Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose

Biotechnology for Biofuels

Volumn 7, Issue 1, 2014, Pages

  Li, Jingen ^a,c   Lin, Liangcai ^a   Li, Huiyan ^a   Tian, Chaoguang ^a   Ma, Yanhe ^a,b  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b INSTITUTE OF MICROBIOLOGY   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

GLT 1; HCR 1; L arabinose; Neurospora crassa; RNA seq; XAT 1; XYT 1

Indexed keywords

CARBON; DATA PROCESSING; FUNGI; GENES; METABOLISM; TRANSCRIPTION FACTORS;

GLT-1; HCR-1; L-ARABINOSE; NEUROSPORA CRASSA; RNA-SEQ; XAT-1; XYT-1;

GLUCOSE;

CELL ORGANELLE; CONCENTRATION (COMPOSITION); EXPERIMENTAL STUDY; FUNGUS; GENE EXPRESSION; GLUCOSE; MONOSACCHARIDE; RNA;

FUNGI; NEUROSPORA CRASSA;

EID: 84898049901     PISSN: 17546834     EISSN: None     Source Type: Journal    
DOI: 10.1186/1754-6834-7-31     Document Type: Article

References (56)

1. Using a model filamentous fungus to unravel mechanisms of lignocellulose deconstruction. Znameroski EA, Glass NL, Biotechnol Biofuels 2013 6 6 10.1186/1754-6834-6-6 23339486
2. Molecular cloning and functional expression of a novel Neurospora crassa xylose reductase in Saccharomyces cerevisiae in the development of a xylose fermenting strain. Gururajan VT, Pretorius IS, Otero RRC, Ann Microbiol 2007 57 223 231 10.1007/BF03175211
3. High activity of xylose reductase and xylitol dehydrogenase improves xylose fermentation by recombinant Saccharomyces cerevisiae. Karhumaa K, Fromanger R, Hahn-Hagerdal B, Gorwa-Grauslund MF, Appl Microbiol Biotechnol 2007 73 1039 1046 16977466
4. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, LaButti KM, Sun H, Clum A, Pangilinan JL, Lindquist EA, Lucas S, Lapidus A, Jin M, Gunawan C, Balan V, Dale BE, Jeffries TW, Zinkel R, Barry KW, Grigoriev IV, Gasch AP, Proc Natl Acad Sci USA 2011 108 13212 13217 10.1073/pnas.1103039108 21788494
5. DNA microarray analysis of the expression of the genes encoding the major enzymes in ethanol production during glucose and xylose co-fermentation by metabolically engineered Saccharomyces yeast. Sedlak M, Edenberg HJ, Ho NWY, Enzyme Microb Tech 2003 33 19 28 10.1016/S0141-0229(03)00067-X
6. RNA-Seq of the xylose-fermenting yeast Scheffersomyces stipitis cultivated in glucose or xylose. Yuan T, Ren Y, Meng K, Feng Y, Yang P, Wang S, Shi P, Wang L, Xie D, Yao B, Appl Microbiol Biotechnol 2011 92 1237 1249 10.1007/s00253-011-3607-6 22086068
7. Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway. Jorgensen TR, Goosen T, Hondel CA, Ram AF, Iversen JJ, BMC Genomics 2009 10 44 10.1186/1471-2164-10-44 19166577
8. Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa. Sun J, Tian C, Diamond S, Glass NL, Eukaryot Cell 2012 11 482 493 10.1128/EC.05327-11 22345350
9. Discovery and characterization of novel d-xylose-specific transporters from Neurospora crassa and Pichia stipitis. Du J, Li S, Zhao H, Mol Biosyst 2010 6 2150 2156 10.1039/c0mb00007h 20714641
10. The glucose/xylose facilitator Gxf1 from Candida intermedia expressed in a xylose-fermenting industrial strain of Saccharomyces cerevisiae increases xylose uptake in SSCF of wheat straw. Fonseca C, Olofsson K, Ferreira C, Runquist D, Fonseca LL, Hahn-Hagerdal B, Liden G, Enzyme Microb Tech 2011 48 518 525 10.1016/j.enzmictec.2011.02.010
11. Improving L-arabinose utilization of pentose fermenting Saccharomyces cerevisiae cells by heterologous expression of L-arabinose transporting sugar transporters. Subtil T, Boles E, Biotechnol Biofuels 2011 4 38 10.1186/1754-6834-4-38 21992610
12. Two cellobiohydrolase-encoding genes from Aspergillus niger require D-xylose and the xylanolytic transcriptional activator XlnR for their expression. Gielkens MMC, Dekkers E, Visser J, de Graaff LH, Appl Environ Microb 1999 65 4340 4345
13. A transcriptional activator, AoXlnR, controls the expression of genes encoding xylanolytic enzymes in Aspergillus oryzae. Marui J, Tanaka A, Mimura S, de Graaff LH, Visser J, Kitamoto N, Kato M, Kobayashi T, Tsukagoshi N, Fungal Genet Biol 2002 35 157 169 10.1006/fgbi.2001.1321 11848678
14. D-Xylose as a repressor or inducer of xylanase expression in Hypocrea jecorina (Trichoderma reesei). Mach-Aigner AR, Pucher ME, Mach RL, Appl Environ Microbiol 2010 76 1770 1776 10.1128/AEM.02746-09 20097821
15. Functional analysis of the transcriptional activator XlnR from Aspergillus niger. Hasper AA, Trindade LM, van der Veen D, van Ooyen AJ, de Graaff LH, Microbiology 2004 150 1367 1375 10.1099/mic.0.26557-0 15133098
16. Xyr1 (xylanase regulator 1) regulates both the hydrolytic enzyme system and D-xylose metabolism in Hypocrea jecorina. Stricker AR, Grosstessner-Hain K, Wurleitner E, Mach RL, Eukaryot Cell 2006 5 2128 2137 10.1128/EC.00211-06 17056741
17. Fungal arabinan and L-arabinose metabolism. Seiboth B, Metz B, Appl Microbiol Biotechnol 2011 89 1665 1673 10.1007/s00253-010-3071-8 21212945
18. Analysis of regulation of pentose utilisation in Aspergillus niger reveals evolutionary adaptations in Eurotiales. Battaglia E, Visser L, Nijssen A, van Veluw GJ, Wosten HA, de Vries RP, Stud Mycol 2011 69 31 38 10.3114/sim.2011.69.03 21892241
19. Regulation of pentose utilisation by AraR, but not XlnR, differs in Aspergillus nidulans and Aspergillus niger. Battaglia E, Hansen SF, Leendertse A, Madrid S, Mulder H, Nikolaev I, de Vries RP, Appl Microbiol Biotechnol 2011 91 387 397 10.1007/s00253-011-3242-2 21484208
20. Neurospora: a model of model microbes. Davis RH, Perkins DD, Nat Rev Genet 2002 3 397 403 11988765
21. Structure and engineering of L-arabinitol 4-dehydrogenase from Neurospora crassa. Bae B, Sullivan RP, Zhao H, Nair SK, J Mol Biol 2010 402 230 240 10.1016/j.jmb.2010.07.033 20655316
22. Heterologous expression, purification, and characterization of a highly active xylose reductase from Neurospora crassa. Woodyer R, Simurdiak M, van der Donk WA, Zhao H, Appl Environ Microbiol 2005 71 1642 1647 10.1128/AEM.71.3.1642- 1647.2005 15746370
23. Biochemical characterization of an L-xylulose reductase from Neurospora crassa. Nair N, Zhao H, Appl Environ Microbiol 2001-2004 2007 73
24. Cloning, characterization, and mutational analysis of a highly active and stable L-arabinitol 4-dehydrogenase from Neurospora crassa. Sullivan R, Zhao H, Appl Microbiol Biotechnol 2007 77 845 852 10.1007/s00253-007-1225-0 17938906
25. Molecular regulation of arabinan and L-arabinose metabolism in Hypocrea jecorina (Trichoderma reesei). Akel E, Metz B, Seiboth B, Kubicek CP, Eukaryot Cell 1837-1844 2009 8
26. Genetic and microbiological research techniques for Neurospora crassa. Davis RH, De Serres FJ, Methods Enzymol 1970 17 65
27. Differential expression analysis for sequence count data. Anders S, Huber W, Genome Biol 2010 11 106 10.1186/gb-2010-11-10-r106 20979621
28. RNA-seq: technical variability and sampling. McIntyre LM, Lopiano KK, Morse AM, Amin V, Oberg AL, Young LJ, Nuzhdin SV, BMC Genomics 2011 12 293 10.1186/1471-2164-12-293 21645359
29. Open source clustering software. de Hoon MJL, Imoto S, Nolan J, Miyano S, Bioinformatics 2004 20 1453 1454 10.1093/bioinformatics/bth078 14871861
30. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M, Mewes HW, Nucleic Acids Res 2004 32 5539 5545 10.1093/nar/gkh894 15486203
31. rco-3, a gene involved in glucose transport and conidiation in Neurospora crassa. Madi L, McBride SA, Bailey LA, Ebbole DJ, Genetics 1997 146 499 508 9178001
32. Cellodextrin transport in yeast for improved biofuel production. Galazka JM, Tian C, Beeson WT, Martinez B, Glass NL, Cate JH, Science 2010 330 84 86 10.1126/science.1192838 20829451
33. A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations. Benz JP, Chau BH, Zheng D, Bauer S, Glass NL, Somerville CR, Mol Microbiol 2014 91 275 299 10.1111/mmi.12459 24224966
34. Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins. Znameroski EA, Coradetti ST, Roche CM, Tsai JC, Iavarone AT, Cate JH, Glass NL, Proc Natl Acad Sci USA 2012 109 6012 6017 10.1073/pnas.1118440109 22474347
35. Competition between pentoses and glucose during uptake and catabolism in recombinant Saccharomyces cerevisiae. Subtil T, Boles E, Biotechnol Biofuels 2012 5 14 10.1186/1754-6834-5-14 22424089
36. Expression of the Gxf1 transporter from Candida intermedia improves fermentation performance in recombinant xylose-utilizing Saccharomyces cerevisiae. Runquist D, Fonseca C, Radstrom P, Spencer-Martins I, Hahn-Hagerdal B, Appl Microbiol Biotechnol 2009 82 123 130 10.1007/s00253-008-1773-y 19002682
37. Expression of a heterologous xylose transporter in a Saccharomyces cerevisiae strain engineered to utilize xylose improves aerobic xylose consumption. Hector RE, Qureshi N, Hughes SR, Cotta MA, Appl Microbiol Biotechnol 2008 80 675 684 10.1007/s00253-008-1583-2 18629494
38. Comparison of heterologous xylose transporters in recombinant Saccharomyces cerevisiae. Runquist D, Hahn-Hagerdal B, Radstrom P, Biotechnol Biofuels 2010 3 5 10.1186/1754-6834-3-5 20236521
39. Improvement of ethanol productivity during xylose and glucose co-fermentation by xylose-assimilating S. cerevisiae via expression of glucose transporter Sut1. Katahira S, Ito M, Takema H, Fujita Y, Tanino T, Tanaka T, Fukuda H, Kondo A, Enzyme Microb Tech 2008 43 115 119 10.1016/j.enzmictec.2008. 03.001
40. TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Ren Q, Chen K, Paulsen IT, Nucleic Acids Res 2007 35 274 D279 10.1093/nar/gkl925 17135193
41. Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa. Xie X, Wilkinson HH, Correa A, Lewis ZA, Bell-Pedersen D, Ebbole DJ, Fungal Genet Biol 2004 41 1104 1119 10.1016/j.fgb.2004.08.009 15531214
42. L-arabitol is the actual inducer of xylanase expression in Hypocrea jecorina (Trichoderma reesei). Mach-Aigner AR, Gudynaite-Savitch L, Mach RL, Appl Environ Microbiol 2011 77 5988 5994 10.1128/AEM.05427-11 21742908
43. Cellulase activity mapping of Trichoderma reesei cultivated in sugar mixtures under fed-batch conditions. Jourdier E, Cohen C, Poughon L, Larroche C, Monot F, Chaabane FB, Biotechnol Biofuels 2013 6 79 10.1186/1754-6834-6-79 23680258
44. The influence of Aspergillus niger transcription factors AraR and XlnR in the gene expression during growth in d-xylose, l-arabinose and steam-exploded sugarcane bagasse. de Souza WR, Maitan-Alfenas GP, de Gouvea PF, Brown NA, Savoldi M, Battaglia E, Goldman MH, de Vries RP, Goldman GH, Fungal Genet Biol 2013 60 29 45 23892063
45. Improved xylanase production by Trichoderma reesei grown on L-arabinose and lactose or D-glucose mixtures. Xiong H, Turunen O, Pastinen O, Leisola M, von Weymarn N, Appl Microbiol Biotechnol 2004 64 353 358 10.1007/s00253-003- 1548-4 14740196
46. Xylanase production by Trichoderma reesei Rut C-30 grown on L-arabinose-rich plant hydrolysates. Xiong H, von Weymarn N, Turunen O, Leisola M, Pastinen O, Bioresour Technol 2005 96 753 759 10.1016/j.biortech.2004.08.007 15607187
47. Xylanase gene transcription in Trichoderma reesei is triggered by different inducers representing different hemicellulosic pentose polymers. Herold S, Bischof R, Metz B, Seiboth B, Kubicek CP, Eukaryot Cell 2013 12 390 398 10.1128/EC.00182-12 23291620
48. A convenient growth medium for Neurospora. Vogel HJ, Microb Genet Bull 1956 13 42 46
49. Concurrent knock-out of at least 20 transporter genes is required to block uptake of hexoses in Saccharomyces cerevisiae. Wieczorke R, Krampe S, Weierstall T, Freidel K, Hollenberg CP, Boles E, Febs Letters 1999 464 123 128 10.1016/S0014-5793(99)01698-1 10618490
50. Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa. Tian C, Beeson WT, Iavarone AT, Sun J, Marletta MA, Cate JH, Glass NL, Proc Natl Acad Sci USA 2009 106 22157 22162 10.1073/pnas.0906810106 20018766
51. FastQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
52. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. Patel RK, Jain M, PLoS One 2012 7 30619 10.1371/journal.pone. 0030619 22312429
53. The genome sequence of the filamentous fungus Neurospora crassa. 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, Schulte U, Kothe GO, Jedd G, Mewes W, et al. Nature 2003 422 859 868 10.1038/nature01554 12712197
54. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L, Nat Protoc 2012 7 562 578 10.1038/nprot.2012.016 22383036
55. Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Gietz RD, Woods RA, Methods Enzymol 2002 350 87 96 12073338
56. Involvement of kinases in glucose and fructose uptake by Saccharomyces cerevisiae. Bisson LF, Fraenkel DG, Proc Natl Acad Sci USA 1983 80 1730 1734 10.1073/pnas.80.6.1730 6300872