Optimized protein extraction methods for proteomic analysis of Rhizoctonia solani

Mycologia

Volumn 100, Issue 6, 2008, Pages 867-875

  Lakshman, Dilip K ^a   Natarajan, Savithiry S ^b   Lakshman, Sukla ^b   Garrett, Wesley M ^c   Dhar, Arun K ^d  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b Soybean Genomics and Improvement Laboratory   (United States)

^c Animal Biosciences and Biotechnology Laboratory   (United States)

^d Advanced BioNutrition Corporation   (United States)

Author keywords

2 D PAGE; MALDI TOFS MS; Proteomics; Rhizoctonia solani; Thanatephorus cucumeris

Indexed keywords

EXTRACTION METHOD; FUNGAL DISEASE; FUNGUS; MONOCOTYLEDON; OPTIMIZATION; PROTEIN; PROTEOMICS; SOIL ORGANIC MATTER;

FUNGI; HYPHOMYCETES; ORCHIDACEAE; RHIZOCTONIA; THANATEPHORUS CUCUMERIS;

ACETONE; FUNGAL PROTEIN; PHOSPHATE; TRICHLOROACETIC ACID;

ARTICLE; CHEMISTRY; EVALUATION; HOST PATHOGEN INTERACTION; HYPHOMYCETES; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; PLANT DISEASE; PLANT ROOT; PRECIPITATION; PROTEOMICS; SOLUBILITY; TECHNIQUE; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ACETONE; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; FUNGAL PROTEINS; HOST-PATHOGEN INTERACTIONS; METHODS; PHOSPHATES; PLANT DISEASES; PLANT ROOTS; PRECIPITATION; PROTEOMICS; RHIZOCTONIA; SOLUBILITY; TRICHLOROACETIC ACID;

EID: 63449136441     PISSN: 00275514     EISSN: 15572536     Source Type: Journal    
DOI: 10.3852/08-065     Document Type: Article

References (55)

1. Akino S, Ogoshi A. 1995. Pathogenicity and host specificity in Rhizoctonia solani. In: Singh US, ed. Pathogenesis and host specificity in plant diseases, histopathological, biochemical, genetic and molecular bases. Vol. II Eukaryotes. New York: Elsevier Science Inc. p 7-49.
2. Anderson NA. 1982. The genetics and pathology of Rhizoctonia solani. Ann Rev Phytopathology 20:329-347.
3. Asif AR, Oellerich M, Amstrong VW, Riemenschneider B, Monod M, Reichard U. 2006. Proteome of conidial surface associated proteins of Aspergillus fumigatus reflecting potential vaccine candidates and allergens. J Proteome Res 5:954-962.
4. Balai G, Kowsari M. 2004. Pectic zymogram variation and pathogenicity of Rhizoctonia solani AG-4 to bean (Phaseolus vulgaris) isolates in Isfahn, Iran. Myco-pathologia 158:377-384.
5. Bertagnolli BL, Soglio FKD, Sinclair JB. 1996. Extracellular enzyme profiles of the fungal pathogen Rhizoctonia solani isolate 2B-12 and of two antagonists, Bacillus megaterium strain B153-2-2 and Trichoderma harzianum isolate Th008. I. Possible correlations with inhibition of growth and biocontrol. Physiol Mol Plant Path 48:145-160.
6. Birrel GW, Brown JA, Wu HI, Giaever G, Chu AM, Davis RW. 2002. Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. PNAS USA 99: 8778-83.
7. Blencowe BJ, Khanna M. 2007. RNA in control. Nature 447: 391-393.
8. Bora PS, Ribeiro D. 2004. Note: Influence of pH on the extraction yield and functional properties of Macadamia (Macadamia integrofolia) protein isolates. Food Sc Tech Int 10:263-267.
9. -, Hardy GESJ, O'Brien PA. 2005. Laccase activity and maceration of lupin tissue by Rhizoctonia solani is inhibited by arginine. Australasian Plant Path 34:591-594.
10. Bradford MM. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248-254.
11. Carling DE, Baird RE, Gitaitis RD, Brainard KA, Kuninaga S. 2002. Characterization of AG-13, a newly reported anastomosis group of Rhizoctonia solani. Phytopathology 92:893-899.
12. Cheah MT, Wachter A, Sudarsan N, Breaker RR. 2007. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447:497-500.
13. Cubeta MA, Vilgalys R. 2001. Rhizoctonia. In: Ledeber J, ed. Encyclopedia of microbiology. Vol. 4. San Diego: Academic Press. p 109-116.
14. Davison DB. 2002. The number of human genes and proteins. Nanotech 2:6-11.
15. Elbakali AM, Lilja A, Hanutula J, Martin MP. 2003. Identification of Spanish isolates of Rhizoctonia solani from potato by anastomosis grouping, ITS-RFLP and RAMS fingerprinting. Phytopathol Mediterr 42:167-176.
16. Evangelista RL, Kusnadi AR, Howard JA, Nikolov ZL. 1998. Process and economic evaluation of the extraction and purification of recombinant β-glucuronidase from transgenic corn. Biotechnol Prog 14:607-614.
17. Dodman RL, Flintze NT. 1970. The mechanism and physiology of plant penetration by Rhizoctonia solani. In: Parmeter JR, ed. Rhizoctonia solani, biology and pathology. Berkeley: Univ California Press. p 149-160.
18. Dubey H, Grover A. 2001. Current initiatives in proteomics research: the plant perspective. Curr Sci 80:262-269.
19. Fernández-Acero FJ, Jorge I, Calvo E, Vallejo I, Carbu M, Camafeita E, Lopez JA, Cantoral JM, Jorrin J. 2006. Two-dimensional electrophoresis protein profile of the phytopathogenic fungus Botrytis cinerea. Proteomics 6: S88-S96.
20. Gao L, Smith FA, Smith SE. 2006. The rmc locus does not affect plant interactions or defence-related gene expression when tomato (Solanum lycopersicum) is infected with the root fungal parasite, Rhizoctonia. Funct Plant Biol 33(3):289-296.
21. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387-391.
22. Gorg A, Obermaier C, Boguth G, Harder A, Scheibe B, Wildgruber R, Weiss W. 2000. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21:1037-1053.
23. Gygi SP, Rochon Y, Franza BR, Aebersold R. 1999. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720-30.
24. Habermann B, Oegema J, Sunyaev S, Shevchenko A. 2004. The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches. Mol Cell Proteomics 3:238-49.
25. Jia J, Lakshman DK, Tavantzis SM. 1997. Association of distinct double-stranded RNAs with enhanced or diminished virulence in Rhizoctonia solani infecting potato. Mol Plant-Microbe Interact 10:1002-1009.
26. -, -, -. 1998. A virulence-associated, 6.4-kb, double-stranded RNA from Rhizoctonia solani is phylo-genetically related to plant bromoviruses and electron transport enzymes. Mol Plant-Microbe Interact 11:601-609.
27. Keijer J. 1996. The initial steps of the infection process in Rhizoctonia solani. In: Sneh B, Jabaji-Hare S, Neate S, Dijst G, eds. Rhizoctonia species: taxonomy, molecular biology, ecology, pathology and disease control. Dordrecht: Kluwer Academic Publishers. p 149-162.
28. Kim Y, Nandakumar MP, Marten MR. 2007. Proteomics of filamentous fungi. Trends Biotechnol 25:395-400.
29. Laemmli UK. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
30. Lakshman DK, Tavantzis SM. 1994. Spontaneous appearance of genetically distinct double-stranded RNA elements in Rhizoctonia solani. Phytopathology 84: 633-639.
31. -, Jian J, Tavantzis SM. 1998. A double-stranded RNA element from a hypovirulent strain of Rhizoctonia solani occurs in DNA form and is genetically related to the pentafunctional AROM protein of the shikimate pathway. PNAS USA 95:6425-6429.
32. -, Liu C, Mishra PK, Tavantzis SM. 2006. Characterization of the arom gene in Rhizoctonia solani, and transcription patterns under stable and induced hypovirulence conditions. Curr Genet 49:166-177.
33. Lehesranta SJ, Davies HV, Shepherd LV, Nunan N, McNicol JW, Auriola S, Koistinen KM, Suomalainen S, Kokko HI, Kärenlampi SO. 2005. Comparison of tuber proteomes of potato varieties, landraces and genetically modified lines. Plant Physiol 138(3):1690-1699.
34. Lewis JA, Papavizas GC. 1987. Reduction of inoculum of Rhizoctonia solani in soil by germlings of Trichoderma hamatum. Soil Biol Biochem 19:195-201.
35. -, -. 1991. Biocontrol of plant diseases: the approach for tomorrow. Crop Protect 10:95-102.
36. Liska AJ, Shevchenko A. 2003. Expanding the organismal scope of proteomics: cross-species protein identification by mass spectrometry and its implications. Proteo-mics 3:19-28.
37. Lumsden RD, Lewis JA, Fravel DR. 1995. Formulation and delivery of biocontrol agents for use against soilborne plant pathogens. In: Hall FR, Barry JW, eds. Biorational pest control agents: formulation and delivery. Washington DC: American Chemical Society. p 166-182.
38. Manibhushanrao K, Zuber M, Manian S. 1981. Phytotoxic metabolites of Rhizoctonia solani. J Sci Ind Res 40:602.
39. Marra R, Ambrosino P, Carbone V, Vinale F, Woo SL, Ruocco M, Ciliento R, Lanzuise S, Ferraioli S, Soriente I, Gigante S, Turrà D, Fogliano V, Scala F, Lorito M. 2006. Study of the three-way interaction between Trichoderma atroviride, plant and fungal pathogens by using a proteomic approach. Curr Genet 50:307-321.
40. Medina ML, Haynes PA, Breci L, Francisco WA. 2005. Analysis of secreted proteins from Aspergillus flavus. Proteomics 5:3153-3161.
41. -, Kiernan UA, Francisco WA. 2004. Proteomic analysis of rutin-induced secreted proteins from Aspergillus flavus. Fungal Genet Biol 41:327-335.
42. Nandakumar MP, Marten MR. 2002. Comparison of lysis methods and preparation protocols for one- and two-dimensional electrophoresis of Aspergillus oryzae intracellular proteins. Electrophoresis 23:2194-2202.
43. Natarajan S, Xu C, Caperna TJ, Garrett WM. 2005. Comparison of protein solubilization methods suitable for proteomic analysis of soybean seed proteins. Anal Biochem 342:214-220.
44. Newsholme SJ, Maleeft BF, Steiner S, Anderson NL, Schwartz LW. 2000. Two-dimensional electrophoresis of liver proteins: characterization of a drug-induced hepatomegaly in rats. Electrophoresis 21:2122-2128.
45. Paper JM, Scott-Craig JS, Adhikari ND, Cuomo CA, Walton JD. 2007. Comparative proteomics of extracellular proteins in vitro and in planta from the pathogenic fungus Fusarium graminearum. Proteomics 7:3171-83.
46. Perkins DN, Pappinl DJC, Creasy DM, Cottrell JS. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551-3567.
47. Rampitsch C, Bykova NV, McCallum B, Beimcik E, Ens W. 2006. Analysis of the wheat and Puccinia triticina (leaf rust) proteomes during a susceptible host-pathogen interaction. Proteomics 6:1897-1907.
48. Rodríguez-Piñeiro AM, Álvarez-Chaver P, Martínez-Zorzano VS, Rodríguez-Berrocal FJ, de la Cadena MP. 2007. Relevance of protein isoforms in proteomic studies. Curr Proteomics 4:235-252.
49. Ruebelt MC, Leimgruber NK, Lipp M, Reynolds TL, Nemeth MA, Astwood JD, Engel KH, Jany KD. 2006. Application of two-dimensional gel electrophoresis to interrogate alterations in the proteome of genetically modified crops 1. Assessing analytical validation. J Agric Food Chem 54:2154-61.
50. Shimizu M, Wariishi H. 2005. Development of a sample preparation method for fungal proteomics. FEMS Microbiol Lett 247:17.
51. Sneh B, Burpee LL, Ogoshi A. 1991. Identification of Rhizoctonia species. St Paul: The American Phytopath-ological Society.
52. Suárez MB, Sanz L, Chamorro MI, Rey M, González FJ, Llobell A, Monte E. 2005. Proteomic analysis of secreted proteins from Trichoderma harzianum. Identification of a fungal cell wall-induced aspartic protease. Fungal Genet Biol 42:924-934.
53. Thurston G, Regan S, Rampitsch C, Xing T. 2005. Proteomic and phosphoproteomic approaches to understand plant-pathogen interactions. Physiol Mol Plant Path 66:3-11.
54. Tsai-Morris CH, Sheng Y, Lee E, Lei Kj, Dufau ML. 2004. Gonadotropin-regulated testicular RNA helicase (GRTH/Ddx25) is essential for spermatid development and completion of spermatogenesis. PNAS USA 101: 6373-6378.
55. Weinhold AR, Sinclair JB. 1996. Rhizoctonia solani: penetration, colonization and host response. In: Sneh B, Jabaji-Hare S, Neate S, Dijst G, eds. Rhizoctonia species: taxonomy, molecular biology, ecology, pathology and disease control. Dordrecht: Kluwer Academic Publishers. p 163-174.