Protein abundance in multiplexed samples (PAMUS) for quantitation of Trichoderma reesei secretome

Journal of Proteomics

Volumn 83, Issue , 2013, Pages 180-196

  Adav, Sunil S ^a   Chao, Lim Tze ^a   Sze, Siu Kwan ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

Bioenergy; Cellulose; PAMUS; Protein abundance; Secretome; Trichoderma reesei

Indexed keywords

CELLULOSE; GLUCOSE; STARCH;

ANALYTIC METHOD; ARTICLE; BIOSYNTHESIS; CARBON SOURCE; FUNGAL STRAIN; HYPOCREA JECORINA; LIQUID CHROMATOGRAPHY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ABUNDANCE IN THE MULTIPLEXED SAMPLE; PROTEIN ANALYSIS; ZYMOGRAPHY;

CULTURE MEDIA; FUNGAL PROTEINS; HUMANS; PROTEOME; PROTEOMICS; TRICHODERMA;

HYPOCREA JECORINA;

EID: 84876700652     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.03.023     Document Type: Article

References (76)

1. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17:994-999.
2. Schmidt A., Beck M., Malmstrom J., Lam H., Claassen M., Campbell D., et al. Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Mol Syst Biol 2011, 7.
3. Griffin T.J., Gygi S.P., Ideker T., Rist B., Eng J., Hood L., et al. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 2002, 1:323-333.
4. MacKay V.L., Li X.H., Flory M.R., Turcott E., Law G.L., Serikawa K.A., et al. Gene expression analyzed by high-resolution state array analysis and quantitative proteomics - response of yeast to mating pheromone. Mol Cell Proteomics 2004, 3:478-489.
5. Stoughton R.B., Friend S.H. Innovation - how molecular profiling could revolutionize drug discovery. Nat Rev Drug Discov 2005, 4:345-350.
6. Kramer R., Cohen D. Functional genomics to new drug targets. Nat Rev Drug Discov 2004, 3:965-972.
7. Guo T.N., Zhu Y., Gan C.S., Lee S.S., Zhu J.A., Wang H.X., et al. Quantitative proteomics discloses MET expression in mitochondria as a direct target of MET kinase inhibitor in cancer cells. Mol Cell Proteomics 2010, 9:2629-2641.
8. Adav S.S., Li A.A., Manavalan A., Punt P., Sze S.K. Quantitative iTRAQ secretome analysis of Aspergillus niger reveals novel hydrolytic enzymes. J Proteome Res 2010, 9:3932-3940.
9. Adav S.S., Ng C.S., Arulmani M., Sze S.K. Quantitative iTRAQ secretome analysis of cellulolytic Thermobifida fusca. J Proteome Res 2010, 9:3016-3024.
10. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376-386.
11. Soufi B., Kumar C., Gnad F., Mann M., Mijakovic I., Macek B. Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis. J Proteome Res 2010, 9:3638-3646.
12. Hanke S., Besir H., Oesterhelt D., Mann M. Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. J Proteome Res 2008, 7:1118-1130.
13. Thompson A., Schafer J., Kuhn K., Kienle S., Schwarz J., Schmidt G., et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003, 75:1895-1904.
14. Ross P.L., Huang Y.L.N., Marchese J.N., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3:1154-1169.
15. Adav S.S., Chao L.T., Sze S.K. Quantitative secretomic analysis of Trichoderma reesei strains reveals enzymatic composition for lignocellulosic biomass degradation. Mol Cell Proteomics 2012, [in press] [11:M111.012419].
16. Adav S.S., Ng C.S., Sze S.K. iTRAQ-based quantitative proteomic analysis of Thermobifida fusca reveals metabolic pathways of cellulose utilization. J Proteomics 2011, 74:2112-2122.
17. Adav S.S., Ravindran A., Sze S.K. Quantitative proteomic analysis of lignocellulolytic enzymes by Phanerochaete chrysosporium on different lignocellulosic biomass. J Proteomics 2012, 75:1493-1504.
18. Dayon L., Sanchez J.C. Relative protein quantification by MS/MS using the tandem mass tag technology. Methods Mol Biol 2012, 893:115-127.
19. Datta A., Park J.E., Li X., Zhang H., Ho Z.S., Heese K., et al. Phenotyping of an in vitro model of ischemic penumbra by iTRAQ-based shotgun quantitative proteomics. J Proteome Res 2010, 9:472-484.
20. Wuhr M., Haas W., McAlister G.C., Peshkin L., Rad R., Kirschner M.W., et al. Accurate multiplexed proteomics at the MS2 level using the complement reporter ion cluster. Anal Chem 2012, 84:9214-9221.
21. Evans C., Noirel J., Ow S.Y., Salim M., Pereira-Medrano A.G., Couto N., et al. An insight into iTRAQ: where do we stand now?. Anal Bioanal Chem 2012, 404:1011-1027.
22. Silva J.C., Gorenstein M.V., Li G.Z., Vissers J.P.C., Geromanos S.J. Absolute quantification of proteins by LCMSE - a virtue of parallel MS acquisition. Mol Cell Proteomics 2006, 5:144-156.
23. Kumar R., Singh S., Singh O.V. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol 2008, 35:377-391.
24. Gao D.H., Chundawat S.P.S., Krishnan C., Balan V., Dale B.E. Mixture optimization of six core glycosyl hydrolases for maximizing saccharification of ammonia fiber expansion (AFEX) pretreated corn stover. Bioresour Technol 2010, 101:2770-2781.
25. Selig M.J., Knoshaug E.P., Adney W.S., Himmel M.E., Decker S.R. Synergistic enhancement of cellobiohydrolase performance on pretreated corn stover by addition of xylanase and esterase activities. Bioresour Technol 2008, 99:4997-5005.
26. Banerjee G., Car S., Scott-Craig J.S., Borrusch M.S., Aslam N., Walton J.D. Synthetic enzyme mixtures for biomass deconstruction: production and optimization of a core set. Biotechnol Bioeng 2010, 106:707-720.
27. Banerjee G., Car S., Scott-Craig J.S., Borrusch M.S., Walton J.D. Rapid optimization of enzyme mixtures for deconstruction of diverse pretreatment/biomass feedstock combinations. Biotechnol Biofuels 2010, 3:22.
28. Phillips C.M., Iavarone A.T., Marletta M.A. Quantitative proteomic approach for cellulose degradation by Neurospora crassa. J Proteome Res 2011, 10:4177-4185.
29. Elliott M.H., Smith D.S., Parker C.E., Borchers C. Current trends in quantitative proteomics. J Mass Spectrom 2009, 44:1637-1660.
30. Wilm M. Quantitative proteomics in biological research. Proteomics 2009, 9:4590-4605.
31. Ishihama Y., Oda Y., Tabata T., Sato T., Nagasu T., Rappsilber J., et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 2005, 4:1265-1272.
32. Montenecourt B.S., Eveleigh D.E. Preparation of mutants of Trichoderma reesei with enhanced cellulase production. Appl Environ Microbiol 1977, 34:777-782.
33. Durand H., Clanet M., Tiraby G. Genetic improvement of Trichoderma reesei for large scale cellulase production. Enzyme Microb Technol 1988, 10:341-346.
34. Jun H., Bing Y., Keying Z., Xuemei D., Daiwen C. Strain improvement of Trichoderma reesei Rut C-30 for increased cellulase production. Indian J Microbiol 2009, 49:188-195.
35. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein dye binding. Anal Biochem 1976, 72:248-254.
36. Hao P., Guo T., Li X., Adav S.S., Yang J., Wei M., et al. Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: comprehensive profiling of rat kidney proteome. J Proteome Res 2010, 9:3520-3526.
37. Bendtsen J.D., Kiemer L., Fausbøll A., Brunak S. Non-classical protein secretion in bacteria. BMC Microbiol 2005, 5.
38. Nombela C., Gil C., Chaffin W.L. Non-conventional protein secretionin yeast. Trends Microbiol 2006, 14:15-21.
39. Lum G., Min X.J. FunSecKB: the fungal secretome knowledgebase 2011, 2011.
40. Bendtsen J.D., Nielsen H., von Heijne G., Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340:783-795.
41. Reese E.T., Parrish F.W., Mandels M. Beta-D-1, 6-glucanases in fungi. Can J Microbiol 1962, 8:327-334.
42. Liu H.B., Sadygov R.G., Yates J.R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004, 76:4193-4201.
43. Ong S.E., Mann M. Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 2005, 1:252-262.
44. Kusmierz J.J., Sumrada R., Desiderio D.M. Fast atom bombardment mass spectrometric quantitative analysis of methionine-enkephalin in human pituitary tissues. Anal Chem 1990, 62:2395-2400.
45. Brun V., Masselon C., Garin J., Dupuis A. Isotope dilution strategies for absolute quantitative proteomics. J Proteomics 2009, 72:740-749.
46. Kettenbach A.N., Rush J., Gerber S.A. Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides. Nat Protoc 2011, 6:175-186.
47. Julka S., Regnier F. Quantification in proteomics through stable isotope coding: a review. J Proteome Res 2004, 3:350-363.
48. Anderson N.L., Anderson N.G., Haines L.R., Hardie D.B., Olafson R.W., Pearson T.W. Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA). J Proteome Res 2004, 3:235-244.
49. Winther B., Moi P., Nordlund M.S., Lunder N., Paus E., Reubsaet J.L.E. Absolute ProGRP quantification in a clinical relevant concentration range using LC-MS/MS and a comprehensive internal standard. J Chromatogr B 2009, 877:1359-1365.
50. Abdel Rahmana A.M., Lopata A.L., Randell E.W., Helleur R.J. Absolute quantification method and validation of airborne snow crab allergen tropomyosin using tandem mass spectrometry. Anal Chim Acta 2010, 681:49-55.
51. Seppala U., Dauly C., Robinson S., Hornshaw M., Larsen J.N., Ipsen H. Absolute quantification of allergens from complex mixtures: a new sensitive tool for standardization of allergen extracts for specific immunotherapy. J Proteome Res 2011, 10:2113-2122.
52. Karp N.A., Huber W., Sadowski P.G., Charles P.D., Hester S.V., Lilley K.S. Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics 2010, 9:1885-1897.
53. Köcher T., Pichler P., Schutzbier M., Stingl C., Kaul A., Teucher N., et al. High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all. J Proteome Res 2009, 8:4743-4752.
54. Cunningham C., Glish G.L., Burinsky D.J. High amplitude short time excitation: a method to form and detect low mass product ions in a quadrupole ion trap mass spectrometer. J Am Soc Mass Spectrom 2006, 17:81-84.
55. Vincent C.E., Rensvold J.W., Westphall M.S., Pagliarini D.J., Coon J.J. Automated gas-phase purification for accurate, multiplexed quantification on a stand-alone ion-trap mass spectrometer. Anal Chem 2013, 85:2079-2086.
56. Ting L., Rad R., Gygi S.P., Haas W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods 2011, 8:937-940.
57. Gerber S.A., Rush J., Stemman O., Kirschner M.W., Gygi S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 2003, 100:6940-6945.
58. Chundawat S.P.S., Lipton M.S., Purvine S.O., Uppugundla N., Gao D.H., Balan V., et al. Proteomics-based compositional analysis of complex cellulase-hemicellulase mixtures. J Proteome Res 2011, 10:4365-4372.
59. Adav S.S., Ravindran A., Chao L.T., Tan L., Singh S., Sze S.K. Proteomic analysis of pH and strains dependent protein secretion of Trichoderma reesei. J Proteome Res 2011, 10:4579-4596.
60. Olsson L., Christensen T.M.I.E., Hansen K.P., Palmqvist E.A. Influence of the carbon source on production of cellulases, hemicellulases and pectinases by Trichoderma reesei Rut C-30. Enzyme Microb Technol 2003, 33:612-619.
61. Ahamed A., Vermette P. Culture-based strategies to enhance cellulase enzyme production from Trichoderma reesei RUT-C30 in bioreactor culture conditions. Biochem Eng J 2008, 40:399-407.
62. Suto M., Tomita F. Induction and catabolite repression mechanisms of cellulase in fungi. J Biosci Bioeng 2001, 92:305-311.
63. 4 with explosive decomposition. Biotechnol Bioeng 1990, 36:446-452.
64. Le Crom S., Schackwitz W., Pennacchio L., Magnuson J.K., Culley D.E., Collett J.R., et al. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc Natl Acad Sci U S A 2009, 106:16151-16156.
65. Martinez D., Berka R.M., Henrissat B., Saloheimo M., Arvas M., Baker S.E., et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 2008, 26:553-560.
66. Woodward J., Hayes M.K., Lee N.E. Hydrolysis of cellulose by saturating and non-saturating concentrations of cellulase - implications for synergism. Bio-Technol 1988, 6:301-304.
67. Merino S.T., Cherry J. Progress and challenges in enzyme development for biomass utilization. Adv Biochem Eng Biotechnol 2007, 108:95-120.
68. Lynd L.R., Weimer P.J., van Zyl W.H., Pretorius I.S. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 2002, 66:506-739.
69. Leathers T.D., Detroy R.W., Bothast R.J. Induction and glucose repression of xylanase from a color variant strain of Aureobasidium-Pullulans. Biotechnol Lett 1986, 8:867-872.
70. Royer J.C., Nakas J.P. Xylanase production by Trichoderma longibrachiatum. Enzyme Microb Technol 1989, 11:405-410.
71. Selig M.J., Knoshaug E.P., Decker S.R., Baker J.O., Himmel M.E., Adney W.S. Heterologous expression of Aspergillus niger beta-D-xylosidase (XlnD): characterization on lignocellulosic substrates. Appl Biochem Biotechnol 2008, 146:57-68.
72. Kaji A. L-Arabinases. Adv Carbohydr Chem Biochem 1984, 42:383-394.
73. Vanden Wymelenberg A., Gaskell J., Mozuch M., Kersten P., Sabat G., Martinez D., et al. Transcriptome and secretome analyses of Phanerochaete chrysosporium reveal complex patterns of gene expression. Appl Environ Microbiol 2009, 75:4058-4068.
74. Ander P., Marzullo L. Sugar oxidoreductases and veratryl alcohol oxidase as related to lignin degradation. J Biotechnol 1997, 53:115-131.
75. Constam D., Muheim A., Zimmermann W., Fiechter A. Purification and partial characterization of an intracellular NADH-Quinone oxidoreductase from Phanerochaete-Chrysosporium. J Gen Microbiol 1991, 137:2209-2214.
76. Punt P.J., van Biezen N., Conesa A., Albers A., Mangnus J., van den Hondel C. Filamentous fungi as cell factories for heterologous protein production. Trends Biotechnol 2002, 20:200-206.