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Transcription Analysis of Recombinant Trichoderma reesei HJ-48 to Compare the Molecular Basis for Fermentation of Glucose and Xylose

  • Huang, Jun (National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences) ;
  • Lin, Mei (National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences) ;
  • Liang, Shijie (National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences) ;
  • Qin, Qiurong (National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences) ;
  • Liao, Siming (National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences) ;
  • Lu, Bo (National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences) ;
  • Wang, Qingyan (National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences)
  • Received : 2020.04.06
  • Accepted : 2020.07.15
  • Published : 2020.10.28

Abstract

Profiling the transcriptome changes involved in xylose metabolism by the fungus Trichoderma reesei allows for the identification of potential targets for ethanol production processing. In the present study, the transcriptome of T. reesei HJ-48 grown on xylose versus glucose was analyzed using next-generation sequencing technology. During xylose fermentation, numerous genes related to central metabolic pathways, including xylose reductase (XR) and xylitol dehydrogenase (XDH), were expressed at higher levels in T. reesei HJ-48. Notably, growth on xylose did not fully repress the genes encoding enzymes of the tricarboxylic acid and respiratory pathways. In addition, increased expression of several sugar transporters was observed during xylose fermentation. This study provides a valuable dataset for further investigation of xylose fermentation and provides a deeper insight into the various genes involved in this process.

Keywords

References

  1. Zheng JN, Negi A, Khomlaem C, Kim BS. 2019. Comparison of bioethanol production by Candida molischiana and Saccharomyces cerevisiae from glucose, cellobiose, and cellulose. J. Microbiol. Biotechnol. 29: 905-912. https://doi.org/10.4014/1904.04014
  2. Kumar V, Binod P, Sindhu R, Gnansounou E, Ahluwalia V. 2018. Bioconversion of pentose sugars to value added chemicals and fuels: Recent trends, challenges and possibilities. Bioresour. Technol. 269: 443-451. https://doi.org/10.1016/j.biortech.2018.08.042
  3. Tang HT, Hou J, Shen Y, Xu LL, Yang H, Fang X, et al. 2013. High beta-glucosidase secretion in Saccharomyces cerevisiae improves the efficiency of cellulase hydrolysis and ethanol production in simultaneous saccharification and fermentation. J. Microbiol. Biotechnol. 23: 1577-1585. https://doi.org/10.4014/jmb.1305.05011
  4. Nijland JG, Vos E, Shin HY, de Waal PP, Klaassen P, Driessen AJ. 2016. Improving pentose fermentation by preventing ubiquitination of hexose transporters in Saccharomyces cerevisiae. Biotechnol. Biofuels 9: 158. https://doi.org/10.1186/s13068-016-0573-3
  5. Liu H, Sun J, Chang JS, Shukla P. 2018. Engineering microbes for direct fermentation of cellulose to bioethanol. Crit. Rev. Biotechnol. 38: 1089-1105. https://doi.org/10.1080/07388551.2018.1452891
  6. Zou ZS, Zhao YY, Zhang TZ, Xu JX, He AY, Deng Y. 2018. Efficient isolation and characterization of a cellulase hyperproducing mutant strain of Trichoderma reesei. J. Microbiol. Biotechnol. 28: 1473-1481. https://doi.org/10.4014/jmb.1805.05009
  7. Xu Q, Singh A, Himmel ME. 2009. Perspectives and new directions for the production of bioethanol using consolidated bioprocessing of lignocellulose. Curr. Opin. Biotechnol. 20: 364-371. https://doi.org/10.1016/j.copbio.2009.05.006
  8. Li YH, Zhang XY, Zhang F, Peng LC, Zhang DB, Kondo A, et al. 2018. Optimization of cellulolytic enzyme components through engineering Trichoderma reesei and on-site fermentation using the soluble inducer for cellulosic ethanol production from corn stover. Biotechnol. Biofuels 11: 49. https://doi.org/10.1186/s13068-018-1048-5
  9. Huang J, Chen D, Wei Y, Wang Q, Li Z, Chen Y, et al. 2014. Direct ethanol production from lignocellulosic sugars and sugarcane bagasse by a recombinant Trichoderma reesei strain HJ48. ScientificWorldJournal. 2014: 798683.
  10. Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, et al. 2014. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 15: 552. https://doi.org/10.1186/1471-2164-15-552
  11. Matsushika A, Goshima T, Hoshino T. 2014. Transcription analysis of recombinant industrial and laboratory Saccharomyces cerevisiae strains reveals the molecular basis for fermentation of glucose and xylose. Microb. Cell Fact. 13: 16. https://doi.org/10.1186/1475-2859-13-16
  12. Huang J, Wu R, Chen D, Wang Q, Huang R. 2016. Transcriptional profiling of the Trichoderma reesei recombinant strain HJ48 by RNA-Seq. J. Microbiol. Biotechnol. 26: 1242-1251.13. https://doi.org/10.4014/jmb.1602.02003
  13. Yang M, Xu L, Liu Y, Yang P. 2015. RNA-Seq uncovers SNPs and alternative splicing events in asian lotus (Nelumbo nucifera). PLoS One. 10: e0125702. https://doi.org/10.1371/journal.pone.0125702
  14. Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, et al. 2008. Genome sequencing and analysis of the biomassdegrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat. Biotechnol. 26: 553-560. https://doi.org/10.1038/nbt1403
  15. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14: R36. https://doi.org/10.1186/gb-2013-14-4-r36
  16. Anders S, Pyl PT, Huber W. 2015. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31: 166-169. https://doi.org/10.1093/bioinformatics/btu638
  17. Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5: 621-628. https://doi.org/10.1038/nmeth.1226
  18. Wang L, Feng Z, Wang X, Wang X, Zhang X. 2010. DEGseq: an R package for identifying differentially expressed genes from RNAseq data. Bioinformatics 26: 136-138. https://doi.org/10.1093/bioinformatics/btp612
  19. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B 1: 289-300.
  20. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol. 11: R106. https://doi.org/10.1186/gb-2010-11-10-r106
  21. Mao XZ, Cai T, Olyarchuk JG, Wei LP. 2005. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21: 3787-3793. https://doi.org/10.1093/bioinformatics/bti430
  22. Li J, Lin L, Li H, Tian C, Ma Y. 2014. Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose. Biotechnol. Biofuels 7: 31. https://doi.org/10.1186/1754-6834-7-31
  23. Stincone A, Prigione A, Cramer T, Wamelink MM, Campbell K, Cheung E, et al. 2015. The return of metabolism: biochemistry and physiology of the pentose phosphate pathway. Biol. Rev. Camb. Philos. Soc. 90: 927-963. https://doi.org/10.1111/brv.12140
  24. Matsushika A, Goshima T, Hoshino T. 2014. Transcription analysis of recombinant industrial and laboratory Saccharomyces cerevisiae strains reveals the molecular basis for fermentation of glucose and xylose. Microb. Cell Fact. 13: 16. https://doi.org/10.1186/1475-2859-13-16
  25. Runquist D, Hahn-Hagerdal B, Bettiga M. 2009. Increased expression of the oxidative pentose phosphate pathway and gluconeogenesis in anaerobically growing xylose-utilizing Saccharomyces cerevisiae. Microb. Cell Fact. 8: 49. https://doi.org/10.1186/1475-2859-8-49
  26. Rodriguez A, de la Cera T, Herrero P, Moreno F. 2001. The hexokinase 2 protein regulates the expression of the GLK1, HXK1 and HXK2 genes of Saccharomyces cerevisiae. Biochem. J. 355: 625-631. https://doi.org/10.1042/bj3550625
  27. Brown SR, Staff M, Lee R, Love J, Parker DA, Aves SJ, et al. 2018. Design of experiments methodology to build a multifactorial statistical model describing the metabolic interactions of alcohol dehydrogenase isozymes in the ethanol biosynthetic pathway of the yeast Saccharomyces cerevisiae. Acs Synth. Biol. 7: 1676-1684. https://doi.org/10.1021/acssynbio.8b00112
  28. Yao YX, Li M, Zhai H, You CX, Hao YJ. 2011. Isolation and characterization of an apple cytosolic malate dehydrogenase gene reveal its function in malate synthesis. J. Plant Physiol. 168: 474-480. https://doi.org/10.1016/j.jplph.2010.08.008
  29. Zeng WY, Tang YQ, Gou M, Xia ZY, Kida K. 2016. Transcriptomes of a xylose-utilizing industrial flocculating Saccharomyces cerevisiae strain cultured in media containing different sugar sources. AMB Express 6: 51. https://doi.org/10.1186/s13568-016-0223-y
  30. Hossain S, Svec D, Mrsa V, Teparic R. 2018. Overview of catalytic properties of fungal xylose reductases and molecular engineering approaches for improved xylose utilisation in yeast. Appl. Food Biotechnol. 5: 47-58.
  31. Li HB, Schmitz O, Alper HS. 2016. Enabling glucose/xylose co-transport in yeast through the directed evolution of a sugar transporter. Appl. Microbiol. Biotechnol. 100: 10215-10223. https://doi.org/10.1007/s00253-016-7879-8
  32. Moyses DN, Reis VC, de Almeida JR, de Moraes LM, Torres FA. 2016. Xylose fermentation by Saccharomyces cerevisiae: challenges and prospects. Int. J. Mol. Sci. 17: 207. https://doi.org/10.3390/ijms17030207
  33. Yang BX , Xie CY , Xia ZY, Wu YJ. 2020. The effect of xylose reductase genes on xylitol production by industrial Saccharomyces cerevisiae in fermentation of glucose and xylose. Process Biochem. 95: 122-130. https://doi.org/10.1016/j.procbio.2020.05.023
  34. Hong Y, Dashtban M, Kepka G, Chen S, Qin W. 2014. Overexpression of D-xylose reductase (xyl1) gene and antisense inhibition of D-xylulokinase (xyiH) gene increase xylitol production in Trichoderma reesei. Biomed. Res. Int. 2014: 169705.
  35. Perl A, Hanczko R, Telarico T, Oaks Z, Landas S. 2011. Oxidative stress, inflammation and carcinogenesis are controlled through the pentose phosphate pathway by transaldolase. Trends Mol. Med. 17: 395-403. https://doi.org/10.1016/j.molmed.2011.01.014
  36. Souto-Maior AM, Runquist D, Hahn-Hagerdal B. 2009. Crabtree-negative characteristics of recombinant xylose-utilizing Saccharomyces cerevisiae. J. Biotechnol. 143: 119-123. https://doi.org/10.1016/j.jbiotec.2009.06.022
  37. Kobayashi Y, Sahara T, Suzuki T, Kamachi S, Matsushika A, Hoshino T, et al. 2017. Genetic improvement of xylose metabolism by enhancing the expression of pentose phosphate pathway genes in Saccharomyces cerevisiae IR-2 for high-temperature ethanol production. J. Ind. Microbiol. Biotechnol. 44: 879-891. https://doi.org/10.1007/s10295-017-1912-5
  38. Feng Q, Liu ZL, Weber SA, Li S. 2018. Signature pathway expression of xylose utilization in the genetically engineered industrial yeast Saccharomyces cerevisiae. PLoS One 13: e0195633. https://doi.org/10.1371/journal.pone.0195633
  39. Chomvong K, Bauer S, Benjamin DI, Li X, Nomura DK, Cate JHD. 2016. Bypassing the pentose phosphate pathway: towards modular utilization of xylose. PLoS One 11: e0158111. https://doi.org/10.1371/journal.pone.0158111
  40. Kurylenko OO, Ruchala J, Vasylyshyn RV, Stasyk OV, Dmytruk OV, Dmytruk KV, et al. 2018. Peroxisomes and peroxisomal transketolase and transaldolase enzymes are essential for xylose alcoholic fermentation by the methylotrophic thermotolerant yeast, Ogataea (Hansenula) polymorpha. Biotechnol. Biofuels 11: 197. https://doi.org/10.1186/s13068-018-1203-z
  41. Jeppsson M, Johansson B, Hahn-Hagerdal B, Gorwa-Grauslund MF. 2002. Reduced oxidative pentose phosphate pathway flux in recombinant xylose-utilizing Saccharomyces cerevisiae strains improves the ethanol yield from xylose. Appl. Environ. Microbiol. 68: 1604-1609. https://doi.org/10.1128/AEM.68.4.1604-1609.2002
  42. Miskovic L, Alff-Tuomala S, Soh KC, Barth D, Salusjarvi L, Pitkanen JP, et al. 2017. A design-build-test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models. Biotechnol. Biofuels 10: 166. https://doi.org/10.1186/s13068-017-0838-5
  43. Matsushika A, Nagashima A, Goshima T, Hoshino T. 2013. Fermentation of xylose causes inefficient metabolic state due to carbon/ energy starvation and reduced glycolytic flux in recombinant industrial Saccharomyces cerevisiae. PLoS One 8: e69005. https://doi.org/10.1371/journal.pone.0069005
  44. Hortschansky P, Eisendle M, Al-Abdallah Q, Schmidt AD, Bergmann S, Thon M, et al. 2007. Interaction of HapX with the CCAATbinding complex-a novel mechanism of gene regulation by iron. EMBO J. 26: 3157-3168. https://doi.org/10.1038/sj.emboj.7601752
  45. Zeilinger S, Ebner A, Marosits T, Mach R, Kubicek CP. 2001. The Hypocrea jecorina HAP 2/3/5 protein complex binds to the inverted CCAAT-box (ATTGG) within the cbh2 (cellobiohydrolase II-gene) activating element. Mol. Genet. Genomics 266: 56-63. https://doi.org/10.1007/s004380100518
  46. Buschlen S, Amillet JM, Guiard B, Fournier A, Marcireau C, Bolotin-Fukuhara M. 2003. The S. cerevisiae HAP complex, a key regulator of mitochondrial function, coordinates nuclear and mitochondrial gene expression. Comp. Funct. Genomics 4: 37-46. https://doi.org/10.1002/cfg.254
  47. Kato M. 2014. An overview of the CCAAT-Box binding factor in filamentous fungi: assembly, nuclear translocation, and transcriptional enhancement. Biosci. Biotechnol. Biochem. 69: 663-672. https://doi.org/10.1271/bbb.69.663
  48. Young EM, Tong A, Bui H, Spofford C, Alper HS. 2014. Rewiring yeast sugar transporter preference through modifying a conserved protein motif. Proc. Natl. Acad. Sci. USA 111: 131-136. https://doi.org/10.1073/pnas.1311970111
  49. Colabardini AC, Ries LNA, Brown NA, Reis TFd, Savoldi M, Goldman MHS, et al. 2014. Functional characterization of a xylose transporter in Aspergillus nidulans. Biotechnol. Biofuels. 7: 46. https://doi.org/10.1186/1754-6834-7-46
  50. Ozcan S, Johnston M. 1999. Function and regulation of yeast hexose transporters. Microbiol. Mol. Biol. Rev. 63: 554-569. https://doi.org/10.1128/MMBR.63.3.554-569.1999
  51. MH Saier Jr, Beatty JT, Goffeau A, Harley KT, Heijne WHM, Huang SC, et al. 1999. The major facilitator superfamily. J. Mol. Microbiol. Biotechnol. 1: 257-279.
  52. Sharma NK, Behera S, Arora R, Kumar S, Sani RK. 2018. Xylose transport in yeast for lignocellulosic ethanol production: current status. J. Biosci. Bioeng. 125: 259-267. https://doi.org/10.1016/j.jbiosc.2017.10.006
  53. Du J, Li S, Zhao H. 2010. Discovery and characterization of novel d-xylose-specific transporters from Neurospora crassa and Pichia stipitis. Mol. Biosyst. 6: 2150-2156. https://doi.org/10.1039/c0mb00007h
  54. Sloothaak J, Tamayo-Ramos JA, Odoni DI, Laothanachareon T, Derntl C, Mach-Aigner AR, et al. 2016. Identification and functional characterization of novel xylose transporters from the cell factories Aspergillus niger and Trichoderma reesei. Biotechnol. Biofuels 9: 148. https://doi.org/10.1186/s13068-016-0564-4