Abstract
The production of biofuels from plant biomass is dependent on the availability of enzymes that can hydrolyze the plant cell wall polysaccharides to their monosaccharides. These enzyme mixtures are formed by microorganisms but their native compositions and properties are often not ideal for application. Genetic engineering of these microorganisms is therefore necessary, in which introduction of DNA is an essential precondition. The filamentous fungus Trichoderma reesei—the main producer of plant-cell-wall-degrading enzymes for biofuels and other industries—has been subjected to intensive genetic engineering toward this goal and has become one of the iconic examples of the successful genetic improvement of fungi. However, the genetic manipulation of other enzyme-producing Trichoderma species is frequently less efficient and, therefore, rarely managed. In this chapter, we therefore describe the two potent methods of Trichoderma transformation mediated by either (a) polyethylene glycol (PEG) or (b) Agrobacterium. The methods are optimized for T. reesei but can also be applied for such transformation-resilient species as T. harzianum and T. guizhouense, which are putative upcoming alternatives for T. reesei in this field. The protocols are simple, do not require extensive training or special equipment, and can be further adjusted for T. reesei mutants with particular properties.
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Notes
- 1.
Only the pioneering publications are cited here.
References
Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Stahlberg J, Beckham GT (2015) Fungal cellulases. Chem Rev 115(3):1308–1448. https://doi.org/10.1021/cr500351c
Gupta VK, Kubicek CP, Berrin JG, Wilson DW, Couturier M, Berlin A, Filho EXF, Ezeji T (2016) Fungal enzymes for bio-products from sustainable and waste biomass. Trends Biochem Sci 41(7):633–645. https://doi.org/10.1016/j.tibs.2016.04.006
Kubicek CP, Kubicek EM (2016) Enzymatic deconstruction of plant biomass by fungal enzymes. Curr Opin Chem Biol 35:51–57. https://doi.org/10.1016/j.cbpa.2016.08.028
Steiger MG, Vitikainen M, Uskonen P, Brunner K, Adam G, Pakula T, Penttila M, Saloheimo M, Mach RL, Mach-Aigner AR (2011) Transformation system for Hypocrea jecorina (Trichoderma reesei) that favors homologous integration and employs reusable bidirectionally selectable markers. Appl Environ Microbiol 77(1):114–121. https://doi.org/10.1128/AEM.02100-10
Peterson R, Nevalainen H (2012) Trichoderma reesei RUT-C30—thirty years of strain improvement. Microbiology 158(Pt 1):58–68. https://doi.org/10.1099/mic.0.054031-0
Malmierca MG, Cardoza RE, Gutiérrez S (2015) Trichoderma transformation methods. In: van den Berg MA, Maruthachalam K (eds) Genetic transformation systems in fungi, vol 1. Springer International Publishing, Cham, pp 41–48. https://doi.org/10.1007/978-3-319-10142-2_3
Bischof RH, Ramoni J, Seiboth B (2016) Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei. Microb Cell Factories 15(1):106. https://doi.org/10.1186/s12934-016-0507-6
Gupta VK, Steindorff AS, de Paula RG, Silva-Rocha R, Mach-Aigner AR, Mach RL, Silva RN (2016) The post-genomic era of Trichoderma reesei: what’s next? Trends Biotechnol 34(12):970–982. https://doi.org/10.1016/j.tibtech.2016.06.003
Druzhinina IS, Kubicek CP (2017) Genetic engineering of Trichoderma reesei cellulases and their production. Microb Biotechnol 10(6):1485–1499. https://doi.org/10.1111/1751-7915.12726
Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 26(5):553–560. https://doi.org/10.1038/nbt1403
Le Crom S, Schackwitz W, Pennacchio L, Magnuson JK, Culley DE, Collett JR, Martin J, Druzhinina IS, Mathis H, Monot F, Seiboth B, Cherry B, Rey M, Berka R, Kubicek CP, Baker SE, Margeot A (2009) Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc Natl Acad Sci U S A 106(38):16151–16156. https://doi.org/10.1073/pnas.0905848106
Vitikainen M, Arvas M, Pakula T, Oja M, Penttila M, Saloheimo M (2010) Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties. BMC Genomics 11:441. https://doi.org/10.1186/1471-2164-11-441
Lichius A, Bidard F, Buchholz F, Le Crom S, Martin J, Schackwitz W, Austerlitz T, Grigoriev IV, Baker SE, Margeot A, Seiboth B, Kubicek CP (2015) Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics 16:326. https://doi.org/10.1186/s12864-015-1526-0
Ivanova C, Ramoni J, Aouam T, Frischmann A, Seiboth B, Baker SE, Le Crom S, Lemoine S, Margeot A, Bidard F (2017) Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction. Biotechnol Biofuels 10:209. https://doi.org/10.1186/s13068-017-0897-7
Li WC, Huang CH, Chen CL, Chuang YC, Tung SY, Wang TF (2017) Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. Biotechnol Biofuels 10:170. https://doi.org/10.1186/s13068-017-0825-x
Jourdier E, Baudry L, Poggi-Parodi D, Vicq Y, Koszul R, Margeot A, Marbouty M, Bidard F (2017) Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes. Biotechnol Biofuels 10:151. https://doi.org/10.1186/s13068-017-0837-6
Zou Z, Zhao Y, Zhang T, Xu J, He A, Deng Y (2018) Efficient isolation and characterization of a cellulase hyperproducing mutant strain of Trichoderma reesei. J Microbiol Biotechnol 28(9):1473–1481. https://doi.org/10.4014/jmb.1805.05009
Liu P, Lin A, Zhang G, Zhang J, Chen Y, Shen T, Zhao J, Wei D, Wang W (2019) Enhancement of cellulase production in Trichoderma reesei RUT-C30 by comparative genomic screening. Microb Cell Factories 18(1):81. https://doi.org/10.1186/s12934-019-1131-z
Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillen N, Margeot A, Zimmer C, Koszul R (2014) High-quality genome (re)assembly using chromosomal contact data. Nat Commun 5:5695. https://doi.org/10.1038/ncomms6695
Druzhinina IS, Kopchinskiy AG, Kubicek EM, Kubicek CP (2016) A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness. Biotechnol Biofuels 9:75. https://doi.org/10.1186/s13068-016-0488-z
Ferreira Filho JA, Horta MAC, Beloti LL, Dos Santos CA, de Souza AP (2017) Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry. BMC Genomics 18(1):779. https://doi.org/10.1186/s12864-017-4181-9
Grujic M, Dojnov B, Potocnik I, Atanasova L, Duduk B, Srebotnik E, Druzhinina IS, Kubicek CP, Vujcic Z (2019) Superior cellulolytic activity of Trichoderma guizhouense on raw wheat straw. World J Microbiol Biotechnol 35(12):194. https://doi.org/10.1007/s11274-019-2774-y
Druzhinina IS, Chenthamara K, Zhang J, Atanasova L, Yang DQ, Miao YZ, Rahimi MJ, Grujic M, Cai F, Pourmehdi S, Abu Salim K, Pretzer C, Kopchinskiy AG, Henrissat B, Kuo A, Hundley H, Wang M, Aerts A, Salamov A, Lipzen A, LaButti K, Barry K, Grigoriev IV, Shen QR, Kubicek CP (2018) Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLoS Genet 14(4):e1007322. https://doi.org/10.1371/journal.pgen.1007322
Kubicek CP, Steindorff AS, Chenthamara K, Manganiello G, Henrissat B, Zhang J, Cai F, Kopchinskiy AG, Kubicek EM, Kuo A, Baroncelli R, Sarrocco S, Noronha EF, Vannacci G, Shen Q, Grigoriev IV, Druzhinina IS (2019) Evolution and comparative genomics of the most common Trichoderma species. BMC Genomics 20(1):485. https://doi.org/10.1186/s12864-019-5680-7
Zhang J, Bayram Akcapinar G, Atanasova L, Rahimi MJ, Przylucka A, Yang D, Kubicek CP, Zhang R, Shen Q, Druzhinina IS (2016) The neutral metallopeptidase NMP1 of Trichoderma guizhouense is required for mycotrophy and self-defence. Environ Microbiol 18(2):580–597. https://doi.org/10.1111/1462-2920.12966
Zhang J, Miao Y, Rahimi MJ, Zhu H, Steindorff A, Schiessler S, Cai F, Pang G, Chenthamara K, Xu Y, Kubicek CP, Shen Q, Druzhinina IS (2019) Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi. Environ Microbiol 21(8):2644–2658. https://doi.org/10.1111/1462-2920.14575
Gao R, Ding M, Jiang S, Zhao Z, Chenthamara K, Shen Q, Cai F, Druzhinina IS (2020) The evolutionary and functional paradox of cerato-platanins in fungi. Appl Environ Microbiol. https://doi.org/10.1128/AEM.00696-20
Penttilä M, Nevalainen H, Rättö M, Salminen E, Knowles J (1987) A versatile transformation system for the cellulolytic filamentous fungus Trichoderma reesei. Gene 61(2):155–164. https://doi.org/10.1016/0378-1119(87)90110-7
Gruber F, Visser J, Kubicek CP, de Graaff LH (1990) The development of a heterologous transformation system for the cellulolytic fungus Trichoderma reesei based on a pyrG-negative mutant strain. Curr Genet 18(1):71–76. https://doi.org/10.1007/BF00321118
Smith JL, Bayliss FT, Ward M (1991) Sequence of the cloned pyr4 gene of Trichoderma reesei and its use as a homologous selectable marker for transformation. Curr Genet 19(1):27–33. https://doi.org/10.1007/BF00362084
Lorito M, Hayes CK, Di Pietro A, Harman GE (1993) Biolistic transformation of Trichoderma harzianum and Gliocladium virens using plasmid and genomic DNA. Curr Genet 24(4):349–356. https://doi.org/10.1007/BF00336788
Zeilinger S (2004) Gene disruption in Trichoderma atroviride via Agrobacterium-mediated transformation. Curr Genet 45(1):54–60. https://doi.org/10.1007/s00294-003-0454-8
Schuster A, Bruno KS, Collett JR, Baker SE, Seiboth B, Kubicek CP, Schmoll M (2012) A versatile toolkit for high throughput functional genomics with Trichoderma reesei. Biotechnol Biofuels 5(1):1. https://doi.org/10.1186/1754-6834-5-1
Magana-Ortiz D, Coconi-Linares N, Ortiz-Vazquez E, Fernandez F, Loske AM, Gomez-Lim MA (2013) A novel and highly efficient method for genetic transformation of fungi employing shock waves. Fungal Genet Biol 56:9–16. https://doi.org/10.1016/j.fgb.2013.03.008
Eveleigh DE, Montenecourt BS (1979) Increasing yields of extracellular enzymes. Adv Appl Microbiol 25:57–74. https://doi.org/10.1016/s0065-2164(08)70146-1
Reagents, Buffers, and Indicators (2017) ACS Reagent Chemicals. Am Chem Soc. https://doi.org/10.1021/acsreagents.3001
Ogawa Y, Mii M (2004) Screening for highly active β-lactam antibiotics against Agrobacterium tumefaciens. Arch Microbiol 181(4):331–336. https://doi.org/10.1007/s00203-004-0650-z
Fincham JR (1989) Transformation in fungi. Microbiol Rev 53(1):148–170
Li D, Tang Y, Lin J, Cai W (2017) Methods for genetic transformation of filamentous fungi. Microb Cell Factories 16(1):168. https://doi.org/10.1186/s12934-017-0785-7
Flores-Felix JD, Menendez E, Peix A, Garcia-Fraile P, Velazquez E (2020) History and current taxonomic status of genus Agrobacterium. Syst Appl Microbiol 43(1):126046. https://doi.org/10.1016/j.syapm.2019.126046
Barton IS, Fuqua C, Platt TG (2018) Ecological and evolutionary dynamics of a model facultative pathogen: Agrobacterium and crown gall disease of plants. Environ Microbiol 20(1):16–29. https://doi.org/10.1111/1462-2920.13976
Gelvin SB (2003) Agrobacterium-mediated plant transformation: the biology behind the “gene-jockeying” tool. Microbiol Mol Biol Rev 67(1):16–37, table of contents. https://doi.org/10.1128/mmbr.67.1.16-37.2003
Dunn-Coleman N, Wang H (1998) Agrobacterium T-DNA: a silver bullet for filamentous fungi? Nat Biotechnol 16(9):817–818. https://doi.org/10.1038/nbt0998-817
de Groot MJ, Bundock P, Hooykaas PJ, Beijersbergen AG (1998) Agrobacterium tumefaciens-mediated transformation of filamentous fungi. Nat Biotechnol 16(9):839–842. https://doi.org/10.1038/nbt0998-839
Michielse CB, Hooykaas PJ, van den Hondel CA, Ram AF (2005) Agrobacterium-mediated transformation as a tool for functional genomics in fungi. Curr Genet 48(1):1–17. https://doi.org/10.1007/s00294-005-0578-0
Idnurm A, Bailey AM, Cairns TC, Elliott CE, Foster GD, Ianiri G, Jeon J (2017) A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi. Fungal Biol Biotechnol 4:6. https://doi.org/10.1186/s40694-017-0035-0
Friedl MA, Schmoll M, Kubicek CP, Druzhinina IS (2008) Photostimulation of Hypocrea atroviridis growth occurs due to a cross-talk of carbon metabolism, blue light receptors and response to oxidative stress. Microbiology 154(Pt 4):1229–1241. https://doi.org/10.1099/mic.0.2007/014175-0
Carreras-Villasenor N, Sanchez-Arreguin JA, Herrera-Estrella AH (2012) Trichoderma: sensing the environment for survival and dispersal. Microbiology 158(Pt 1):3–16. https://doi.org/10.1099/mic.0.052688-0
Hood EE, Gelvin SB, Melchers LS, Hoekema A (1993) New Agrobacterium helper plasmids for gene transfer to plants. Transgenic Res 2(4):208–218. https://doi.org/10.1007/BF01977351
Kunamneni A, Plou FJ, Alcalde M, Ballesteros A (2014) Chapter 24: Trichoderma enzymes for food industries. In: Gupta VK, Schmoll M, Herrera-Estrella A, Upadhyay RS, Druzhinina I, Tuohy MG (eds) Biotechnology and biology of Trichoderma. Elsevier, Amsterdam, pp 339–344. https://doi.org/10.1016/B978-0-444-59576-8.00024-2
Druzhinina IS, Kubicek CP, Komon-Zelazowska M, Mulaw TB, Bissett J (2010) The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages. BMC Evol Biol 10:94. https://doi.org/10.1186/1471-2148-10-94
Chaverri P, Branco-Rocha F, Jaklitsch W, Gazis R, Degenkolb T, Samuels GJ (2015) Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains. Mycologia 107(3):558–590. https://doi.org/10.3852/14-147
Sandoval-Denis M, Sutton DA, Cano-Lira JF, Gené J, Fothergill AW, Wiederhold NP, Guarro J (2014) Phylogeny of the clinically relevant species of the emerging fungus Trichoderma and their antifungal susceptibilities. J Clin Microbiol 52(6):2112–2125. https://doi.org/10.1128/JCM.00429-14
Blochlinger K, Diggelmann H (1984) Hygromycin B phosphotransferase as a selectable marker for DNA transfer experiments with higher eucaryotic cells. Mol Cell Biol 4(12):2929. https://doi.org/10.1128/MCB.4.12.2929
Hua J, Meyer JD, Lodge JK (2000) Development of positive selectable markers for the fungal pathogen Cryptococcus neoformans. Clin Diagn Lab Immunol 7(1):125–128. https://doi.org/10.1128/cdli.7.1.125-128.2000
Solis-Escalante D, Kuijpers NGA, Nadine B, Bolat I, Bosman L, Pronk JT, Daran J-M, Pascale D-L (2013) amdSYM, a new dominant recyclable marker cassette for Saccharomyces cerevisiae. FEMS Yeast Res 13(1):126–139. https://doi.org/10.1111/1567-1364.12024
Guangtao Z, Seiboth B, Wen C, Yaohua Z, Xian L, Wang T (2010) A novel carbon source-dependent genetic transformation system for the versatile cell factory Hypocrea jecorina (anamorph Trichoderma reesei). FEMS Microbiol Lett 303(1):26–32. https://doi.org/10.1111/j.1574-6968.2009.01851.x
Acknowledgments
The authors wish to thank Renwei Gao, Siqi Jiang, Jian Zhang, and Zheng Zhao (Nanjing Agricultural University, Nanjing, China) for the materials used for images and useful comments. This work was supported by grants from the National Natural Science Foundation of China (31801939) and the Ministry of Science & Technology of Jiangsu Province (BK20180533), China, to FC, and grants from the Austrian Science Fund (FWF) P25613-B20 and P25745-B20, to ISD.
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Cai, F., Kubicek, C.P., Druzhinina, I.S. (2021). Genetic Transformation of Trichoderma spp.. In: Basu, C. (eds) Biofuels and Biodiesel. Methods in Molecular Biology, vol 2290. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1323-8_12
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