Skip to main content
SpringerLink
Log in

Exploring Fungi-Associated Lignocellulose Degradation: Secretomic and Proteomic Approaches

  • Chapter
  • First Online:
Advancing Frontiers in Mycology & Mycotechnology

Abstract

Filamentous fungi of phyla Basidiomycota and Ascomycota are the group of microorganisms that are capable of secreting a variety of proteins and other secondary metabolites depending on the environment and culture conditions. The protein constitutes the hydrolytic enzymes which cause the deconstruction of the plant cell wall and has applicability in several biotechnological processes including second-generation ethanol production. Secretomic and proteomic analysis of the fungi is an excellent tool to find out the biological mechanisms of lignocellulose degradation. Furthermore, it is also an important tool to search for novel enzymes or metabolites of the biotechnology field. Extracellular secretion of the protein from different fungal species has been studied using different high-throughput techniques such as 2-D PAGE, MALDI-ToF/ToF, LC-MS/MS, iTRAQ technique using LC-MS/MS, and Nano-LC-MS/MS protein mass spectrometry. Bioinformatics tools have equal importance in the prediction and profiling of the expressed proteins, according to the current database. For this reason, publications documenting the fungal secretome and proteome have increased significantly in the past few years. Herein, we have updated the development and evolution of the proteome/secretome technology and its application in the protein profiling and functional genomics of the economically important filamentous fungi.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abbas A, Koc H, Liu F, Tien M (2005) Fungal degradation of wood: initial proteomic analysis of extracellular proteins of Phanerochaete chrysosporium grown on oak substrate. Curr Genet 47:49–56

    Article  CAS  PubMed  Google Scholar 

  • Abdallah C, Dumas-Gaudot E, Renaut J, Sergeant K (2012) Gel-based and gel-free quantitative proteomics approaches at a glance. Int J Plant Genom 2012:494572

    Google Scholar 

  • 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(8):3932–3940

    Article  CAS  PubMed  Google Scholar 

  • Adav SS, Ravindran A, Chao LT, Tan L, Singh S, Sze SK (2011) Proteomic analysis of pH and strains dependent protein secretion of Trichoderma reesei. J Proteome Res 10:4579–4596

    Article  CAS  PubMed  Google Scholar 

  • Adav SS, Ravindran A, Cheow ES, Sze SK (2012a) Quantitative proteomic analysis of secretome of microbial consortium during saw dust utilization. J Proteome 75(18):5590–5603

    Article  CAS  Google Scholar 

  • Adav SS, Ravindran A, Sze SK (2012b) Quantitative proteomic analysis of lignocellulolytic enzymes by Phanerochaete chrysosporium on different lignocellulosic biomass. J Proteome 75(5):1493–1504

    Article  CAS  Google Scholar 

  • Adav SS, Ravindran A, Sze SK (2014) Study of Phanerochaete chrysosporium secretome revealed protein glycosylation as a substrate-dependent post-translational modification. J Proteome Res 13(10):4272–4280

    Article  CAS  PubMed  Google Scholar 

  • Adav SS, Ravindran A, Sze SK (2015) Quantitative proteomic study of Aspergillus fumigatus secretome revealed deamidation of secretory enzymes. J Proteome 119:154–168

    Article  CAS  Google Scholar 

  • Adsul MG, Bastawde KB, Varma AJ, Gokhale DV (2007) Strain improvement of Penicillium janthinellum NCIM 1171 for increased cellulase production. Bioresour Technol 98(7):1467–1473

    Article  CAS  PubMed  Google Scholar 

  • Alfaro M, Oguiza JA, Ramirez L, Pisabarro AG (2014) Comparative analysis of secretomes in basidiomycete fungi. J Proteome 102:28–43

    Article  CAS  Google Scholar 

  • Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B (2007) Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 389(4):1017–1031

    Article  CAS  PubMed  Google Scholar 

  • Bianco L, Perrotta G (2016) Fruit development and ripening: proteomic as an approach to study Olea Europaea and other non-model organisms. Agric Proteomics 1:53–65

    Article  Google Scholar 

  • Bouws H, Wattenberg A, Zorn H (2008) Fungal secretomes-nature’s toolbox for white biotechnology. Appl Microbiol Biotechnol 80(3):381

    Article  CAS  PubMed  Google Scholar 

  • Cai Y, Gong Y, Liu W, Hu Y, Chen L, Yan L, Zhou Y, Bian Y (2017) Comparative secretomic analysis of lignocelluloses degradation by Lentinula edodes grown on microcrystalline cellulose, lignosulfonate and glucose. J Proteome 163:92–101

    Article  CAS  Google Scholar 

  • Carvalho W, Canilha L, Ferraz A, Milagres AM (2009) An overview of wood structure, composition and biodegradation. Nova Chem 32(8):1–5

    Google Scholar 

  • Chen S, Xu J, Liu C, Zhu Y, Nelson DR, Zhou S, Li C, Wang L, Guo X, Sun Y, Luo H (2012) Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nat Commun 3:913

    Article  PubMed  CAS  Google Scholar 

  • Chutani P, Sharma KK (2015) Biochemical evaluation of xylanases from various filamentous fungi and their application for the deinking of ozone treated newspaper pulp. Carbohydr Polym 127:54–63

    Article  CAS  PubMed  Google Scholar 

  • Chutani P, Sharma KK (2016) Concomitant production of xylanases and cellulases from Trichoderma longibrachiatum MDU-6 selected for the deinking of paper waste. Bioprocess Biosyst Eng 39(5):747–758

    Article  CAS  PubMed  Google Scholar 

  • Claus H (2004) Laccases: structure, reactions, distribution. Micron 35(1-2):93–96

    Article  CAS  PubMed  Google Scholar 

  • Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou S, Schwartz DC (2009) The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5(8):e1000618

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Collier TS, Hawkridge AM, Georgianna DR, Payne GA, Muddiman DC (2008) Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer. Anal Chem 80(13):4994–5001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Couturier M, Navarro D, Favel A, Haon M, Lechat C, Lesage-Meessen L, Chevret D, Lombard V, Henrissat B, Berrin JG (2016) Fungal secretomics of ascomycete fungi for biotechnological applications. Mycosphere J 7(10):1546–1553

    Article  Google Scholar 

  • Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20(9):1466–1467

    Article  CAS  PubMed  Google Scholar 

  • de Gouvea PF, Bernardi AV, Gerolamo LE, de Souza SE, Riano-Pachon DM, Uyemura SA, Dinamarco TM (2018) Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse. BMC Genomics 19(1):232

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • de Oliveira JM, van Passel MW, Schaap PJ, de Graaff LH (2011) Proteomic analysis of the secretory response of Aspergillus niger to D-maltose and D-xylose. PLoS One 6(6):e20865

    Article  PubMed  CAS  Google Scholar 

  • de Souza WR, de Gouvea PF, Savoldi M, Malavazi I, de Souza Bernardes LA, Goldman MHS, Goldman GH (2011) Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse. Biotechnol Biofuels 4(1):40

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dix NJ, Webster J (1995) Colonization and decay of wood. In: Fungal ecology. Springer, Dordrecht, pp 145–171

    Chapter  Google Scholar 

  • Doyle S (2011) Fungal proteomics: from identification to function. FEMS Microbiol Lett 321(1):1–9

    Article  CAS  PubMed  Google Scholar 

  • Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M (2011) The plant cell wall–decomposing machinery underlies the functional diversity of forest fungi. Science 333(6043):762–765

    Article  CAS  PubMed  Google Scholar 

  • Efstathiou G, Antonakis AN, Pavlopoulos GA, Theodosiou T, Divanach P, Trudgian DC, Thomas B, Papanikolaou N, Aivaliotis M, Acuto O, Iliopoulos I (2017) ProteoSign: an end-user online differential proteomics statistical analysis platform. Nucleic Acids Res 45(W1):W300–W306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Erden E, Ucar MC, Gezer T, Pazarlioglu NK (2009) Screening for ligninolytic enzymes from autochthonous fungi and applications for decolorization of Remazole Marine Blue. Braz J Microbiol 40(2):346–353

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fernandez-Fueyo E, Ruiz-Duenas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P (2012) Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci U S A 109:5458–5463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fernandez-Fueyo E, Ruiz-Duenas FJ, Lopez-Lucendo MF, Perez-Boada M, Rencoret J, Gutierrez A, Pisabarro AG, Ramirez L, Martinez AT (2016) A secretomic view of woody and nonwoody lignocellulose degradation by Pleurotus ostreatus. Biotechnol Biofuels 9(1):49

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336(6089):1715–1719

    Article  CAS  PubMed  Google Scholar 

  • Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Chulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422(6934):859–868

    Article  CAS  PubMed  Google Scholar 

  • Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, BaÅŸturkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Penalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438(7071):1105–1115

    Article  CAS  PubMed  Google Scholar 

  • Glenn JK, Morgan MA, Mayfield MB, Kuwahara M, Gold MH (1983) An extracellular H2O2-requiring enzyme preparation involved in lignin biodegradation by the white rot basidiomycete Phanerochaete chrysosporium. Biochem Biophys Res Commun 114(3):1077–1083

    Article  CAS  PubMed  Google Scholar 

  • Graham C, McMullan G, Graham RL (2011) Proteomics in the microbial sciences. Bioeng Bugs 2(1):17–30

    Article  PubMed  Google Scholar 

  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 10:994

    Article  CAS  Google Scholar 

  • Hagglund P, Bunkenborg J, Maeda K, Svensson B (2008) Identification of thioredoxin disulfide targets using a quantitative proteomics approach based on isotope-coded affinity tags. J Proteome Res 7(12):5270–5276

    Article  PubMed  CAS  Google Scholar 

  • Hakkinen M, Arvas M, Oja M, Aro N, Penttilä M, Saloheimo M, Pakula TM (2012) Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates. Microb Cell Factories 11(1):134

    Article  CAS  Google Scholar 

  • Han X, Aslanian A, Yates JR III (2008) Mass spectrometry for proteomics. Curr Opin Chem Biol 12(5):483–490

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henriksson G, Johansson G, Pettersson G (2000a) A critical review of cellobiose dehydrogenases. J Biotechnol 78(2):93–113

    Article  CAS  PubMed  Google Scholar 

  • Henriksson G, Zhang L, Li J, Ljungquist P, Reitberger T, Pettersson G, Johansson G (2000b) Is cellobiose dehydrogenase from Phanerochaete chrysosporium a lignin degrading enzyme? Biochim Biophys Acta Protein Struct Mol Enzymol 1480(1–2):83–91

    Article  CAS  Google Scholar 

  • Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci 90(11):5011–5015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hibbett DS, Donoghue MJ (2001) Analysis of character correlations among wood decay mechanisms, mating systems, and substrate ranges in homobasidiomycetes. Syst Biol 50(2):215–242

    Article  CAS  PubMed  Google Scholar 

  • Hoegger PJ, Kilaru S, James TY, Thacker JR, Kües U (2006) Phylogenetic comparison and classification of laccase and related multicopper oxidase protein sequences. FEBS J 273(10):2308–2326

    Article  CAS  PubMed  Google Scholar 

  • Hoegger P, Majcherczyk A, Dwivedi R, Svobodova K, Kilaru S, Kües U (2007) Enzymes in wood degradation. In: Kües U (ed) Wood prod. Wood technol. Biotechnol. Impacts. Universitätsverlag Göttingen, Göttingen, pp 383–432

    Google Scholar 

  • Hofrichter M (2002) Lignin conversion by manganese peroxidase (MnP). Enzym Microb Technol 30(4):454–466

    Article  CAS  Google Scholar 

  • Hori C, Igarashi K, Katayama A, Samejima M (2011) Effects of xylan and starch on secretome of the basidiomycete Phanerochaete chrysosporium grown on cellulose. FEMS Microbiol Lett 321(1):14–23

    Article  CAS  PubMed  Google Scholar 

  • Hori C, Gaskell J, Igarashi K, Samejima M, Hibbett D, Henrissat B, Cullen D (2013) Genome wide analysis of polysaccharides degrading enzymes in 11 white-and brown-rot Polyporales provides insight into mechanisms of wood decay. Mycologia 105(6):1412–1427

    Article  CAS  PubMed  Google Scholar 

  • Hori C, Gaskell J, Igarashi K, Kersten P, Mozuch M, Samejima M, Cullen D (2014) Temporal alterations in secretome of selective ligninolytic fungi Ceriporiopsis subvermispora during growth on aspen wood reveal its strategy of degrading lignocellulose. Appl Environ Microbiol 17:AEM-03652

    Google Scholar 

  • Horth P, Miller CA, Preckel T, Wenz C (2006) Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol Cell Proteomics 5(10):1968–1974

    Article  PubMed  CAS  Google Scholar 

  • Jain KK, Kumar A, Shankar A, Pandey D, Chaudhary B, Sharma KK (2019) De novo transcriptome assembly and protein profiling of copper-induced lignocellulolytic fungus Ganoderma lucidum MDU-7 reveals genes involved in lignocellulose degradation and terpenoid biosynthetic pathways. Genomics. https://doi.org/10.1016/j.ygeno.2019.01.012

  • Ji XL, Zhang WT, Gai YP, Lu BY, Yuan CZ, Liu QX, Mu ZM (2012) Patterns of lignocellulose degradation and secretome analysis of Trametes trogii MT. Int Biodeterior Biodegradation 75:55–62

    Article  CAS  Google Scholar 

  • Juhasz T, Szengyel Z, Reczey K, Siika-Aho M, Viikari L (2005) Characterization of cellulases and hemicellulases produced by Trichoderma reesei on various carbon sources. Process Biochem 40(11):3519–3525

    Article  CAS  Google Scholar 

  • Jungblut PR, Holzhütter HG, Apweiler R, Schlüter H (2008) The speciation of the proteome. Chem Cent J 2(1):16

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kellner H, Vandenbol M (2010) Fungi unearthed: transcripts encoding lignocellulolytic and chitinolytic enzymes in forest soil. PLoS One 5(6):e10971

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kersten P, Cullen D (2007) Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium. Fungal Genet Biol 44(2):77–87

    Article  CAS  PubMed  Google Scholar 

  • Kim Y, Nandakumar MP, Marten MR (2007) Proteomics of filamentous fungi. Trends Biotechnol 25(9):395–400

    Article  CAS  PubMed  Google Scholar 

  • Knezević A, Milovanović I, Stajić M, Vukojević J (2013) Potential of Trametes species to degrade lignin. Int Biodeterior Biodegradation 85:52–56

    Article  CAS  Google Scholar 

  • Krijger JJ, Thon MR, Deising HB, Wirsel SG (2014) Compositions of fungal secretomes indicate a greater impact of phylogenetic history than lifestyle adaptation. BMC Genomics 15(1):722

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar A, Sharma KK, Kumar P, Ramchiary N (2015) Laccase isozymes from Ganoderma lucidum MDU-7: isolation, characterization, catalytic properties and differential role during oxidative stress. J Mol Catal B Enzym 113:68–75

    Article  CAS  Google Scholar 

  • Kumar A, Singh D, Sharma KK, Arora S, Singh AK, Gill SS, Singhal B (2017) Gel-based purification and biochemical study of laccase isozymes from Ganoderma sp. and its role in enhanced cotton callogenesis. Front Microbiol 8:674

    Article  PubMed  PubMed Central  Google Scholar 

  • Lamer S, Jungblut PR (2001) Matrix-assisted laser desorption-ionization mass spectrometry peptide mass fingerprinting for proteome analysis: identification efficiency after on-blot or in-gel digestion with and without desalting procedures. J Chromatogr B Biomed Sci Appl 752(2):311–322

    Article  CAS  PubMed  Google Scholar 

  • Le Marquer M, Clemente HS, Roux C, Savelli B, dit Frey NF (2019) Identification of new signalling peptides through a genome-wide survey of 250 fungal secretomes. BMC Genomics 20(1):64. https://doi.org/10.1186/s12864-018-5414-2

    Article  PubMed  PubMed Central  Google Scholar 

  • Lebrun JD, Demont-Caulet N, Cheviron N, Laval K, Trinsoutrot-Gattin I, Mougin C (2011) Secretion profiles of fungi as potential tools for metal ecotoxicity assessment: a study of enzymatic system in Trametes versicolor. Chemosphere 82(3):340–345

    Article  CAS  PubMed  Google Scholar 

  • Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR (1999) Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17(7):676

    Article  CAS  PubMed  Google Scholar 

  • Liu D, Li J, Zhao S, Zhang R, Wang M, Miao Y, Shen Y, Shen Q (2013) Secretome diversity and quantitative analysis of cellulolytic Aspergillus fumigatus Z5 in the presence of different carbon sources. Biotechnology for Biofuels 6(1):149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu X, Sun J, Nimtz M, Wissing J, Zeng AP, Rinas U (2010) The intra-and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate. Microb Cell Factories 9(1):23

    Article  CAS  Google Scholar 

  • Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto KI, Arima T, Akita O, Kashiwagi Y, Abe K (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature 438(7071):1157

    Article  PubMed  Google Scholar 

  • Maciel MJ, Ribeiro HC (2010) Industrial and biotechnological applications of ligninolytic enzymes of the basidiomycota: a review. Electron J Biotechnol 13(6):14–15

    Google Scholar 

  • Manavalan A, Adav SS, Sze SK (2011) iTRAQ-based quantitative secretome analysis of Phanerochaete chrysosporium. J Proteome 75(2):642–654

    Article  CAS  Google Scholar 

  • Manavalan T, Manavalan A, Thangavelu KP, Heese K (2012) Secretome analysis of Ganoderma lucidum cultivated in sugarcane bagasse. J Proteom 77:298–309

    Article  CAS  Google Scholar 

  • Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC, Larimer F, Coutinho PM (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol 22(6):695

    Article  CAS  PubMed  Google Scholar 

  • Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Danchin EG (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnol 26(5):553

    Article  CAS  Google Scholar 

  • Martínez D, Challacombe J, Morgenstern I, Hibbett DS, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden-Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Bondurant SS, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, Lavin JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker SE, Bruno K, Kenealy W, Hoegger PJ, Kues U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee CL, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev IV, Brettin T, Rokhsar D, Berka R, Cullen D (2009) Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci U S A 106:1954–1959

    Article  PubMed  PubMed Central  Google Scholar 

  • Mathieu Y, Piumi F, Valli R, Aramburu JC, Ferreira P, Faulds C, Record E (2016) Secreted aryl alcohol quinone oxidoreductases from Pycnoporus cinnabarinus provides new activities and insights into fungal degradation of plant biomass. Appl Environ Microbiol 12:AEM-03761

    Google Scholar 

  • Mattow J, Schaible UE, Schmidt F, Hagens K, Siejak F, Brestrich G, Haeselbarth G, Müller EC, Jungblut PR, Kaufmann SH (2003) Comparative proteome analysis of culture supernatant proteins from virulent Mycobacterium tuberculosis H37Rv and attenuated M. bovis BCG Copenhagen. Electrophoresis 24(19-20):3405–3420

    Article  CAS  PubMed  Google Scholar 

  • Mayer AM, Staples RC (2002) Laccase: new functions for an old enzyme. Phytochemistry 60(6):551–565

    Article  CAS  PubMed  Google Scholar 

  • Minden J (2007) Comparative proteomics and difference gel electrophoresis. Biotechniques 43(6):739–745

    Article  CAS  PubMed  Google Scholar 

  • Minussi RC, Miranda MA, Silva JA, Ferreira CV, Aoyama H, Marangoni S, Rotilio D, Pastore GM, Durán N (2007) Purification, characterization and application of laccase from Trametes versicolor for colour and phenolic removal of olive mill wastewater in the presence of 1-hydroxybenzotriazole. Afr J Biotechnol 6(2):1–10

    Google Scholar 

  • Miura N, Ueda M (2018) Evaluation of unconventional protein secretion by Saccharomyces cerevisiae and other fungi. Cell 7(9):128

    Article  CAS  Google Scholar 

  • Mukherjee P, Mani S (2013) Methodologies to decipher the cell secretome. Biochim Biophys Acta Protein Proteomics 1834(11):2226–2232

    Article  CAS  Google Scholar 

  • Nagele E, Vollmer M, Hörth P (2003) Two-dimensional nano-liquid chromatography-mass spectrometry system for applications in proteomics. J Chromatogr A 1009(1-2):197–205

    Article  CAS  PubMed  Google Scholar 

  • Nitsche BM, Jørgensen TR, Akeroyd M, Meyer V, Ram AF (2012) The carbon starvation response of Aspergillus niger during submerged cultivation: insights from the transcriptome and secretome. BMC Genomics 13(1):380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250(10):4007–4021

    PubMed  Google Scholar 

  • Pellegrin C, Morin E, Martin FM, Veneault-Fourrey C (2015) Comparative analysis of secretomes from ectomycorrhizal fungi with an emphasis on small-secreted proteins. Front Microbiol 18(6):1278

    Google Scholar 

  • Phalip V, Delalande F, Carapito C, Goubet F, Hatsch D, Leize-Wagner E, Dupree P, Van Dorsselaer A, Jeltsch JM (2005) Diversity of the exoproteome of Fusarium graminearum grown on plant cell wall. Curr Genet 48(6):366–379

    Article  CAS  PubMed  Google Scholar 

  • Phillips CM, Iavarone AT, Marletta MA (2011) Quantitative proteomic approach for cellulose degradation by Neurospora crassa. J Proteome Res 10(9):4177–4185

    Article  CAS  PubMed  Google Scholar 

  • Piontek K, Smith AT, Blodig W (2001) Lignin peroxidase structure and function. Biochem Soc Trans 29:111–116

    Article  CAS  PubMed  Google Scholar 

  • Poland J, Cahill MA, Sinha P (2003) Isoelectric focusing in long immobilized pH gradient gels to improve protein separation in proteomic analysis. Electrophoresis 24(7–8):1271–1275

    Article  CAS  PubMed  Google Scholar 

  • Ravalason H, Jan G, Molle D, Pasco M, Coutinho PM, Lapierre C, Pollet B, Bertaud F, Petit-Conil M, Grisel S, Sigoillot JC (2008) Secretome analysis of Phanerochaete chrysosporium strain CIRM-BRFM41 grown on softwood. Appl Microbiol Biotechnol 80(4):719–733

    Article  CAS  PubMed  Google Scholar 

  • Rohr CO, Levin LN, Mentaberry AN, Wirth SA (2013) A first insight into Pycnoporus sanguineus BAFC 2126 transcriptome. PLoS One 8(12):e81033

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3(12):1154–1169

    Article  CAS  PubMed  Google Scholar 

  • Ruiz-Dueñas FJ, Martínez AT (2009) Microbial degradation of lignin: how a bulky recalcitrant polymer is efficiently recycled in nature and how we can take advantage of this. Microb Biotechnol 2(2):164–177

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ruiz-Dueñas FJ, Pogni R, Morales M, Giansanti S, Mate MJ, Romero A, Martínez AT (2009) Protein radicals in fungal versatile peroxidase catalytic tryptophan radical in both compound I and compound II and studies on W164Y, W164H, and W164S variants. J Biol Chem 284(12):7986–7994

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • San Ryu J, Shary S, Houtman CJ, Panisko EA, Korripally P, John FJ, Crooks C, Siika-aho M, Magnuson JK, Hammel KE (2011) Proteomic and functional analysis of the cellulase system expressed by Postia placenta during brown rot of solid wood. Appl Environ Microbiol 77:7933–7941

    Article  CAS  Google Scholar 

  • Sato S, Liu F, Koc H, Tien M (2007) Expression analysis of extracellular proteins from Phanerochaete chrysosporium grown on different liquid and solid substrates. Microbiology 153(9):3023–3033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saykhedkar S, Ray A, Ayoubi-Canaan P, Hartson SD, Prade R, Mort AJ (2012) A time course analysis of the extracellular proteome of Aspergillus nidulans growing on sorghum stover. Biotechnology for biofuels. 5(1):52

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma KK (2016) Fungal genome sequencing: basic biology to biotechnology. Crit Rev Biotechnol 36(4):743–759

    CAS  PubMed  Google Scholar 

  • Sharma KK, Kuhad RC (2008) Laccase: enzyme revisited function redefined. Indian J Microbiol 48:309–316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma KK, Singh D, Singh B, Kuhad RC (2013) Ligninolytic enzymes in environmental management. In: Biotechnology for environmental management and resource recovery. Springer, India, pp 219–238

    Chapter  Google Scholar 

  • Shevchenko A, Wilm M, Vorm O, Mann M (1996) Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal Chem 68(5):850–858

    Article  CAS  PubMed  Google Scholar 

  • Sripuan T, Aoki K, Yamamoto K, Tongkao D, Kumagai H (2003) Purification and characterization of thermostable α-galactosidase from Ganoderma lucidum. Biosci Biotechnol Biochem 67(7):1485–1491

    Article  CAS  PubMed  Google Scholar 

  • Steffen W, Crutzen PJ, McNeill JR (2007) The Anthropocene: are humans now overwhelming the great forces of nature. AMBIO 36(8):614–621

    Article  CAS  PubMed  Google Scholar 

  • Stroher E, Dietz KJ (2006) Concepts and approaches towards understanding the cellular redox proteome. Plant Biol 8(4):407–418

    Article  CAS  PubMed  Google Scholar 

  • Tomsovsky M, Homolka L (2003) Laccase and other ligninolytic enzyme activities of selected strains of Trametes spp. from different localities and substrates. Folia Microbiol 48(3):413

    Article  CAS  Google Scholar 

  • Trejo-Hernandez MR, Lopez-Munguia A, Ramirez RQ (2001) Residual compost of Agaricus bisporus as a source of crude laccase for enzymic oxidation of phenolic compounds. Process Biochem 36(7):635–639

    Article  CAS  Google Scholar 

  • Vasina DV, Pavlov AR, Koroleva OV (2016) Extracellular proteins of Trametes hirsuta s t. 072 induced by copper ions and a lignocellulose substrate. BMC Microbiol 16(1):106

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vincent D, Kohler A, Claverol S, Solier E, Joets J, Gibon J, Lebrun MH, Plomion C, Martin F (2011) Secretome of the free-living mycelium from the ectomycorrhizal basidiomycete Laccaria bicolor. J Proteome Res 11(1):157–171

    Article  PubMed  CAS  Google Scholar 

  • Vasina DV, Loginov DS, Koroleva OV (2013) Comparative proteomic study of the basidiomycete Trametes hirsuta grown on different substrates. Biochem Mosc 78(5):477–484

    Article  CAS  Google Scholar 

  • Waanders LF, Hanke S, Mann M (2007) Top-down quantitation and characterization of SILAC-labeled proteins. J Am Soc Mass Spectrom 18(11):2058–2064

    Article  CAS  PubMed  Google Scholar 

  • Wang B, Cai P, Sun W, Li J, Tian C, Ma Y (2015) A transcriptomic analysis of Neurospora crassa using five major crop residues and the novel role of the sporulation regulator rca-1 in lignocellulase production. Biotechnology for Biofuels 8(1):21

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Washburn MP, Wolters D, Yates JR III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19(3):242

    Article  CAS  PubMed  Google Scholar 

  • Wiese S, Reidegeld KA, Meyer HE, Warscheid B (2007) Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics 7(3):340–350

    Article  CAS  PubMed  Google Scholar 

  • Wymelenberg AV, Minges P, Sabat G, Martinez D, Aerts A, Salamov A, Grigoriev I, Shapiro H, Putnam N, Belinky P, Dosoretz C (2006) Computational analysis of the Phanerochaete chrysosporium v2. 0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins. Fungal Genet Biol 43(5):343–356

    Article  CAS  Google Scholar 

  • Wymelenberg AV, Gaskell J, Mozuch M, Kersten P, Sabat G, Martinez D, Cullen D (2009) Transcriptome and secretome analyses of Phanerochaete chrysosporium reveal complex patterns of gene expression. Appl Environ Microbiol 75(12):4058–4068

    Article  CAS  Google Scholar 

  • Wymelenberg AV, Gaskell J, Mozuch M, Sabat G, Ralph J, Skyba O, Mansfield SD, Blanchette RA, Martinez D, Grigoriev I, Kersten PJ (2010) Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium. Appl Environ Microbiol 76(11):3599–3610

    Article  CAS  Google Scholar 

  • Wymelenberg AV, Gaskell J, Mozuch M, BonDurant SS, Sabat G, Ralph J, Skyba O, Mansfield SD, Blanchette RA, Grigoriev IV, Kersten PJ (2011) Significant alteration of gene expression in wood decay fungi Postia placenta and Phanerochaete chrysosporium by plant species. Appl Environ Microbiol 77(13):4499–4507

    Article  CAS  Google Scholar 

  • Xie F, Liu T, Qian WJ, Petyuk VA, Smith RD (2011) Liquid chromatography-mass spectrometry-based quantitative proteomics. J Biol Chem 286:25443–25449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu GJ, Yin YL, Yu WH, Liu W, Jin YX, Shrestha A, Yang Q, Ye XD, Sun H (2015) Proteome exploration to provide a resource for the investigation of Ganoderma lucidum. PLoS One 10(3):e0119439

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zargar SM, Gupta N, Mir RA, Rai V (2016) Shift from gel based to gel free proteomics to unlock unknown regulatory network in plants: a comprehensive review. J Adv Res Biotechnol 1(1):19

    Google Scholar 

  • Zeiner CA, Purvine SO, Zink EM, Pasa-Tolic L, Chaput DL, Haridas S, Wu S, LaButti K, Grigoriev IV, Henrissat B, Santelli CM (2016) Comparative analysis of secretome profiles of manganese (II)-oxidizing Ascomycete fungi. PLoS One 11(7):e0157844

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR III (2013) Protein analysis by shotgun/bottom-up proteomics. Chem Rev 113(4):2343–2394

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu N, Liu J, Yang J, Lin Y, Yang Y, Ji L, Li M, Yuan H (2016) Comparative analysis of the secretomes of Schizophyllum commune and other wood-decay basidiomycetes during solid-state fermentation reveals its unique lignocellulose-degrading enzyme system. Biotechnol Biofuels 9(1):42

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Znameroski EA, Coradetti ST, Roche CM, Tsai JC, Iavarone AT, Cate JH, Glass NL (2012) Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins. Proc Natl Acad Sci 109(16):6012–6017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zorn H, Bouws H, Takenberg M, Nimtz M, Getzlaff R, Breithaupt DE, Berger RG (2005) An extracellular carboxylesterase from the basidiomycete Pleurotus sapidus hydrolyses xanthophyll esters. Biol Chem 386(5):435–440

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgment

The authors acknowledge Maharshi Dayanand University for the infrastructure facilities. FIST-DST grant to the Department of Microbiology is sincerely acknowledged.

Author information

Authors and Affiliations

  1. Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India

    Akshay Shankar, Shruti Ahlawat & Krishna Kant Sharma

Authors
  1. Akshay Shankar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shruti Ahlawat
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Krishna Kant Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Krishna Kant Sharma .

Editor information

Editors and Affiliations

  1. Division of Biological Science and Engineering, Netaji Subhas University of Technology, New Delhi, Delhi, India

    Tulasi Satyanarayana

  2. Biotech & Management of Bioresources Div, The Energy and Resources Institute, New Delhi, Delhi, India

    Sunil Kumar Deshmukh

  3. Division of Biological Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, India

    Mukund V. Deshpande

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Shankar, A., Ahlawat, S., Sharma, K.K. (2019). Exploring Fungi-Associated Lignocellulose Degradation: Secretomic and Proteomic Approaches. In: Satyanarayana, T., Deshmukh, S., Deshpande, M. (eds) Advancing Frontiers in Mycology & Mycotechnology. Springer, Singapore. https://doi.org/10.1007/978-981-13-9349-5_10

Download citation

Publish with us

Policies and ethics

Search

Navigation