Long-term strain improvements accumulate mutations in regulatory elements responsible for hyper-production of cellulolytic enzymes

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Liu, Guodong ^a   Zhang, Lei ^b   Qin, Yuqi ^a   Zou, Gen ^b   Li, Zhonghai ^a   Yan, Xing ^b   Wei, Xiaomin ^a   Chen, Mei ^a   Chen, Ling ^b   Zheng, Kai ^a   Zhang, Jun ^b   Ma, Liang ^b   Li, Jie ^a   Liu, Rui ^b   Xu, Hai ^a   Bao, Xiaoming ^a   Fang, Xu ^a   Wang, Lushan ^a   Zhong, Yaohua ^a   Liu, Weifeng ^b   Zheng, Huajun ^c   Wang, Shengyue ^c   Wang, Chengshu ^b   Xun, Luying ^a,d   Zhao, Guo Ping ^b,c   Wang, Tianhong ^a   Zhou, Zhihua ^b   Qu, Yinbo ^a   more..

^a SHANDONG UNIVERSITY   (China)

^b INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^c CHINESE NATIONAL HUMAN GENOME CENTER AT SHANGHAI   (China)

^d WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULASE; GLYCOSIDASE; HEMICELLULASE; TRANSCRIPTOME;

ARTICLE; BIOSYNTHESIS; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; ENZYMOLOGY; GENETICS; NUCLEOTIDE SEQUENCE; PENICILLIUM; PROMOTER REGION;

BASE SEQUENCE; CELLULASES; GLYCOSIDE HYDROLASES; PENICILLIUM; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME;

EID: 84875769164     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep01569     Document Type: Article

References (52)

1. Somerville, C. The billion-ton biofuels vision. Science 312, 1277 (2006). (Pubitemid 43839509)
2. Fernando, S., Adhikari, S., Chandrapal, C. & Murali, N. Biorefineries: current status, challenges, and future direction. Energy & Fuels 20, 1727-1737 (2006). (Pubitemid 44193596)
3. Sanchez, C. Lignocellulosic residues: biodegradation and bioconversion by fungi. Biotechnol Adv 27, 185-194 (2009).
4. Cherry, J. R. & Fidantsef, A. L. Directed evolution of industrial enzymes: an update. Curr Opin Biotechnol 14, 438-443 (2003). (Pubitemid 37011326)
5. Gusakov, A. V. Alternatives to Trichoderma reesei in biofuel production. Trends Biotechnol 29, 419-425 (2011).
6. Esterbauer, H., Steiner, W., Labudova, I., Hermann, A. & Hayn, M. Production of Trichoderma cellulase in laboratory and pilot scale. Bioresour Technol 36, 51-65 (1991).
7. Ilmen, M., Thrane, C. & Penttila, M. The glucose repressor gene cre1 of Trichoderma: Isolation and expression of a full-length and a truncated mutant form. Mol Gen Genet 251, 451-460 (1996).
8. Nitta, M. et al. A new Zn(II)(2)Cys(6)-type transcription factor BglR regulates beta-glucosidase expression in Trichoderma reesei. Fungal Genet Biol 49, 388-397 (2012).
9. Geysens, S. et al. Cloning and characterization of the glucosidase II alpha subunit gene of Trichoderma reesei: a frameshift mutation results in the aberrant glycosylation profile of the hypercellulolytic strain Rut-C30. Appl Environ Microbiol 71, 2910-2924 (2005). (Pubitemid 40807194)
10. Le Crom, S. et al. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc Natl Acad Sci USA 106, 16151-16156 (2009).
11. Vitikainen, M. et al. Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties. BMC Genomics 11, 441 (2010).
12. Gusakov, A. V. & Sinitsyn, A. P. Cellulases from Penicillium species for producing fuels from biomass. Biofuels 3, 463-477 (2012).
13. Liu, G. et al. Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens. PLoS One 8, e55185 (2013).
14. Qu, Y., Gao, P. &Wang, Z. Screening of catabolite repression-resistantmutants of cellulase producing Penicillium spp. Acta Mycol Sinica 3, 238-243 (1984).
15. Qu, Y., Zhao, X.,Gao, P.&Wang, Z. Cellulase production from spent sulfite liquor and paper-mill waste fiber. Appl Biochem Biotechnol 28-29, 363-368 (1991).
16. Fang, X., Shen, Y., Zhao, J., Bao, X. & Qu, Y. Status and prospect of lignocellulosic bioethanol production in China. Bioresour Technol 101, 4814-4819 (2010).
17. Sun, X., Liu, Z., Qu, Y. & Li, X. The effects of wheat bran composition on the production of biomass-hydrolyzing enzymes by Penicillium decumbens. Appl Biochem Biotechnol 146, 119-128 (2008).
18. Andersen, M. R. et al. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res 21, 885-897 (2011).
19. Marcet-Houben, M. et al. Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus. BMC Genomics 13, 646 (2012).
20. Fedorova, N. D. et al. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genetics 4, e1000046 (2008).
21. Kumar, P., Henikoff, S. & Ng, P. C. Predicting the effects of coding nonsynonymous variants on protein function using the SIFT algorithm. Nat Protoc 4, 1073-1081 (2009).
22. Li, R. X. et al. Localized-statistical quantification of human serum proteome associated with type 2 diabetes. PLoS One 3, e3224 (2008).
23. Aro, N., Pakula, T. & Penttila, M. Transcriptional regulation of plant cell wall degradation by filamentous fungi. FEMS Microbiol Rev 29, 719-739 (2005). (Pubitemid 41139180)
24. Cubero, B. & Scazzocchio, C. Two different, adjacent and divergent zinc finger binding sites are necessary for CREA-mediated carbon catabolite repression in the proline gene cluster of Aspergillus nidulans. EMBO J 13, 407-415 (1994). (Pubitemid 24034224)
25. Sun, J. & Glass, N. L. Identification of the CRE-1 cellulolytic regulon in Neurospora crassa. PLoS One 6, e25654 (2011).
26. Petersen, K. L., Lehmbeck, J. & Christensen, T. A new transcriptional activator for amylase genes in Aspergillus. Mol Gen Genet 262, 668-676 (1999). (Pubitemid 30018809)
27. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. & Hirakawa, M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38, D355-360 (2010).
28. vanKuyk, P. A., Benen, J. A.,Wosten, H. A., Visser, J. & de Vries, R. P. A broader role for AmyR in Aspergillus niger: regulation of the utilisation of D-glucose or Dgalactose containing oligo-and polysaccharides. Appl Microbiol Biotechnol 93, 285-293 (2012).
29. Watanabe, J. et al. Loss of Aspergillus oryzae amyR function indirectly affects hemicellulolytic and cellulolytic enzyme production. J Biosci Bioeng 111, 408-413 (2011).
30. Foreman, P. K. et al. Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei. J Biol Chem 278, 31988-31997 (2003). (Pubitemid 37048387)
31. Margulies, M. et al. Genome sequencing inmicrofabricated high-density picolitre reactors. Nature 437, 376-380 (2005). (Pubitemid 41613494)
32. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J Mol Biol 215, 403-410 (1990).
33. Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676 (2005). (Pubitemid 41264107)
34. Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nat Genet 25, 25-29 (2000). (Pubitemid 30257031)
35. Hunter, S. et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40, D306-312 (2012).
36. Park, J. et al. FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors. Bioinformatics 24, 1024-1025 (2008). (Pubitemid 351448042)
37. Khaldi, N. et al. SMURF: Genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol 47, 736-741 (2010).
38. Mao, X., Cai, T., Olyarchuk, J. G. & Wei, L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21, 3787-3793 (2005). (Pubitemid 41535528)
39. Darling, A. C.,Mau, B., Blattner, F. R.&Perna, N. T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14, 1394-1403 (2004). (Pubitemid 39029237)
40. Darling, A. E., Mau, B. & Perna, N. T. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5, e11147 (2010).
41. Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol 5, R12 (2004).
42. Li, H.& Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
43. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
44. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).
45. Rumble, S. M. et al. SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol 5, e1000386 (2009).
46. Koboldt, D. C. et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25, 2283-2285 (2009).
47. Chundawat, S. P. et al. Proteomics-based compositional analysis of complex cellulase-hemicellulase mixtures. J Proteome Res 10, 4365-4372 (2011).
48. AC't Hoen, P. et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 36, e141-e141 (2008).
49. Audic, S. & Claverie, J. M. The significance of digital gene expression profiles. Genome Res 7, 986-995 (1997). (Pubitemid 27487763)
50. Benjamini, Y. & Yekutieli, D. The control of the false discovery rate in multiple testing under dependency. Ann Stat, 1165-1188 (2001). (Pubitemid 33575263)
51. Li, Z., Du, C., Zhong, Y. & Wang, T. Development of a highly efficient gene targeting system allowing rapid genetic manipulations in Penicillium decumbens. Appl Microbiol Biotechnol 87, 1065-1076 (2010).
52. Kubodera, T., Yamashita, N. & Nishimura, A. Transformation of Aspergillus sp. and Trichoderma reesei using the pyrithiamine resistance gene (ptrA) of Aspergillus oryzae. Biosci Biotechnol Biochem 66, 404-406 (2002). (Pubitemid 39251064)