Methods for investigating the UPR in filamentous fungi

Methods in Enzymology

Volumn 490, Issue C, 2011, Pages 1-29

  Guillemette, Thomas ^a   Ram, Arthur F J ^b   Carvalho, Neuza D S P ^b   Joubert, Aymeric ^a   Simoneau, Philippe ^a   Archer, David B ^c  

^a Agrocampus Ouest Centre d'Angers INHP   (France)

^b LEIDEN UNIVERSITY   (Netherlands)

^c UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; MESSENGER RNA; SECRETORY PROTEIN;

ARTICLE; ASPERGILLUS NIGER; BIOTECHNOLOGY; CANDIDA ALBICANS; CONTROLLED STUDY; ENDOPLASMIC RETICULUM STRESS; FUNGAL VIRULENCE; FUNGUS; GENE DELETION; GENE EXPRESSION; GENE REPLACEMENT THERAPY; GENE SEQUENCE; GENE TARGETING; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; NONHUMAN; POLYSOME; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROCESSING; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; UNFOLDED PROTEIN RESPONSE; WILD TYPE;

ALTERNARIA BRASSICICOLA; ASPERGILLUS NIGER; FUNGI; SACCHAROMYCES CEREVISIAE;

EID: 79251530770     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385114-7.00001-5     Document Type: Chapter

References (49)

1. H. Akamatsu, Y. Itoh, M. Kodama, H. Otani, and K. Kohmoto AAL-toxin-deficient mutants of alternaria alternata tomato pathotype by restriction enzyme-mediated integration Phytopathology 87 1997 967 972
2. H. Al-Sheikh, A.J. Watson, G.A. Lacey, P.J. Punt, D.A. MacKenzie, D.J. Jeenes, T. Pakula, M. Penttila, M.J. Alcocer, and D.B. Archer Endoplasmic reticulum stress leads to the selective transcriptional downregulation of the glucoamylase gene in Aspergillus niger Mol. Microbiol. 53 2004 1731 1742
3. M.R. Andersen, W. Vongsangnak, G. Panagiotou, M.P. Salazar, L. Lehmann, and J. Nielsen A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species Proc. Natl. Acad. Sci. USA 105 2008 4387 4392
4. Y. Arava Isolation of polysomal RNA for microarray analysis Methods Mol. Biol. 224 2003 79 87
5. D.B. Archer, and G. Turner Genomics of protein secretion and hyphal growth in Aspergillus A. Brown, The Mycota XIII, Fungal Genomics 2006 Springer, New york 75 96
6. M. Arvas, T. Pakula, K. Lanthaler, M. Saloheimo, M. Valkonen, T. Suortti, G. Robson, and M. Penttila Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae BMC Genomics 7 2006 32
7. A. Bashir, V. Bansal, and V. Bafna Designing deep sequencing experiments: Detecting structural variation and estimating transcript abundance BMC Genomics 11 2010 385
8. A. Breakspear, and M. Momany The first fifty microarray studies in filamentous fungi Microbiology 153 2007 7 15
9. N.D. Carvalho, M. Arentshorst, M. Jin Kwon, V. Meyer, and A.F. Ram Expanding the ku70 toolbox for filamentous fungi: Establishment of complementation vectors and recipient strains for advanced gene analyses Appl. Microbiol. Biotechnol. 87 2010 1463 1473
10. A. Conesa, P.J. Punt, N. van Luijk, and C.A. van den Hondel The secretion pathway in filamentous fungi: A biotechnological view Fungal Genet. Biol. 33 2001 155 171
11. Y.M. de Ruiter-Jacobs, M. Broekhuijsen, S.E. Unkles, E.I. Campbell, J.R. Kinghorn, R. Contreras, P.H. Pouwels, and C.A. van den Hondel A gene transfer system based on the homologous pyrG gene and efficient expression of bacterial genes in Aspergillus oryzae Curr. Genet. 16 1989 159 163
12. R. Fischer, N. Zekert, and N. Takeshita Polarized growth in fungiInterplay between the cytoskeleton, positional markers and membrane domains Mol. Microbiol. 68 2008 813 826
13. S. Geysens, G. Whyteside, and D.B. Archer Genomics of protein folding in the endoplasmic reticulum, secretion stress and glycosylation in the aspergilli Fungal Genet. Biol. 46 2009 S121 S140
14. R.J. Gouka, P.J. Punt, and C.A. van den Hondel Efficient production of secreted proteins by Aspergillus: Progress, limitations and prospects Appl. Microbiol. Biotechnol. 47 1997 1 11
15. T. Guillemette, N.N. van Peij, T. Goosen, K. Lanthaler, G.D. Robson, C.A. van den Hondel, H. Stam, and D.B. Archer Genomic analysis of the secretion stress response in the enzyme-producing cell factory Aspergillus niger BMC Genomics 8 2007 158
16. S.D. Harris Branching of fungal hyphae: Regulation, mechanisms and comparison with other branching systems Mycologia 100 2008 823 832
17. M. Hirota, M. Kitagaki, H. Itagaki, and S. Aiba Quantitative measurement of spliced XBP1 mRNA as an indicator of endoplasmic reticulum stress J. Toxicol. Sci. 31 2006 149 156
18. D.I. Jacobs, M.M. Olsthoorn, I. Maillet, M. Akeroyd, S. Breestraat, S. Donkers, R.A. van der Hoeven, C.A. van den Hondel, R. Kooistra, T. Lapointe, H. Menke, and R. Meulenberg Effective lead selection for improved protein production in Aspergillus niger based on integrated genomics Fungal Genet. Biol. 46 Suppl. 1 2009 S141 S152
19. T.R. Jorgensen, T. Goosen, C.A. Hondel, A.F. Ram, and J.J. Iversen Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway BMC Genomics 10 2009 44
20. A. Joubert, B. Calmes, R. Berruyer, M. Pihet, J.P. Bouchara, P. Simoneau, and T. Guillemette Laser nephelometry applied in an automated microplate system to study filamentous fungus growth Biotechniques 48 2010 399 404
21. K. Kohno Stress-sensing mechanisms in the unfolded protein response: Similarities and differences between yeast and mammals J. Biochem. 147 2010 27 33
22. S. Le Crom, W. Schackwitz, L. Pennacchio, J.K. Magnuson, D.E. Culley, J.R. Collett, J. Martin, I.S. Druzhinina, H. Mathis, F. Monot, B. Seiboth, and B. Cherry Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing Proc. Natl. Acad. Sci. USA 106 2009 16151 16156
23. D. Lubertozzi, and J.D. Keasling Developing Aspergillus as a host for heterologous expression Biotechnol. Adv. 27 2009 53 75
24. M. Machida, K. Asai, M. Sano, T. Tanaka, T. Kumagai, G. Terai, K. Kusumoto, T. Arima, O. Akita, Y. Kashiwagi, K. Abe, and K. Gomi Genome sequencing and analysis of Aspergillus oryzae Nature 438 2005 1157 1161
25. J.E. McCarthy Posttranscriptional control of gene expression in yeast Microbiol. Mol. Biol. Rev. 62 1998 1492 1553
26. V. Meyer, R.A. Damveld, M. Arentshorst, U. Stahl, C.A. van den Hondel, and A.F. Ram Survival in the presence of antifungals: Genome-wide expression profiling of Aspergillus niger in response to sublethal concentrations of caspofungin and fenpropimorph J. Biol. Chem. 282 2007 32935 32948
27. V. Meyer, M. Arentshorst, S.J. Flitter, B.M. Nitsche, M.J. Kwon, C.G. Reynaga-Pena, S. Bartnicki-Garcia, C.A. van den Hondel, and A.F. Ram Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics Eukaryot. Cell 8 2009 1677 1691
28. V. Meyer, A. Ram, and P.J. Punt Genetics, genetic manipulation, and approaches to strain improvement of filamentous fungi A.L. Demain, J.L. Davies, Manual of Industrial Microbiology and Biotechnology 3rd edn. 2010 Wiley New York 318 329
29. C.B. Michielse, P.J. Hooykaas, C.A. van den Hondel, and A.F. Ram Agrobacterium-mediated transformation of the filamentous fungus Aspergillus awamori Nat. Protoc. 3 2008 1671 1678
30. H.J. Mulder, and I. Nikolaev HacA-dependent transcriptional switch releases hacA mRNA from a translational block upon endoplasmic reticulum stress Eukaryot. Cell 8 2009 665 675
31. H.J. Mulder, M. Saloheimo, M. Penttila, and S.M. Madrid The transcription factor HACA mediates the unfolded protein response in Aspergillus niger, and up-regulates its own transcription Mol. Genet. Genomics 271 2004 130 140
32. T.M. Pakula, M. Laxell, A. Huuskonen, J. Uusitalo, M. Saloheimo, and M. Penttila The effects of drugs inhibiting protein secretion in the filamentous fungus Trichoderma reesei. Evidence for down-regulation of genes that encode secreted proteins in the stressed cells J. Biol. Chem. 278 2003 45011 45020
33. H.J. Pel, J.H. de Winde, D.B. Archer, P.S. Dyer, G. Hofmann, P.J. Schaap, G. Turner, R.P. de Vries, R. Albang, K. Albermann, M.R. Andersen, and J.D. Bendtsen Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 Nat. Biotechnol. 25 2007 221 231
34. B. Pradet-Balade, F. Boulme, H. Beug, E.W. Mullner, and J.A. Garcia-Sanz Translation control: Bridging the gap between genomics and proteomics? Trends Biochem. Sci. 26 2001 225 229
35. D.L. Richie, L. Hartl, V. Aimanianda, M.S. Winters, K.K. Fuller, M.D. Miley, S. White, J.W. McCarthy, J.P. Latge, M. Feldmesser, J.C. Rhodes, and D.S. Askew A role for the unfolded protein response (UPR) in virulence and antifungal susceptibility in Aspergillus fumigatus PLoS Pathog. 5 2009 e1000258
36. U. Ruegsegger, J.H. Leber, and P. Walter Block of HAC1 mRNA translation by long-range base pairing is released by cytoplasmic splicing upon induction of the unfolded protein response Cell 107 2001 103 114
37. J.Y. Shoji, M. Arioka, and K. Kitamoto Dissecting cellular components of the secretory pathway in filamentous fungi: Insights into their application for protein production Biotechnol. Lett. 30 2008 7 14
38. A.H. Sims, M.E. Gent, K. Lanthaler, N.S. Dunn-Coleman, S.G. Oliver, and G.D. Robson Transcriptome analysis of recombinant protein secretion by Aspergillus nidulans and the unfolded-protein response in vivo Appl. Environ. Microbiol. 71 2005 2737 2747
39. C.W. Smith, J.G. Klaasmeyer, J.B. Edeal, T.L. Woods, and S.J. Jones Effects of serum deprivation, insulin and dexamethasone on polysome percentages in C2C12 myoblasts and differentiating myoblasts Tissue Cell 31 1999 451 458
40. J.A. Sweigard, A.M. Carroll, S. Kang, L. Farrall, F.G. Chumley, and B. Valent Identification, cloning, and characterization of PWL2, a gene for host species specificity in the rice blast fungus Plant Cell 7 1995 1221 1233
41. K.J. Travers, C.K. Patil, L. Wodicka, D.J. Lockhart, J.S. Weissman, and P.\ Walter Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation Cell 101 2000 249 258
42. M. Valkonen, M. Ward, H. Wang, M. Penttila, and M. Saloheimo Improvement of foreign-protein production in Aspergillus niger var. awamori by constitutive induction of the unfolded-protein response Appl. Environ. Microbiol. 69 2003 6979 6986
43. R.F. van Gorcom, and C.A. van den Hondel Expression analysis vectors for Aspergillus niger Nucleic Acids Res. 16 1988 9052
44. W. van Hartingsveldt, I.E. Mattern, C.M. van Zeijl, P.H. Pouwels, and C.A. van den Hondel Development of a homologous transformation system for Aspergillus niger based on the pyrG gene Mol. Gen. Genet. 206 1987 71 75
45. W. Vishniac, and M. Santer The thiobacilli Bacteriol. Rev. 21 1957 195 213
46. W. Vongsangnak, I. Nookaew, M. Salazar, and J. Nielsen Analysis of genome-wide coexpression and coevolution of Aspergillus oryzae and Aspergillus niger OMICS 14 2010 165 175
47. Z. Wang, M. Gerstein, and M. Snyder RNA-Seq: A revolutionary tool for transcriptomics Nat. Rev. Genet. 10 2009 57 63
48. T.T. Wimalasena, B. Enjalbert, T. Guillemette, A. Plumridge, S. Budge, Z. Yin, A.J. Brown, and D.B. Archer Impact of the unfolded protein response upon genome-wide expression patterns, and the role of Hac1 in the polarized growth, of Candida albicans Fungal Genet. Biol. 45 2008 1235 1247
49. J.H. Yu, Z. Hamari, K.H. Han, J.A. Seo, Y. Reyes-Dominguez, and C. Scazzocchio Double-joint PCR: A PCR-based molecular tool for gene manipulations in filamentous fungi Fungal Genet. Biol. 41 2004 973 981