Skip to main content
SpringerLink
Log in

13 Functional Genomics to Characterize Opportunistic Pathogens

  • Chapter
  • First Online:
Fungal Genomics

Part of the book series: The Mycota ((MYCOTA,volume 13))

  • 2104 Accesses

Abstract

Fungal pathogens cause a wide range of diseases, from allergies and superficial infections to life-threatening invasive mycoses. Often, the outcome of a fungal infection depends on the immune status of the host organism. The most important causes of life-threatening invasive mycoses are infections caused by the yeast Candida albicans and the filamentous fungus Aspergillus fumigatus. To date, neither reliable diagnostic tools nor effective treatment options are available, resulting in unacceptably high mortality rates of patients suffering from invasive fungal infections. Knowledge of the DNA sequence of microorganisms and the application of functional genomics is a promising tool to understand the interplay between pathogens and host cells and to improve diagnosis, identify new drug targets, and develop tailor-made drugs.

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

  • Adams MD, Soares MB, Kerlavage AR, Fields C, Venter JC (1993) Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library. Nat Genet 4:373–380

    PubMed  CAS  Google Scholar 

  • Albrecht D, Guthke R, Brakhage AA, Kniemeyer O (2010) Integrative analysis of the heat shock response in Aspergillus fumigatus. BMC Genomics 11:32

    PubMed Central  PubMed  Google Scholar 

  • Albuquerque PC, Nakayasu ES, Rodrigues ML, Frases S, Casadevall A, Zancope-Oliveira RM, Almeida IC, Nosanchuk JD (2008) Vesicular transport in Histoplasma capsulatum: an effective mechanism for trans-cell wall transfer of proteins and lipids in ascomycetes. Cell Microbiol 10:1695–1710

    PubMed Central  PubMed  CAS  Google Scholar 

  • Alter O, Brown PO, Botstein D (2003) Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci U S A 100:3351–3356

    PubMed Central  PubMed  CAS  Google Scholar 

  • Altwasser R, Linde J, Buyko E, Hahn U, Guthke R (2012) Genome-wide scale-free network inference for Candida albicans. Front Microbiol 3:51

    PubMed Central  PubMed  Google Scholar 

  • Alwine JC, Kemp DJ, Stark GR (1977) Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci U S A 74:5350–5354

    PubMed Central  PubMed  CAS  Google Scholar 

  • Andersen MR, Nielsen JB, Klitgaard A, Petersen LM, Zachariasen M, Hansen TJ, Blicher LH, Gotfredsen CH, Larsen TO, Nielsen KF, Mortensen UH (2013) Accurate prediction of secondary metabolite gene clusters in filamentous fungi. Proc Natl Acad Sci U S A 110:E99–E107

    PubMed Central  PubMed  CAS  Google Scholar 

  • Arnaud MB, Chibucos MC, Costanzo MC, Crabtree J, Inglis DO, Lotia A, Orvis J, Shah P, Skrzypek MS, Binkley G, Miyasato SR, Wortman JR, Sherlock G (2010) The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Res 38:D420–D427

    PubMed Central  PubMed  CAS  Google Scholar 

  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25:25–29

    PubMed Central  PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Askew DS (2008) Aspergillus fumigatus: virulence genes in a street-smart mold. Curr Opin Microbiol 11:331–337

    PubMed Central  PubMed  CAS  Google Scholar 

  • Barker KS, Crisp S, Wiederhold N, Lewis RE, Bareither B, Eckstein J, Barbuch R, Bard M, Rogers PD (2004) Genome-wide expression profiling reveals genes associated with amphotericin B and fluconazole resistance in experimentally induced antifungal resistant isolates of Candida albicans. J Antimicrob Chemother 54:376–385

    PubMed  CAS  Google Scholar 

  • Barker BM, Kroll K, Vodisch M, Mazurie A, Kniemeyer O, Cramer RA (2012) Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter. BMC Genomics 13:62

    PubMed Central  PubMed  CAS  Google Scholar 

  • Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara ECM, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O’Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59

    PubMed Central  PubMed  CAS  Google Scholar 

  • Bergmann S, Schumann J, Scherlach K, Lange C, Brakhage AA, Hertweck C (2007) Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat Chem Biol 3:213–217

    PubMed  CAS  Google Scholar 

  • Bok JW, Keller NP (2004) LaeA, a regulator of secondary metabolism in Aspergillus spp. Eukaryot Cell 3:527–535

    PubMed Central  PubMed  CAS  Google Scholar 

  • Bok JW, Chiang YM, Szewczyk E, Reyes-Dominguez Y, Davidson AD, Sanchez JF, Lo HC, Watanabe K, Strauss J, Oakley BR, Wang CC, Keller NP (2009) Chromatin-level regulation of biosynthetic gene clusters. Nat Chem Biol 5:462–464

    PubMed Central  PubMed  CAS  Google Scholar 

  • Brakhage AA (2005) Systemic fungal infections caused by Aspergillus species: epidemiology, infection process and virulence determinants. Curr Drug Targets 6:875–886

    PubMed  CAS  Google Scholar 

  • Brakhage AA (2013) Regulation of fungal secondary metabolism. Nat Rev Microbiol 11:21–32

    PubMed  CAS  Google Scholar 

  • Brakhage AA, Schuemann J, Bergmann S, Scherlach K, Schroeckh V, Hertweck C (2008) Activation of fungal silent gene clusters: a new avenue to drug discovery. Prog Drug Res 66(1):3–12

    Google Scholar 

  • Brakhage AA, Thon M, Sprote P, Scharf DH, Al-Abdallah Q, Wolke SM, Hortschansky P (2009) Aspects on evolution of fungal beta-lactam biosynthesis gene clusters and recruitment of trans-acting factors. Phytochemistry 70:1801–1811

    PubMed  CAS  Google Scholar 

  • Brown JS, Aufauvre-Brown A, Brown J, Jennings JM, Arst H Jr, Holden DW (2000) Signature-tagged and directed mutagenesis identify PABA synthetase as essential for Aspergillus fumigatus pathogenicity. Mol Microbiol 36:1371–1380

    PubMed  CAS  Google Scholar 

  • Brown GD, Denning DW, Gow NA, Levitz SM, Netea MG, White TC (2012) Hidden killers: human fungal infections. Sci Transl Med 4:165rv13

    PubMed  Google Scholar 

  • Bruns S, Seidler M, Albrecht D, Salvenmoser S, Remme N, Hertweck C, Brakhage AA, Kniemeyer O, Muller FM (2010) Functional genomic profiling of Aspergillus fumigatus biofilm reveals enhanced production of the mycotoxin gliotoxin. Proteomics 10:3097–3107

    PubMed  CAS  Google Scholar 

  • Castillo L, Calvo E, Martinez AI, Ruiz-Herrera J, Valentin E, Lopez JA, Sentandreu R (2008) A study of the Candida albicans cell wall proteome. Proteomics 8:3871–3881

    PubMed  CAS  Google Scholar 

  • Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bahler J (2003) Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell 14:214–229

    PubMed Central  PubMed  CAS  Google Scholar 

  • Chiang YM, Lee KH, Sanchez JF, Keller NP, Wang CC (2009) Unlocking fungal cryptic natural products. Nat Prod Commun 4:1505–1510

    PubMed Central  PubMed  CAS  Google Scholar 

  • Chooi YH, Fang J, Liu H, Filler SG, Wang P, Tang Y (2013) Genome mining of a prenylated and immunosuppressive polyketide from pathogenic fungi. Org Lett 15:780–783

    PubMed Central  PubMed  CAS  Google Scholar 

  • Cichewicz RH (2010) Epigenome manipulation as a pathway to new natural product scaffolds and their congeners. Nat Prod Rep 27:11–22

    PubMed Central  PubMed  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 80:4994–5001

    PubMed Central  PubMed  CAS  Google Scholar 

  • Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, Weiss RL, Borkovich KA, Dunlap JC (2006) A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci U S A 103:10352–10357

    PubMed Central  PubMed  CAS  Google Scholar 

  • Cormack BP, Ghori N, Falkow S (1999) An adhesin of the yeast pathogen Candida glabrata mediating adherence to human epithelial cells. Science 285:578–582

    PubMed  CAS  Google Scholar 

  • Crestani J, Carvalho PC, Han X, Seixas A, Broetto L, Fischer Jde S, Staats CC, Schrank A, Yates JR 3rd, Vainstein MH (2012) Proteomic profiling of the influence of iron availability on Cryptococcus gattii. J Proteome Res 11:189–205

    PubMed Central  PubMed  CAS  Google Scholar 

  • da Silva Ferreira ME, Malavazi I, Savoldi M, Brakhage AA, Goldman MH, Kim HS, Nierman WC, Goldman GH (2006) Transcriptome analysis of Aspergillus fumigatus exposed to voriconazole. Curr Genet 50:32–44

    PubMed  Google Scholar 

  • da Silva Ferreira ME, Heinekamp T, Hartl A, Brakhage AA, Semighini CP, Harris SD, Savoldi M, de Gouvea PF, de Souza Goldman MH, Goldman GH (2007) Functional characterization of the Aspergillus fumigatus calcineurin. Fungal Genet Biol 44:219–230

    PubMed  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • De Backer MD, Ilyina T, Ma XJ, Vandoninck S, Luyten WH, Vanden Bossche H (2001) Genomic profiling of the response of Candida albicans to itraconazole treatment using a DNA microarray. Antimicrob Agents Chemother 45:1660–1670

    PubMed Central  PubMed  Google Scholar 

  • de Groot PW, de Boer AD, Cunningham J, Dekker HL, de Jong L, Hellingwerf KJ, de Koster C, Klis FM (2004) Proteomic analysis of Candida albicans cell walls reveals covalently bound carbohydrate-active enzymes and adhesins. Eukaryot Cell 3:955–965

    PubMed Central  PubMed  Google Scholar 

  • Doedt T, Krishnamurthy S, Bockmuhl DP, Tebarth B, Stempel C, Russell CL, Brown AJ, Ernst JF (2004) APSES proteins regulate morphogenesis and metabolism in Candida albicans. Mol Biol Cell 15:3167–3180

    PubMed Central  PubMed  CAS  Google Scholar 

  • Domon B, Aebersold R (2006) Mass spectrometry and protein analysis. Science 312:212–217

    PubMed  CAS  Google Scholar 

  • Ene IV, Heilmann CJ, Sorgo AG, Walker LA, de Koster CG, Munro CA, Klis FM, Brown AJ (2012) Carbon source-induced reprogramming of the cell wall proteome and secretome modulates the adherence and drug resistance of the fungal pathogen Candida albicans. Proteomics 12:3164–3179

    PubMed Central  PubMed  CAS  Google Scholar 

  • Fedorova ND, Nierman WC, Turner G, Joardar V, Maiti R, Anderson MJ, Denning DW, Wortman JR (2008) A comparative view of the genome of Aspergillus fumigatus. In: Osmani SA, Goldman GH (eds) The aspergilli: genomics, medical aspects, biotechnology, and research methods. CRC Press, Boca Raton, pp 25–42

    Google Scholar 

  • Gacek A, Strauss J (2012) The chromatin code of fungal secondary metabolite gene clusters. Appl Microbiol Biotechnol 95:1389–1404

    PubMed Central  PubMed  CAS  Google Scholar 

  • Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Basturkmen 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 438:1105–1115

    PubMed  CAS  Google Scholar 

  • Gallagher L, Owens RA, Dolan SK, O’Keeffe G, Schrettl M, Kavanagh K, Jones GW, Doyle S (2012) The Aspergillus fumigatus protein GliK protects against oxidative stress and is essential for gliotoxin biosynthesis. Eukaryot Cell 11:1226–1238

    PubMed Central  PubMed  CAS  Google Scholar 

  • Garbis S, Lubec G, Fountoulakis M (2005) Limitations of current proteomics technologies. J Chromatogr A 1077:1–18

    PubMed  CAS  Google Scholar 

  • Gardiner DM, Howlett BJ (2005) Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster of Aspergillus fumigatus. FEMS Microbiol Lett 248:241–248

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Gibbons JG, Beauvais A, Beau R, McGary KL, Latge JP, Rokas A (2012) Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Eukaryot Cell 11:68–78

    PubMed Central  PubMed  CAS  Google Scholar 

  • Grahl N, Shepardson KM, Chung D, Cramer RA (2012) Hypoxia and fungal pathogenesis: to air or not to air? Eukaryot Cell 11:560–570

    PubMed Central  PubMed  CAS  Google Scholar 

  • Haas H (2012) Iron – a key nexus in the virulence of Aspergillus fumigatus. Front Microbiol 3:28

    PubMed Central  PubMed  CAS  Google Scholar 

  • Hartmann T, Dumig M, Jaber BM, Szewczyk E, Olbermann P, Morschhauser J, Krappmann S (2010) Validation of a self-excising marker in the human pathogen Aspergillus fumigatus by employing the beta-rec/six site-specific recombination system. Appl Environ Microbiol 76:6313–6317

    PubMed Central  PubMed  CAS  Google Scholar 

  • Hartmann T, Cairns TC, Olbermann P, Morschhauser J, Bignell EM, Krappmann S (2011) Oligopeptide transport and regulation of extracellular proteolysis are required for growth of Aspergillus fumigatus on complex substrates but not for virulence. Mol Microbiol 82:917–935

    PubMed  CAS  Google Scholar 

  • Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R (2009) Gene regulatory network inference: data integration in dynamic models-a review. Biosystems 96:86–103

    PubMed  CAS  Google Scholar 

  • Heddergott C, Bruns S, Nietzsche S, Leonhardt I, Kurzai O, Kniemeyer O, Brakhage AA (2012) The Arthroderma benhamiae hydrophobin HypA mediates hydrophobicity and influences recognition by human immune effector cells. Eukaryot Cell 11:673–682

    PubMed Central  PubMed  CAS  Google Scholar 

  • Heilmann CJ, Sorgo AG, Siliakus AR, Dekker HL, Brul S, de Koster CG, de Koning LJ, Klis FM (2011) Hyphal induction in the human fungal pathogen Candida albicans reveals a characteristic wall protein profile. Microbiology 157:2297–2307

    PubMed  CAS  Google Scholar 

  • Hernaez ML, Ximenez-Embun P, Martinez-Gomariz M, Gutierrez-Blazquez MD, Nombela C, Gil C (2010) Identification of Candida albicans exposed surface proteins in vivo by a rapid proteomic approach. J Proteomics 73:1404–1409

    PubMed  CAS  Google Scholar 

  • Hernandez R, Nombela C, Diez-Orejas R, Gil C (2004) Two-dimensional reference map of Candida albicans hyphal forms. Proteomics 4:374–382

    PubMed  CAS  Google Scholar 

  • Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH (2009) Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res 19:657–666

    PubMed Central  PubMed  CAS  Google Scholar 

  • Homann OR, Dea J, Noble SM, Johnson AD (2009) A phenotypic profile of the Candida albicans regulatory network. PLoS Genet 5:e1000783

    PubMed Central  PubMed  Google Scholar 

  • Horn F, Heinekamp T, Kniemeyer O, Pollmacher J, Valiante V, Brakhage AA (2012) Systems biology of fungal infection. Front Microbiol 3:108

    PubMed Central  PubMed  CAS  Google Scholar 

  • Hortschansky P, Eisendle M, Al-Abdallah Q, Schmidt AD, Bergmann S, Thon M, Kniemeyer O, Abt B, Seeber B, Werner ER, Kato M, Brakhage AA, Haas H (2007) Interaction of HapX with the CCAAT-binding complex – a novel mechanism of gene regulation by iron. Embo J 26:3157–3168

    PubMed Central  PubMed  CAS  Google Scholar 

  • Ihmels J, Bergmann S, Berman J, Barkai N (2005) Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet 1:e39

    PubMed Central  PubMed  Google Scholar 

  • Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M (2005) Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteom 4:1265–1272

    CAS  Google Scholar 

  • Jacobsen ID, Wilson D, Wachtler B, Brunke S, Naglik JR, Hube B (2012) Candida albicans dimorphism as a therapeutic target. Expert Rev Anti Infect Ther 10:85–93

    PubMed  Google Scholar 

  • Jahn B, Boukhallouk F, Lotz J, Langfelder K, Wanner G, Brakhage AA (2000) Interaction of human phagocytes with pigmentless Aspergillus conidia. Infect Immun 68:3736–3739

    PubMed Central  PubMed  CAS  Google Scholar 

  • Jain R, Valiante V, Remme N, Docimo T, Heinekamp T, Hertweck C, Gershenzon J, Haas H, Brakhage AA (2011) The MAP kinase MpkA controls cell wall integrity, oxidative stress response, gliotoxin production and iron adaptation in Aspergillus fumigatus. Mol Microbiol 82:39–53

    PubMed Central  PubMed  CAS  Google Scholar 

  • Jong AY, Chen SH, Stins MF, Kim KS, Tuan TL, Huang SH (2003) Binding of Candida albicans enolase to plasmin(ogen) results in enhanced invasion of human brain microvascular endothelial cells. J Med Microbiol 52:615–622

    PubMed  CAS  Google Scholar 

  • Kamthan M, Mukhopadhyay G, Chakraborty N, Chakraborty S, Datta A (2012) Quantitative proteomics and metabolomics approaches to demonstrate N-acetyl-D-glucosamine inducible amino acid deprivation response as morphological switch in Candida albicans. Fungal Genet Biol 49:369–378

    PubMed  CAS  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    PubMed Central  PubMed  CAS  Google Scholar 

  • Keller O, Kollmar M, Stanke M, Waack S (2011) A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics 27:757–763

    PubMed  CAS  Google Scholar 

  • Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, Fedorova ND (2010) SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol 47:736–741

    PubMed Central  PubMed  CAS  Google Scholar 

  • Kniemeyer O, Lessing F, Scheibner O, Hertweck C, Brakhage AA (2006) Optimisation of a 2-D gel electrophoresis protocol for the human-pathogenic fungus Aspergillus fumigatus. Curr Genet 49:178–189

    PubMed  CAS  Google Scholar 

  • Kniemeyer O, Schmidt AD, Vodisch M, Wartenberg D, Brakhage AA (2011) Identification of virulence determinants of the human pathogenic fungi Aspergillus fumigatus and Candida albicans by proteomics. Int J Med Microbiol 301:368–377

    PubMed  Google Scholar 

  • Krappmann S, Sasse C, Braus GH (2006) Gene targeting in Aspergillus fumigatus by homologous recombination is facilitated in a nonhomologous end-joining-deficient genetic background. Eukaryot Cell 5:212–215

    PubMed Central  PubMed  CAS  Google Scholar 

  • Kraus PR, Boily MJ, Giles SS, Stajich JE, Allen A, Cox GM, Dietrich FS, Perfect JR, Heitman J (2004) Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarray. Eukaryot Cell 3:1249–1260

    PubMed Central  PubMed  CAS  Google Scholar 

  • Kroll K, Pahtz V, Kniemeyer O (2013) Elucidating the fungal stress response by proteomics. J Proteom pii:S1874–3919(13)00315–1. doi:10.1016/j.jprot.2013.06.001. [Epub ahead of print]

  • Kusch H, Engelmann S, Albrecht D, Morschhauser J, Hecker M (2007) Proteomic analysis of the oxidative stress response in Candida albicans. Proteomics 7:686–697

    PubMed  CAS  Google Scholar 

  • Kusch H, Engelmann S, Bode R, Albrecht D, Morschhauser J, Hecker M (2008) A proteomic view of Candida albicans yeast cell metabolism in exponential and stationary growth phases. Int J Med Microbiol 298:291–318

    PubMed  CAS  Google Scholar 

  • La Hoz RM, Pappas PG (2013) Cryptococcal infections: changing epidemiology and implications for therapy. Drugs 73:495–504

    PubMed  Google Scholar 

  • Langfelder K, Jahn B, Gehringer H, Schmidt A, Wanner G, Brakhage AA (1998) Identification of a polyketide synthase gene (pksP) of Aspergillus fumigatus involved in conidial pigment biosynthesis and virulence. Med Microbiol Immun (Berl) 187:79–89

    CAS  Google Scholar 

  • Langfelder K, Philippe B, Jahn B, Latge JP, Brakhage AA (2001) Differential expression of the Aspergillus fumigatus pksP gene detected in vitro and in vivo with green fluorescent protein. Infect Immun 69:6411–6418

    PubMed Central  PubMed  CAS  Google Scholar 

  • Langfelder K, Streibel M, Jahn B, Haase G, Brakhage AA (2003) Biosynthesis of fungal melanins and their importance for human pathogenic fungi. Fungal Genet Biol 38:143–158

    PubMed  CAS  Google Scholar 

  • Lee I, Oh JH, Shwab EK, Dagenais TR, Andes D, Keller NP (2009) HdaA, a class 2 histone deacetylase of Aspergillus fumigatus, affects germination and secondary metabolite production. Fungal Genet Biol 46:782–790

    PubMed Central  PubMed  CAS  Google Scholar 

  • 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

    PubMed Central  PubMed  CAS  Google Scholar 

  • Liang P, Pardee AB (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257:967–971

    PubMed  CAS  Google Scholar 

  • Liebmann B, Gattung S, Jahn B, Brakhage AA (2003) cAMP signaling in Aspergillus fumigatus is involved in the regulation of the virulence gene pksP and in defense against killing by macrophages. Mol Genet Genomics 269:420–435

    PubMed  CAS  Google Scholar 

  • Linde J, Hortschansky P, Fazius E, Brakhage AA, Guthke R, Haas H (2012) Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a systems biology approach. BMC Syst Biol 6:6

    PubMed Central  PubMed  CAS  Google Scholar 

  • Liu H, Lin D, Yates JR, IIIrd (2002) Multidimensional separations for protein/peptide analysis in the post-genomic era. Biotechniques 32:898, 900, 902 passim

    Google Scholar 

  • Liu TT, Lee RE, Barker KS, Lee RE, Wei L, Homayouni R, Rogers PD (2005) Genome-wide expression profiling of the response to azole, polyene, echinocandin, and pyrimidine antifungal agents in Candida albicans. Antimicrob Agents Chemother 49:2226–2236

    PubMed Central  PubMed  CAS  Google Scholar 

  • Mabey JE, Anderson MJ, Giles PF, Miller CJ, Attwood TK, Paton NW, Bornberg-Bauer E, Robson GD, Oliver SG, Denning DW (2004) CADRE: the central Aspergillus data REpository. Nucleic Acids Res 32:D401–D405

    PubMed Central  PubMed  CAS  Google Scholar 

  • McDonagh A, Fedorova ND, Crabtree J, Yu Y, Kim S, Chen D, Loss O, Cairns T, Goldman G, Armstrong-James D, Haynes K, Haas H, Schrettl M, May G, Nierman WC, Bignell E (2008) Sub-telomere directed gene expression during initiation of invasive aspergillosis. PLoS Pathog 4:e1000154

    PubMed Central  PubMed  Google Scholar 

  • Miller I, Crawford J, Gianazza E (2006) Protein stains for proteomic applications: which, when, why? Proteomics 6:5385–5408

    PubMed  CAS  Google Scholar 

  • Missall TA, Lodge JK, McEwen JE (2004) Mechanisms of resistance to oxidative and nitrosative stress: implications for fungal survival in mammalian hosts. Eukaryot Cell 3:835–846

    PubMed Central  PubMed  CAS  Google Scholar 

  • Missall TA, Pusateri ME, Donlin MJ, Chambers KT, Corbett JA, Lodge JK (2006) Posttranslational, translational, and transcriptional responses to nitric oxide stress in Cryptococcus neoformans: implications for virulence. Eukaryot Cell 5:518–529

    PubMed Central  PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Muller S, Baldin C, Groth M, Guthke R, Kniemeyer O, Brakhage AA, Valiante V (2012) Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression. BMC Genomics 13:519

    PubMed Central  PubMed  Google Scholar 

  • Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51(Pt 1):263–273

    PubMed  CAS  Google Scholar 

  • Murillo LA, Newport G, Lan CY, Habelitz S, Dungan J, Agabian NM (2005) Genome-wide transcription profiling of the early phase of biofilm formation by Candida albicans. Eukaryot Cell 4:1562–1573

    PubMed Central  PubMed  CAS  Google Scholar 

  • Muszkieta L, Beauvais A, Pahtz V, Gibbons JG, Anton Leberre V, Beau R, Shibuya K, Rokas A, Francois JM, Kniemeyer O, Brakhage AA, Latge JP (2013) Investigation of Aspergillus fumigatus biofilm formation by various “omics” approaches. Front Microbiol 4:13

    PubMed Central  PubMed  Google Scholar 

  • Nielsen ML, Albertsen L, Lettier G, Nielsen JB, Mortensen UH (2006) Efficient PCR-based gene targeting with a recyclable marker for Aspergillus nidulans. Fungal Genet Biol 43:54–64

    PubMed  CAS  Google Scholar 

  • Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, Davies R, Dyer PS, Farman M, Fedorova N, Fedorova N, Feldblyum TV, Fischer R, Fosker N, Fraser A, Garcia JL, Garcia MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jimenez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafon A, Latge JP, Li W, Lord A, Lu C, Majoros WH, May GS, Miller BL, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O’Neil S, Paulsen I, Penalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream MA, Reichard U, Renauld H, Robson GD, Rodriguez de Cordoba S, Rodriguez-Pena JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Sanchez-Ferrero JC, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Vazquez de Aldana CR, Weidman J, White O, Woodward J, Yu JH, Fraser C, Galagan JE, Asai K, Machida M, Hall N, Barrell B, Denning DW (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438:1151–1156

    PubMed  CAS  Google Scholar 

  • Nikolov M, Schmidt C, Urlaub H (2012) Quantitative mass spectrometry-based proteomics: an overview. Methods Mol Biol 893:85–100

    PubMed  CAS  Google Scholar 

  • Noble SM, French S, Kohn LA, Chen V, Johnson AD (2010) Systematic screens of a Candida albicans homozygous deletion library decouple morphogenetic switching and pathogenicity. Nat Genet 42:590–598

    PubMed Central  PubMed  CAS  Google Scholar 

  • Nutzmann HW, Reyes-Dominguez Y, Scherlach K, Schroeckh V, Horn F, Gacek A, Schumann J, Hertweck C, Strauss J, Brakhage AA (2011) Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation. Proc Natl Acad Sci U S A 108:14282–14287

    PubMed Central  PubMed  CAS  Google Scholar 

  • Ong SE, Mann M (2005) Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 1:252–262

    PubMed  CAS  Google Scholar 

  • Ormerod KL, Morrow CA, Chow EW, Lee IR, Arras SD, Schirra HJ, Cox GM, Fries BC, Fraser JA (2013) Comparative genomics of serial isolates of Cryptococcus neoformans reveals gene associated with carbon utilization and virulence. G3 (Bethesda) pii:g.113.005660v1. doi:10.1534/g3.113005660. [Epub ahead of print]

  • Palmer JM, Keller NP (2010) Secondary metabolism in fungi: does chromosomal location matter? Curr Opin Microbiol 13:431–436

    PubMed Central  PubMed  CAS  Google Scholar 

  • Palmer JM, Bok JW, Lee S, Dagenais TR, Andes DR, Kontoyiannis DP, Keller NP (2013) Loss of CclA, required for histone 3 lysine 4 methylation, decreases growth but increases secondary metabolite production in Aspergillus fumigatus. Peer J 1:e4

    PubMed Central  PubMed  Google Scholar 

  • Park BJ, Pappas PG, Wannemuehler KA, Alexander BD, Anaissie EJ, Andes DR, Baddley JW, Brown JM, Brumble LM, Freifeld AG, Hadley S, Herwaldt L, Ito JI, Kauffman CA, Lyon GM, Marr KA, Morrison VA, Papanicolaou G, Patterson TF, Perl TM, Schuster MG, Walker R, Wingard JR, Walsh TJ, Kontoyiannis DP (2011) Invasive non-Aspergillus mold infections in transplant recipients, United States, 2001–2006. Emerg Infect Dis 17:1855–1864

    PubMed Central  PubMed  Google Scholar 

  • Patron NJ, Waller RF, Cozijnsen AJ, Straney DC, Gardiner DM, Nierman WC, Howlett BJ (2007) Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes. BMC Evol Biol 7:174

    PubMed Central  PubMed  Google Scholar 

  • Patterson M, Dhand R (2000) Nature insight: functional genomics. Nature 405:819

    Google Scholar 

  • Pechanova O, Pechan T, Rodriguez JM, Williams WP, Brown AE (2013) A two-dimensional proteome map of the aflatoxigenic fungus Aspergillus flavus. Proteomics 13:1513–1518

    PubMed  CAS  Google Scholar 

  • Pfaller MA, Diekema DJ (2007) Epidemiology of invasive candidiasis: a persistent public health problem. Clin Microbiol Rev 20:133–163

    PubMed Central  PubMed  CAS  Google Scholar 

  • Rabilloud T, Lelong C (2011) Two-dimensional gel electrophoresis in proteomics: a tutorial. J Proteomics 74:1829–1841

    PubMed  CAS  Google Scholar 

  • Rai MN, Balusu S, Gorityala N, Dandu L, Kaur R (2012) Functional genomic analysis of Candida glabrata-macrophage interaction: role of chromatin remodeling in virulence. PLoS Pathog 8:e1002863

    PubMed Central  PubMed  CAS  Google Scholar 

  • Reyes-Dominguez Y, Bok JW, Berger H, Shwab EK, Basheer A, Gallmetzer A, Scazzocchio C, Keller N, Strauss J (2010) Heterochromatic marks are associated with the repression of secondary metabolism clusters in Aspergillus nidulans. Mol Microbiol 76:1376–1386

    PubMed Central  PubMed  CAS  Google Scholar 

  • Rispail N, Soanes DM, Ant C, Czajkowski R, Grunler A, Huguet R, Perez-Nadales E, Poli A, Sartorel E, Valiante V, Yang M, Beffa R, Brakhage AA, Gow NA, Kahmann R, Lebrun MH, Lenasi H, Perez-Martin J, Talbot NJ, Wendland J, Di Pietro A (2009) Comparative genomics of MAP kinase and calcium-calcineurin signalling components in plant and human pathogenic fungi. Fungal Genet Biol 46:287–298

    PubMed  CAS  Google Scholar 

  • Rodrigues ML, Nakayasu ES, Oliveira DL, Nimrichter L, Nosanchuk JD, Almeida IC, Casadevall A (2008) Extracellular vesicles produced by Cryptococcus neoformans contain protein components associated with virulence. Eukaryot Cell 7:58–67

    PubMed Central  PubMed  CAS  Google Scholar 

  • Rodrigues ML, Nakayasu ES, Almeida IC, Nimrichter L (2013) The impact of proteomics on the understanding of functions and biogenesis of fungal extracellular vesicles. J Proteomics pii:S1874–3919(13)00182–6. doi:10.1016/j.jprot.2013.04.001. [Epub ahead of print]

  • Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M, Mewes HW (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res 32:5539–5545

    PubMed Central  PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Scharf DH, Remme N, Habel A, Chankhamjon P, Scherlach K, Heinekamp T, Hortschansky P, Brakhage AA, Hertweck C (2011) A dedicated glutathione S-transferase mediates carbon-sulfur bond formation in gliotoxin biosynthesis. J Am Chem Soc 133:12322–12325

    PubMed  CAS  Google Scholar 

  • Scharf DH, Heinekamp T, Remme N, Hortschansky P, Brakhage AA, Hertweck C (2012) Biosynthesis and function of gliotoxin in Aspergillus fumigatus. Appl Microbiol Biotechnol 93:467–472

    PubMed  CAS  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    PubMed  CAS  Google Scholar 

  • Scherlach K, Nutzmann HW, Schroeckh V, Dahse HM, Brakhage AA, Hertweck C (2011) Cytotoxic pheofungins from an engineered fungus impaired in posttranslational protein modification. Angew Chem Int Ed Engl 50:9843–9847

    PubMed  CAS  Google Scholar 

  • Schrettl M, Kim HS, Eisendle M, Kragl C, Nierman WC, Heinekamp T, Werner ER, Jacobsen I, Illmer P, Yi H, Brakhage AA, Haas H (2008) SreA-mediated iron regulation in Aspergillus fumigatus. Mol Microbiol 70:27–43

    PubMed Central  PubMed  CAS  Google Scholar 

  • Schrettl M, Carberry S, Kavanagh K, Haas H, Jones GW, O’Brien J, Nolan A, Stephens J, Fenelon O, Doyle S (2010) Self-protection against gliotoxin – a component of the gliotoxin biosynthetic cluster, GliT, completely protects Aspergillus fumigatus against exogenous gliotoxin. PLoS Pathog 6:e1000952

    PubMed Central  PubMed  Google Scholar 

  • Schwienbacher M, Weig M, Thies S, Regula JT, Heesemann J, Ebel F (2005) Analysis of the major proteins secreted by the human opportunistic pathogen Aspergillus fumigatus under in vitro conditions. Med Mycol 43:623–630

    PubMed  CAS  Google Scholar 

  • Seider K, Heyken A, Luttich A, Miramon P, Hube B (2010) Interaction of pathogenic yeasts with phagocytes: survival, persistence and escape. Curr Opin Microbiol 13:392–400

    PubMed  CAS  Google Scholar 

  • Seneviratne CJ, Jin L, Samaranayake LP (2008) Biofilm lifestyle of Candida: a mini review. Oral Dis 14:582–590

    PubMed  CAS  Google Scholar 

  • Shimizu M, Masuo S, Fujita T, Doi Y, Kamimura Y, Takaya N (2012) Hydrolase controls cellular NAD, sirtuin, and secondary metabolites. Mol Cell Biol 32:3743–3755

    PubMed Central  PubMed  CAS  Google Scholar 

  • Shwab EK, Bok JW, Tribus M, Galehr J, Graessle S, Keller NP (2007) Histone deacetylase activity regulates chemical diversity in Aspergillus. Eukaryot Cell 6:1656–1664

    PubMed Central  PubMed  CAS  Google Scholar 

  • Sorgo AG, Heilmann CJ, Dekker HL, Brul S, de Koster CG, Klis FM (2010) Mass spectrometric analysis of the secretome of Candida albicans. Yeast 27:661–672

    PubMed  CAS  Google Scholar 

  • Sorgo AG, Heilmann CJ, Brul S, de Koster CG, Klis FM (2013) Beyond the wall: Candida albicans secret(e)s to survive. FEMS Microbiol Lett 338:10–17

    PubMed  CAS  Google Scholar 

  • Sosinska GJ, de Groot PW, Teixeira de Mattos MJ, Dekker HL, de Koster CG, Hellingwerf KJ, Klis FM (2008) Hypoxic conditions and iron restriction affect the cell-wall proteome of Candida albicans grown under vagina-simulative conditions. Microbiology 154:510–520

    PubMed  CAS  Google Scholar 

  • Sosinska GJ, de Koning LJ, de Groot PW, Manders EM, Dekker HL, Hellingwerf KJ, de Koster CG, Klis FM (2011) Mass spectrometric quantification of the adaptations in the wall proteome of Candida albicans in response to ambient pH. Microbiology 157:136–146

    PubMed  CAS  Google Scholar 

  • Soukup AA, Chiang YM, Bok JW, Reyes-Dominguez Y, Oakley BR, Wang CC, Strauss J, Keller NP (2012) Overexpression of the Aspergillus nidulans histone 4 acetyltransferase EsaA increases activation of secondary metabolite production. Mol Microbiol 86:314–330

    PubMed Central  PubMed  CAS  Google Scholar 

  • Sriranganadane D, Waridel P, Salamin K, Reichard U, Grouzmann E, Neuhaus JM, Quadroni M, Monod M (2010) Aspergillus protein degradation pathways with different secreted protease sets at neutral and acidic pH. J Proteome Res 9:3511–3519

    PubMed  CAS  Google Scholar 

  • Steen H, Mann M (2004) The ABC’s (and XYZ’s) of peptide sequencing. Nat Rev Mol Cell Biol 5:699–711

    PubMed  CAS  Google Scholar 

  • Steinbach WJ, Cramer RA Jr, Perfect BZ, Asfaw YG, Sauer TC, Najvar LK, Kirkpatrick WR, Patterson TF, Benjamin DK Jr, Heitman J, Perfect JR (2006) Calcineurin controls growth, morphology, and pathogenicity in Aspergillus fumigatus. Eukaryot Cell 5:1091–1103

    PubMed Central  PubMed  CAS  Google Scholar 

  • Teutschbein J, Albrecht D, Potsch M, Guthke R, Aimanianda V, Clavaud C, Latge JP, Brakhage AA, Kniemeyer O (2010) Proteome profiling and functional classification of intracellular proteins from conidia of the human-pathogenic mold Aspergillus fumigatus. J Proteome Res 9:3427–3442

    PubMed  CAS  Google Scholar 

  • Thomas DP, Bachmann SP, Lopez-Ribot JL (2006) Proteomics for the analysis of the Candida albicans biofilm lifestyle. Proteomics 6:5795–5804

    PubMed  CAS  Google Scholar 

  • Thywißen A, Heinekamp T, Dahse H-M, Schmaler-Ripcke J, Nietsche S, Zipfel PF, Brakhage AA (2011) Front Microbiol 2. doi:10.3389/fmicb201100096

  • Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18:2071–2077

    PubMed  CAS  Google Scholar 

  • Valiante V, Heinekamp T, Jain R, Hartl A, Brakhage AA (2008) The mitogen-activated protein kinase MpkA of Aspergillus fumigatus regulates cell wall signaling and oxidative stress response. Fungal Genet Biol 45:618–627

    PubMed  CAS  Google Scholar 

  • Valiante V, Jain R, Heinekamp T, Brakhage AA (2009) The MpkA MAP kinase module regulates cell wall integrity signaling and pyomelanin formation in Aspergillus fumigatus. Fungal Genet Biol 46:909–918

    PubMed  CAS  Google Scholar 

  • Vallejo MC, Nakayasu ES, Matsuo AL, Sobreira TJ, Longo LV, Ganiko L, Almeida IC, Puccia R (2012) Vesicle and vesicle-free extracellular proteome of Paracoccidioides brasiliensis: comparative analysis with other pathogenic fungi. J Proteome Res 11:1676–1685

    PubMed Central  PubMed  CAS  Google Scholar 

  • Viswanathan S, Unlu M, Minden JS (2006) Two-dimensional difference gel electrophoresis. Nat Protoc 1:1351–1358

    PubMed  CAS  Google Scholar 

  • Vodisch M, Albrecht D, Lessing F, Schmidt AD, Winkler R, Guthke R, Brakhage AA, Kniemeyer O (2009) Two-dimensional proteome reference maps for the human pathogenic filamentous fungus Aspergillus fumigatus. Proteomics 9:1407–1415

    PubMed  Google Scholar 

  • Vodisch M, Scherlach K, Winkler R, Hertweck C, Braun HP, Roth M, Haas H, Werner ER, Brakhage AA, Kniemeyer O (2011) Analysis of the Aspergillus fumigatus proteome reveals metabolic changes and the activation of the pseurotin A biosynthesis gene cluster in response to hypoxia. J Proteome Res 10:2508–2524

    PubMed Central  PubMed  CAS  Google Scholar 

  • Vodovotz Y, Constantine G, Faeder J, Mi Q, Rubin J, Bartels J, Sarkar J, Squires RH Jr, Okonkwo DO, Gerlach J, Zamora R, Luckhart S, Ermentrout B, An G (2010) Translational systems approaches to the biology of inflammation and healing. Immunopharmacol Immunotoxicol 32:181–195

    PubMed Central  PubMed  Google Scholar 

  • Volling K, Thywissen A, Brakhage AA, Saluz HP (2011) Phagocytosis of melanized Aspergillus conidia by macrophages exerts cytoprotective effects by sustained PI3K/Akt signalling. Cell Microbiol 13:1130–1148

    PubMed  CAS  Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

    PubMed Central  PubMed  CAS  Google Scholar 

  • Wartenberg D, Lapp K, Jacobsen ID, Dahse HM, Kniemeyer O, Heinekamp T, Brakhage AA (2011) Secretome analysis of Aspergillus fumigatus reveals Asp-hemolysin as a major secreted protein. Int J Med Microbiol 301:602–611

    PubMed  CAS  Google Scholar 

  • Weig M, Jansch L, Gross U, De Koster CG, Klis FM, De Groot PW (2004) Systematic identification in silico of covalently bound cell wall proteins and analysis of protein-polysaccharide linkages of the human pathogen Candida glabrata. Microbiology 150:3129–3144

    PubMed  CAS  Google Scholar 

  • Westermann AJ, Gorski SA, Vogel J (2012) Dual RNA-seq of pathogen and host. Nat Rev Microbiol 10:618–630

    PubMed  CAS  Google Scholar 

  • Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, Williams KL (1996) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13:19–50

    PubMed  CAS  Google Scholar 

  • Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M’Rabet N, Menard P, Mittmann M, Pai C, Rebischung C, Revuelta JL, Riles L, Roberts CJ, Ross-MacDonald P, Scherens B, Snyder M, Sookhai-Mahadeo S, Storms RK, Veronneau S, Voet M, Volckaert G, Ward TR, Wysocki R, Yen GS, Yu K, Zimmermann K, Philippsen P, Johnston M, Davis RW (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901–906

    PubMed  CAS  Google Scholar 

  • Yates JR, Ruse CI, Nakorchevsky A (2009) Proteomics by mass spectrometry: approaches, advances, and applications. Annu Rev Biomed Eng 11:49–79

    PubMed  CAS  Google Scholar 

  • Yin Z, Stead D, Walker J, Selway L, Smith DA, Brown AJ, Quinn J (2009) A proteomic analysis of the salt, cadmium and peroxide stress responses in Candida albicans and the role of the Hog1 stress-activated MAPK in regulating the stress-induced proteome. Proteomics 9:4686–4703

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knoell Institute (HKI), Jena, Germany

    Thorsten Heinekamp, Vito Valiante, Nora Koester-Eiserfunke & Axel A. Brakhage

  2. Department of Molecular and Applied Microbiology, Friedrich Schiller University, Jena, Germany

    Thorsten Heinekamp, Vito Valiante, Nora Koester-Eiserfunke & Axel A. Brakhage

Authors
  1. Thorsten Heinekamp
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vito Valiante
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nora Koester-Eiserfunke
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Axel A. Brakhage
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Axel A. Brakhage .

Editor information

Editors and Affiliations

  1. Department of General and Molecular Bota, Ruhr-University of Bochum, Bochum, Germany

    Minou Nowrousian

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Heinekamp, T., Valiante, V., Koester-Eiserfunke, N., Brakhage, A.A. (2014). 13 Functional Genomics to Characterize Opportunistic Pathogens. In: Nowrousian, M. (eds) Fungal Genomics. The Mycota, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-45218-5_13

Download citation

Publish with us

Policies and ethics

Search

Navigation