Fungal proteomics: From identification to function

FEMS Microbiology Letters

Volumn 321, Issue 1, 2011, Pages 1-9

  Doyle, Sean ^a  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

Aspergillus fumigatus; Fungal proteomics; Gliotoxin; LC MS; MALDI ToF; Protein mass spectrometry

Indexed keywords

FUNGAL PROTEIN; GLIOTOXIN; THIOREDOXIN; THIOREDOXIN REDUCTASE;

ASPERGILLUS FUMIGATUS; BIOTECHNOLOGICAL PRODUCTION; COMPARATIVE STUDY; FUNCTIONAL GENOMICS; FUNGAL EXAMINATION; FUNGAL GENE; FUNGAL VIRULENCE; GENE EXPRESSION REGULATION; HUMAN; IMMUNOREACTIVITY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEOMICS; RNA SEQUENCE; SHORT SURVEY; TRANSCRIPTOMICS;

FUNGAL PROTEINS; FUNGI; GENE EXPRESSION REGULATION, FUNGAL; PROTEOME; PROTEOMICS;

ASPERGILLUS FUMIGATUS; FUNGI; HEXAPODA;

EID: 79959978277     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2011.02292.x     Document Type: Short Survey

References (63)

1. Adav SS, Li AA, Manavalan A, Punt P & Sze SK (2010) Quantitative iTRAQ secretome analysis of Aspergillus niger reveals novel hydrolytic enzymes. J Proteome Res 9: 3932-3940.
2. 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.
3. Barros BH, da Silva SH, dos ReisMarques Edos R, Rosa JC, Yatsuda AP, Roberts DW & Braga GU (2010) A proteomic approach to identifying proteins differentially expressed in conidia and mycelium of the entomopathogenic fungus Metarhizium acridum. Fungal Biol 114: 572-579.
4. Bouws H, Wattenberg A & Zorn H (2008) Fungal secretomes - nature's toolbox for white biotechnology. Appl Microbiol Biot 80: 381-388.
5. Bowyer P & Denning DW (2007) Genomic analysis of allergen genes in Aspergillus spp: the relevance of genomics to everyday research. Med Mycol 45: 17-26.
6. Braaksma M, Martens-Uzunova ES, Punt PJ & Schaap PJ (2010) An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data. BMC Genomics 11: 584.
7. Brewis IA & Brennan P (2010) Proteomics technologies for the global identification and quantification of proteins. Adv Protein Chem Struct Biol 80: 1-44.
8. Bruns S, Seidler M, Albrecht D, Salvenmoser S, Remme N, Hertweck C, Brakhage AA, Kniemeyer O & Müller FM (2010) Functional genomic profiling of Aspergillus fumigatus biofilm reveals enhanced production of the mycotoxin gliotoxin. Proteomics 10: 3097-3107.
9. Burns C, Geraghty R, Neville C, Murphy A, Kavanagh K & Doyle S (2005) Identification, cloning, and functional expression of three glutathione transferase genes from Aspergillus fumigatus. Fungal Genet Biol 42: 319-327.
10. Cagas SE, Jain MR, Li H & Perlin DS (2011) Profiling the Aspergillus fumigatus proteome in response to caspofungin. Antimicrob Agents Ch 55: 146-154.
11. Carberry S, Neville CM, Kavanagh KA & Doyle S (2006) Analysis of major intracellular proteins of Aspergillus fumigatus by MALDI mass spectrometry: identification and characterisation of an elongation factor 1B protein with glutathione transferase activity. Biochem Biophys Res Commun 314: 1096-1104.
12. Costa V, Angelini C, De Feis I & Ciccodicola A (2010) Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol 2010: 853916.
13. Dagenais TR & Keller NP (2009) Pathogenesis of Aspergillus fumigatus in invasive Aspergillosis. Clin Microbiol Rev 22: 447-465.
14. Datta K, Bartlett KH, Baer R et al. (2009) Spread of Cryptococcus gattii into Pacific Northwest region of the United States. Emerg Infect Dis 15: 1185-1191.
15. Davis C, Carberry S, Schrettl M, Singh I, Stephens JC, Barry SM, Kavanagh K, Challis GL, Brougham D & Doyle S (2011) The role of glutathione S-transferase GliG in gliotoxin biosynthesis in Aspergillus fumigatus. Chem Biol 18: 542-552.
16. de Oliveira JM & de Graaff LH (2011) Proteomics of industrial fungi: trends and insights for biotechnology. Appl Microbiol Biot 89: 225-237.
17. Doyle S (2011) Fungal proteomics. Fungi: Biology and Applications (Kavanagh K, eds). Wiley, New York (in press).
18. Dunlap JC, Borkovich KA, Henn MR et al. (2007) Enabling a community to dissect an organism: overview of the neurospora functional genomics project. Adv Genet 57: 49-96.
19. Fernández-Acero FJ, Colby T, Harzen A, Carbú M, Wieneke U, Cantoral JM & Schmidt J (2010) 2-DE proteomic approach to the Botrytis cinerea secretome induced with different carbon sources and plant-based elicitors. Proteomics 10: 2270-2280.
20. Fernández-Arenas E, Cabezón V, Bermejo C, Arroyo J, Nombela C, Diez-Orejas R & Gil C (2007) Integrated proteomics and genomics strategies bring new insight into Candida albicans response upon macrophage interaction. Mol Cell Proteomics 6: 460-478.
21. Ferreira de Oliveira JM, van Passel MW, Schaap PJ & de Graaff LH (2010) Shotgun proteomics of Aspergillus niger microsomes upon d-xylose induction. Appl Environ Microb 76: 4421-4429.
22. Gao Q, Jin K, Ying SH et al. (2011) Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. PLoS Genet 7: e1001264.
23. Gautam P, Sundaram CS, Madan T, Gade WN, Shah A, Sirdeshmukh R & Sarma PU (2007) Identification of novel allergens of Aspergillus fumigatus using immunoproteomics approach. Clin Exp Allergy 37: 1239-1249.
24. Gautam P, Shankar J, Madan T, Sirdeshmukh R, Sundaram CS, Gade WN, Basir SF & Sarma PU (2008) Proteomic and transcriptomic analysis of Aspergillus fumigatus on exposure to amphotericin B. Antimicrob Agents Ch 52: 4220-4227.
25. Georgianna DR, Hawkridge AM, Muddiman DC & Payne GA (2008) Temperature-dependent regulation of proteins in Aspergillus flavus: whole organism stable isotope labeling by amino acids. J Proteome Res 7: 2973-2979.
26. González-Fernández R, Prats E & Jorrín-Novo JV (2010) Proteomics of plant pathogenic fungi. J Biomed Biotechnol 2010: 932527.
27. Ito JI, Lyons JM, Hong TB, Tamae D, Liu YK, Wilczynski SP & Kalkum M (2006) Vaccinations with recombinant variants of Aspergillus fumigatus allergen Asp f 3 protect mice against invasive aspergillosis. Infect Immun 74: 5075-5084.
28. Jobbins SE, Hill CJ, D'Souza-Basseal JM, Padula MP, Herbert BR & Krockenberger MB (2010) Immunoproteomic approach to elucidating the pathogenesis of cryptococcosis caused by Cryptococcus gattii. J Proteome Res 9: 3832-3841.
29. Keller M & Hettich R (2009) Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol Mol Biol R 73: 62-70.
30. Kikot GE, Hours RA & Alconada TM (2009) Contribution of cell wall degrading enzymes to pathogenesis of Fusarium graminearum: a review. J Basic Microb 49: 231-241.
31. Kim Y, Nandakumar MP & Marten MR (2008) The state of proteome profiling in the fungal genus Aspergillus. Brief Funct Genomic Proteomic 7: 87-94.
32. Kim Y, Nandakumar MP & Marten MR (2007) Proteomics of filamentous fungi. Trends Biotechnol 25: 395-400.
33. Kniemeyer O, Lessing F & Brakhage AA (2009) Proteome analysis for pathogenicity and new diagnostic markers for Aspergillus fumigatus. Med Mycol 47 (suppl 1): S248-S254.
34. Lakshman DK, Natarajan SS, Lakshman S, Garrett WM & Dhar AK (2008) Optimized protein extraction methods for proteomic analysis of Rhizoctonia solani. Mycologia 100: 867-875.
35. Lessing F, Kniemeyer O, Wozniok I, Loeffler J, Kurzai O, Haertl A & Brakhage AA (2007) The Aspergillus fumigatus transcriptional regulator AfYap1 represents the major regulator for defense against reactive oxygen intermediates but is dispensable for pathogenicity in an intranasal mouse infection model. Eukaryot Cell 6: 2290-2302.
36. Losada L, Ajayi O, Frisvad JC, Yu J & Nierman WC (2009) Effect of competition on the production and activity of secondary metabolites in Aspergillus species. Med Mycol 47 suppl 1): S88-S96.
37. Martin F, Aerts A, Ahrén D et al. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452: 88-92.
38. Monteoliva L, Martinez-Lopez R, Pitarch A, Hernaez ML, Serna A, Nombela C, Albar JP & Gil C (2011) Quantitative proteome and acidic subproteome profiling of Candida albicans yeast-to-hypha transition. J Proteome Res 10: 502-517.
39. Murad AM, Laumann RA, Lima Tde A, Sarmento RB, Noronha EF, Rocha TL, Valadares-Inglis MC & Franco OL (2006) Screening of entomopathogenic Metarhizium anisopliae isolates and proteomic analysis of secretion synthesized in response to cowpea weevil (Callosobruchus maculatus) exoskeleton. Comp Biochem Physiol C Toxicol Pharmacol 142: 365-370.
40. Murad AM, Noronha EF, Miller RN, Costa FT, Pereira CD, Mehta A, Caldas RA & Franco OL (2008) Proteomic analysis of Metarhizium anisopliae secretion in the presence of the insect pest Callosobruchus maculatus. Microbiology 154: 3766-3774.
41. 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: 3171-3183.
42. Pasquali M, Giraud F, Lasserre JP, Planchon S, Hoffmann L, Bohn T & Renaut J (2010) Toxin induction and protein extraction from Fusarium spp. cultures for proteomic studies. J Vis Exp 16. Available at.
43. Pedrini N, Crespo R & Juárez MP (2007) Biochemistry of insect epicuticle degradation by entomopathogenic fungi. Comp Biochem Physiol C 146: 124-137.
44. Pitarch A, Abian J, Carrascal M, Sánchez M, Nombela C & Gil C (2004) Proteomics-based identification of novel Candida albicans antigens for diagnosis of systemic candidiasis in patients with underlying hematological malignancies. Proteomics 4: 3084-3106.
45. Pitarch A, Jiménez A, Nombela C & Gil C (2006) Decoding serological response to Candida cell wall immunome into novel diagnostic, prognostic, and therapeutic candidates for systemic candidiasis by proteomic and bioinformatic analyses. Mol Cell Proteomics 5: 79-96.
46. Pitarch A, Nombela C & Gil C (2011) Prediction of the clinical outcome in invasive candidiasis patients based on molecular fingerprints of five anti-Candida antibodies in serum. Mol Cell Proteomics 10: in press.
47. Priebe S, Linde J, Albrecht D, Guthke R & Brakhage AA (2011) FungiFun: a web-based application for functional categorization of fungal genes and proteins. Fungal Genet Biol 48: 353-358.
48. Pusztahelyi T, Klement E, Szajli E et al. (2011) Comparison of transcriptional and translational changes caused by long-term menadione exposure in Aspergillus nidulans. Fungal Genet Biol 48: 92-103.
49. Sato I, Shimizu M, Hoshino T & Takaya N (2009) The glutathione system of Aspergillus nidulans involves a fungus-specific glutathione S-transferase. J Biol Chem 284: 8042-8053.
50. Scharf DH, Remme N, Heinekamp T, Hortschansky P, Brakhage AA & Hertweck C (2010) Transannular disulfide formation in gliotoxin biosynthesis and its role in self-resistance of the human pathogen Aspergillus fumigatus. J Am Chem Soc 132: 10136-10141.
51. Schrettl M, Carberry S, Kavanagh K, Haas H, Jones GW, O'Brien J, Stephens J, Fenelon O, Nolan A & Doyle S (2010) Self-protection against gliotoxin - A component of the gliotoxin biosynthetic cluster, GliT, Completely protects Aspergillus fumigatus against exogenous gliotoxin. PLoS Pathogens 6: e1000952.
52. Schuster A & Schmoll M (2010) Biology and biotechnology of Trichoderma. Appl Microbiol Biot 87: 787-799.
53. Shankar J, Gupta PD, Sridhara S, Singh BP, Gaur SN & Arora N (2005) Immunobiochemical analysis of cross-reactive glutathione s-transferase allergen from different fungal sources. Immunol Invest 34: 37-51.
54. Shankar J, Singh BP, Gaur SN & Arora N (2006) Recombinant glutathione-S-transferase a major allergen from Alternaria alternata for clinical use in allergy patients. Mol Immunol 43: 1927-1932.
55. Sheppard DC, Doedt T, Chiang LY, Kim HS, Chen D, Nierman WC & Filler SG (2006) The Aspergillus fumigatus StuA protein governs the up-regulation of a discrete transcriptional program during the acquisition of developmental competence. Mol Biol Cell 16: 5866-5879.
56. Shevchenko A, Tomas H, Havlis J, Olsen JV & Mann M (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1: 2856-2860.
57. Singh B, Sharma GL, Oellerich M, Kumar R, Singh S, Bhadoria DP, Katyal A, Reichard U & Asif AR (2010a) Novel cytosolic allergens of Aspergillus fumigatus identified from germinating conidia. J Proteome Res 9: 5530-5541.
58. Singh B, Oellerich M, Kumar R, Kumar M, Bhadoria DP, Reichard U, Gupta VK, Sharma GL & Asif AR (2010b) Immuno-reactive molecules identified from the secreted proteome of Aspergillus fumigatus. J Proteome Res 9: 5517-5529.
59. Tan KC, Ipcho SV, Trengove RD, Oliver RP & Solomon PS (2009) Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology. Mol Plant Pathol 10: 703-715.
60. Taylor RD, Saparno A, Blackwell B, Anoop V, Gleddie S, Tinker NA & Harris LJ (2008) Proteomic analyses of Fusarium graminearum grown under mycotoxin-inducing conditions. Proteomics 8: 2256-2265.
61. Thön M, Al Abdallah Q, Hortschansky P, Scharf DH, Eisendle M, Haas H & Brakhage AA (2010) The CCAAT-binding complex coordinates the oxidative stress response in eukaryotes. Nucleic Acids Res 38: 1098-1113.
62. Wang S, Leclerque A, Pava-Ripoll M, Fang W & St Leger RJ (2009) Comparative genomics using microarrays reveals divergence and loss of virulence-associated genes in host-specific strains of the insect pathogen Metarhizium anisopliae. Eukaryot Cell 8: 888-898.
63. Zhou W, Eudes F & Laroche A (2006) Identification of differentially regulated proteins in response to a compatible interaction between the pathogen Fusarium graminearum and its host, Triticum aestivum. Proteomics 6: 4599-4609.