H., Hurkman W.J., and Buchanan B.B. Thioredoxin targets of developing wheat seeds identified by complementary proteomic approaches. Phytochemistry 65 (2004) 1629-1640
111. Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K., Zhou Y., Chen L., Wood G.E., Almeida Jr. N.F., Woo L., Chen Y., Paulsen I.T., Eisen J.A., Karp P.D., Bovee Sr. D., Chapman P., Clendenning J., Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R., Li M.J., McClelland E., Palmieri A., Raymond C., Rouse G., Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y., Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S., Hendrick C., Zhao Z.Y., Dolan M., Chumley F., Tingey S.V., Tomb J.F., Gordon M.P., Olson M.V., and Nester E.W. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294 (2001) 2317-2323
112. Yajima W., and Kav N.N. The proteome of the phytopathogenic fungus Sclerotinia sclerotiorum. Proteomics 6 (2006) 5995-6007
113. Yan S.P., Zhang Q.Y., Tang Z.C., Su W.A., and Sun W.N. Comparative proteomic analysis provides new insights into chilling stress responses in rice. Mol. Cell. Proteomics 5 (2006) 484-496
114. Yang C.H., and Ho G.D. Resistance and susceptibility of Arabidopsis thaliana to bacterial wilt caused by Ralstonia solanacearum. Phytopathology 88 (1998) 330-334
115. Yang Q., Wang Y., Zhang J., Shi W., Qian C., and Peng X. Identification of aluminum-responsive proteins in rice roots by a proteomic approach: cysteine synthase as a key player in Al response. Proteomics 7 (2007) 737-749
116. Zeigler, R.S., Leong, S.A., Teeng, P.S., 1994. Rice Blast Disease. CAB International, Wallingford.