Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Morphological Engineering of Filamentous Fungi: Research Progress and Perspectives

  • Zhengwu Lu (College of Life Sciences, Linyi University) ;
  • Zhiqun Chen (College of Life Sciences, Linyi University) ;
  • Yunguo Liu (College of Life Sciences, Linyi University) ;
  • Xuexue Hua (Shandong Fufeng Fermentation Co., Ltd.) ;
  • Cuijuan Gao (College of Life Sciences, Linyi University) ;
  • Jingjing Liu (College of Life Sciences, Linyi University)
  • Received : 2024.02.05
  • Accepted : 2024.03.06
  • Published : 2024.06.28
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Abstract

Filamentous fungi are important cell factories for the production of high-value enzymes and chemicals for the food, chemical, and pharmaceutical industries. Under submerged fermentation, filamentous fungi exhibit diverse fungal morphologies that are influenced by environmental factors, which in turn affect the rheological properties and mass transfer of the fermentation system, and ultimately the synthesis of products. In this review, we first summarize the mechanisms of mycelial morphogenesis and then provide an overview of current developments in methods and strategies for morphological regulation, including physicochemical and metabolic engineering approaches. We also anticipate that rapid developments in synthetic biology and genetic manipulation tools will accelerate morphological engineering in the future.

Keywords

Acknowledgement

This work was supported by the Youth Foundation of Shandong Natural Science Foundation of China (Grant No. ZR2020QC007); the Innovation Project for Major Application Technology in the Agricultural Sector in Shandong Province (Grant No. SD2019ZZ005); and Special Funds for the Central Management of Scientific and Technological Development at the Local Level (Grant No. YDZX2021070).

References

  1. Abarca ML, Accensi F, Cano J, Cabanes FJ. 2004. Taxonomy and significance of black aspergilli. Antonie Van Leeuwenhoek. 86: 33-49. 
  2. Grimm LH, Kelly S, Krull R, Hempel DC. 2005. Morphology and productivity of filamentous fungi. Appl. Microbiol. Biotechnol. 69: 375-384. 
  3. Troiano D, Orsat V, Dumont MJ. 2020. Status of filamentous fungi in integrated biorefineries. Renew. Sustain. Energ. Rev. 117: 109472. 
  4. Meyer V, Andersen MR, Brakhage AA, Braus GH, Caddick MX, Cairns TC, et al. 2016. Current challenges of research on filamentous fungi in relation to human welfare and a sustainable bio-economy: a white paper. Fungal Biol. Biotechnol. 3: 6. 
  5. Cairns TC, Zheng X, Zheng P, Sun J, Meyer V. 2019. Moulding the mould: understanding and reprogramming filamentous fungal growth and morphogenesis for next generation cell factories. Biotechnol. Biofuels 12: 77. 
  6. Palacio-Barrera AM, Areiza D, Zapata P, Atehortua L, Correa C, Penuela-Vasquez M. 2019. Induction of pigment production through media composition, abiotic and biotic factors in two filamentous fungi. Biotechnol. Rep. (Amst) 21: e00308. 
  7. Kalra R, Conlan XA, Goel M. 2020. Fungi as a potential source of pigments: Harnessing filamentous fungi. Front. Chem. 8: 00369. 
  8. Zhang T, Liu H, Lv B, Li C. 2020. Regulating strategies for producing carbohydrate active enzymes by filamentous fungal cell factories. Front. Bioeng. Biotechnol. 8: 691. 
  9. Ward OP. 2012. Production of recombinant proteins by filamentous fungi. Biotechnol. Adv. 30: 1119-1139. 
  10. Liu G, Qu Y. 2019. Engineering of filamentous fungi for efficient conversion of lignocellulose: tools, recent advances and prospects. Biotechnol. Adv. 37: 519-529. 
  11. Wosten HAB. 2019. Filamentous fungi for the production of enzymes, chemicals and materials. Curr. Opin. Biotechnol. 59: 65-70. 
  12. Baron NC, Rigobelo EC, Zied DC. 2019. Filamentous fungi in biological control: current status and future perspectives. Chilean J. Agric. Res. 79: 307-315. 
  13. Alberti F, Foster GD, Bailey AM. 2017. Natural products from filamentous fungi and production by heterologous expression. Appl. Microbiol. Biotechnol. 101: 493-500. 
  14. Cairns TC, Nai C, Meyer V. 2018. How a fungus shapes biotechnology: 100 years of Aspergillus niger research. Fungal Biol. Biotechnol. 5: 13. 
  15. Yu JH, Keller N. 2005. Regulation of secondary metabolism in filamentous fungi. Ann. Rev. Phytopathol. 43: 437-458. 
  16. Ogawa M, Bisson LF, Garcia-Martinez T, Mauricio JC, Moreno-Garcia J. 2019. New insights on yeast and filamentous fungus adhesion in a natural co-immobilization system: proposed advances and applications in wine industry. Appl. Microbiol. Biotechnol. 103: 4723-4731. 
  17. Gonzalez-Saiz JM, Garrido-Vidal D, Pizarro C. 2009. Scale up and design of processes in aerated-stirred fermenters for the industrial production of vinegar. J. Food Eng. 93: 89-100. 
  18. Kossen NWF. 2000. The Morphology of Filamentous Fungi, In History of Modern Biotechnology II, Ed. Springer Berlin Heidelberg, pp. 1-33. 
  19. Cairns TC, Feurstein C, Zheng X, Zheng P, Sun J, Meyer V. 2019. A quantitative image analysis pipeline for the characterization of filamentous fungal morphologies as a tool to uncover targets for morphology engineering: a case study using aplD in Aspergillus niger. Biotechnol. Biofuels 12: 149. 
  20. Miyazawa K, Yoshimi A, Abe K. 2020. The mechanisms of hyphal pellet formation mediated by polysaccharides, α-1,3-glucan and galactosaminogalactan, in Aspergillus species. Fungal Biol. Biotechnol. 7: 10. 
  21. Harris SD. 2006. Cell Polarity in Filamentous Fungi: Shaping the Mold, International Review of Cytology, Ed. Academic Press, pp. 41-77. 
  22. Lichius A, Lord KM. 2014. Chemoattractive Mechanisms in Filamentous Fungi. Open Mycol. J.. 8: 28-57. 
  23. Kurt T, Marba-Ardebol AM, Turan Z, Neubauer P, Junne S, Meyer V. 2018. Rocking Aspergillus: morphology-controlled cultivation of Aspergillus niger in a wave-mixed bioreactor for the production of secondary metabolites. Microb. Cell Fact. 17: 128. 
  24. Riquelme M, Aguirre J, Bartnicki-Garcia S, Braus GH, Feldbrugge M, Fleig U, et al. 2018. Fungal morphogenesis, from the polarized growth of hyphae to complex reproduction and infection structures. Microbiol. Mol. Biol. Rev. 82: 00068-00017. 
  25. Riquelme M. 2013. Tip growth in filamentous fungi: A road trip to the Apex. Ann. Rev. Microbiol. 67: 587-609. 
  26. Steinberg G, Penalva MA, Riquelme M, Wosten HA, Harris SD. 2017. Cell biology of hyphal growth. Microbiol. Spectrum 5: 0034. 
  27. Meyer V, Arentshorst M, Flitter SJ, Nitsche BM, Kwon MJ, Reynaga-Pena CG, et al. 2009. Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics. Eukaryot. Cell 8: 1677-1691. 
  28. Gomes DG, Coelho E, Silva R, Domingues L, Teixeira JA. 2023. 8 - Bioreactors and engineering of filamentous fungi cultivation, pp. 219-250. In Taherzadeh MJ, Ferreira JA, Pandey A (eds.), Current Developments in Biotechnology and Bioengineering, Ed. Elsevier, 
  29. Liu J, Guo T, Luo Y, Chai X, Wu J, Zhao W, et al. 2019. Enhancement of monascus pigment productivity via a simultaneous fermentation process and separation system using immobilized-cell fermentation. Bioresour. Technol. 272: 552-560. 
  30. Gong Z, Zhang S, Liu J. 2023. Recent advances in chitin biosynthesis associated with the morphology and secondary metabolite synthesis of filamentous fungi in submerged fermentation. J. Fungi 9: 205. 
  31. Papagianni M. 2004. Fungal morphology and metabolite production in submerged mycelial processes. Biotechnol. Adv. 22: 189-259. 
  32. Zhang J, Zhang J. 2016. The filamentous fungal pellet and forces driving its formation. Crit. Rev. Biotechnol. 36: 1066-1077. 
  33. Veiter L, Rajamanickam V, Herwig C. 2018. The filamentous fungal pellet-relationship between morphology and productivity. Appl. Microbiol. Biotechnol. 102: 2997-3006. 
  34. Krull R, Wucherpfennig T, Esfandabadi ME, Walisko R, Melzer G, Hempel DC, et al. 2013. Characterization and control of fungal morphology for improved production performance in biotechnology. J. Biotechnol. 163: 112-123. 
  35. Papagianni M, Mattey M. 2006. Morphological development of Aspergillus niger in submerged citric acid fermentation as a function of the spore inoculum level. Application of neural network and cluster analysis for characterization of mycelial morphology. Microb. Cell Fact. 5: 3. 
  36. Driouch H, Hansch R, Wucherpfennig T, Krull R, Wittmann C. 2012. Improved enzyme production by bio-pellets of Aspergillus niger: targeted morphology engineering using titanate microparticles. Biotechnol. Bioeng. 109: 462-471. 
  37. Mantzouridou F, Roukas T, Kotzekidou P. 2002. Effect of the aeration rate and agitation speed on β-carotene production and morphology of Blakeslea trispora in a stirred tank reactor: mathematical modeling. Biochem. Eng. J. 10: 123-135. 
  38. Lan T-Q, Wei D, Yang S-T, Liu X. 2013. Enhanced cellulase production by Trichoderma viride in a rotating fibrous bed bioreactor. Bioresour. Technol. 133: 175-182. 
  39. Carlsen M, Spohr AB, Nielsen J, Villadsen J. 1996. Morphology and physiology of an α-amylase producing strain of Aspergillus oryzae during batch cultivations. Biotechnol. Bioeng. 49: 266-276. 
  40. Paul GC, Priede MA, Thomas CR. 1999. Relationship between morphology and citric acid production in submerged Aspergillus niger fermentations. Biochem. Eng. J. 3: 121-129. 
  41. Ahamed A, Singh A, Ward OP. 2005. Culture-based strategies for reduction of protease activity in filtrates from Aspergillus niger NRRL-3. World J. Microbiol. Biotechnol. 21: 1577-1583. 
  42. Casas Lopez JL, Sanchez Perez JA, Fernandez Sevilla JM, Rodriguez Porcel EM, Chisti Y. 2005. Pellet morphology, culture rheology and lovastatin production in cultures of Aspergillus terreus. J. Biotechnol. 116: 61-77. 
  43. Haack MB, Olsson L, Hansen K, Eliasson Lantz A. 2006. Change in hyphal morphology of Aspergillus oryzae during fed-batch cultivation. Appl. Microbiol. Biotechnol. 70: 482-487. 
  44. Tari C, Gogus N, Tokatli F. 2007. Optimization of biomass, pellet size and polygalacturonase production by Aspergillus sojae ATCC 20235 using response surface methodology. Enzyme Microb. Technol. 40: 1108-1116. 
  45. Liao W, Liu Y, Chen S. 2007. Studying pellet formation of a filamentous fungus Rhizopus oryzae to enhance organic acid production. Appl. Biochem. Biotechnol. 137: 689-701. 
  46. Kaup BA, Ehrich K, Pescheck M, Schrader J. 2008. Microparticle-enhanced cultivation of filamentous microorganisms: Increased chloroperoxidase formation by Caldariomyces fumago as an example. Biotechnol. Bioeng. 99: 491-498. 
  47. Sitanggang AB, Wu HS, Wang SS, Ho YC. 2010. Effect of pellet size and stimulating factor on the glucosamine production using Aspergillus sp. BCRC 31742. Bioresour. Technol. 101: 3595-3601. 
  48. Driouch H, Sommer B, Wittmann C. 2010. Morphology engineering of Aspergillus niger for improved enzyme production. Biotechnol. Bioeng. 105: 1058-1068. 
  49. Lin PJ, Scholz A, Krull R. 2010. Effect of volumetric power input by aeration and agitation on pellet morphology and product formation of Aspergillus niger. Biochem. Eng. J. 49: 213-220. 
  50. Wucherpfennig T, Hestler T, Krull R. 2011. Morphology engineering - Osmolality and its effect on Aspergillus niger morphology and productivity. Microb. Cell Fact. 10: 58. 
  51. Yu L, Chao Y, Wensel P, Chen S. 2012. Hydrodynamic and kinetic study of cellulase production by Trichoderma reesei with pellet morphology. Biotechnol. Bioeng. 109: 1755-1768. 
  52. Wucherpfennig T, Lakowitz A, Driouch H, Krull R, Wittmann C. 2012. Customization of Aspergillus niger morphology through ddition of Talc micro particles. J. Vis. Exp. 15: 4023. 
  53. Gao D, Zeng J, Yu X, Dong T, Chen S. 2014. Improved lipid accumulation by morphology engineering of oleaginous fungus Mortierella isabellina. Biotechnol. Bioeng. 111: 1758-1766. 
  54. Zhang K, Yu C, Yang ST. 2015. Effects of soybean meal hydrolysate as the nitrogen source on seed culture morphology and fumaric acid production by Rhizopus oryzae. Process Biochem. 50: 173-179. 
  55. Yatmaz E, Karahalil E, Germec M, Ilgin M, Turhan I. 2016. Controlling filamentous fungi morphology with microparticles to enhanced β-mannanase production. Bioprocess Biosyst. Eng. 39: 1391-1399. 
  56. Abasian L, Shafiei Alavijeh R, Satari B, Karimi K. 2020. Sustainable and effective chitosan production by dimorphic fungus Mucor rouxii via replacing yeast extract with fungal extract. Appl. Biochem. Biotechnol. 191: 666-678. 
  57. Saberi A, Jalili H, Nikfarjam A, Koohsorkhi J, Jarmoshti J, Bizukojc M. 2020. Monitoring of Aspergillus terreus morphology for the lovastatin production in submerge culture by impedimetry. Biochem. Eng. J. 159: 107615. 
  58. Salvatierra HN, Regner EL, Baigori MD, Pera LM. 2021. Orchestration an extracellular lipase production from Aspergillus niger MYA 135: biomass morphology and fungal physiology. AMB Express 11: 42. 
  59. McIntyre M, Muller C, Dynesen J, Nielsen J. 2001. Metabolic engineering of the morphology of Aspergillus, pp. 103-128. In Metabolic Engineering, Ed. Springer Berlin Heidelberg, Berlin, Germany. 
  60. Muller C, McIntyre M, Hansen K, Nielsen J. 2002. Metabolic engineering of the morphology of Aspergillus oryzae by altering chitin synthesis. Appl. Environ. Microbiol. 68: 1827-1836. 
  61. Weld RJ, Plummer KM, Carpenter MA, Ridgway HJ. 2006. Approaches to functional genomics in filamentous fungi. Cell Res. 16: 31-44. 
  62. Wang S, Chen H, Tang X, Zhang H, Chen W, Chen YQ. 2017. Molecular tools for gene manipulation in filamentous fungi. Appl. Microbiol. Biotechnol. 101: 8063-8075. 
  63. Jin FJ, Takahashi T, Matsushima K-i, Hara S, Shinohara Y, Maruyama J-i, et al. 2011. SclR, a basic helix-loop-helix transcription factor, regulates hyphal morphology and promotes sclerotial formation in Aspergillus oryzae. Eukaryot. Cell 10: 945-955. 
  64. Liu H, Zheng Z, Wang P, Gong G, Wang L, Zhao G. 2013. Morphological changes induced by class III chitin synthase gene silencing could enhance penicillin production of Penicillium chrysogenum. Appl. Microbiol. Biotechnol. 97: 3363-3372. 
  65. Yin C, Wang B, He P, Lin Y, Pan L. 2014. Genomic analysis of the aconidial and high-performance protein producer, industrially relevant Aspergillus niger SH2 strain. Gene 541: 107-114. 
  66. Cai M, Zhang Y, Hu W, Shen W, Yu Z, Zhou W, et al. 2014. Genetically shaping morphology of the filamentous fungus Aspergillus glaucus for production of antitumor polyketide aspergiolide A. Microb. Cell Fact. 13: 73. 
  67. Sun X, Wu H, Zhao G, Li Z, Wu X, Liu H, et al. 2018. Morphological regulation of Aspergillus niger to improve citric acid production by chsC gene silencing. Bioprocess Biosyst. Eng. 41: 1029-1038. 
  68. Chen X, Zhou J, Ding Q, Luo Q, Liu L. 2019. Morphology engineering of Aspergillus oryzae for l-malate production. Biotechnol. Bioeng. 116: 2662-2673. 
  69. Bocking SP, Wiebe MG, Robson GD, Hansen K, Christiansen LH, Trinci APJ. 1999. Effect of branch frequency in Aspergillus oryzae on protein secretion and culture viscosity. Biotechnol. Bioeng. 65: 638-648. 
  70. Bayram O, Krappmann S, Ni M, Bok JW, Helmstaedt K, Valerius O, et al. 2008. VelB/VeA/LaeA complex coordinates light signal with fungal development and secondary metabolism. Science 320: 1504-1506. 
  71. Terfehr D, Dahlmann TA, Kuck U. 2017. Transcriptome analysis of the two unrelated fungal β-lactam producers Acremonium chrysogenum and Penicillium chrysogenum: Velvet-regulated genes are major targets during conventional strain improvement programs. BMC Genomics 18: 272. 
  72. Gong Z, Zhang S, Liu J. 2023. Recent advances in chitin biosynthesis associated with the morphology and secondary metabolite synthesis of filamentous fungi in submerged fermentation. J. Fungi 9: 205. 
  73. Zhang J, Jiang H, Du Y, Keyhani NO, Xia Y, Jin K. 2019. Members of chitin synthase family in Metarhizium acridum differentially affect fungal growth, stress tolerances, cell wall integrity and virulence. PLoS Pathog. 15: e1007964. 
  74. Takeshita, N. 2019. Control of actin and calcium for chitin synthase delivery to the hyphal tip of Aspergillus. Fungal Cell Wall 193: 113-129. 
  75. Fiedler MRM, Lorenz A, Nitsche BM, van den Hondel CA, Ram AFJ, Meyer V. 2014. The capacity of Aspergillus niger to sense and respond to cell wall stress requires at least three transcription factors: RlmA, MsnA and CrzA. Fungal Biol. Biotechnol. 1: 5. 
  76. Spielvogel A, Findon H, Arst Herbert N, Jr, Araujo-Bazan L, Hernandez-Ortiz P, Stahl U, et al. 2008. Two zinc finger transcription factors, CrzA and SltA, are involved in cation homoeostasis and detoxification in Aspergillus nidulans. Biochem. J. 414: 419-429. 
  77. Chen L, Zou G, Wang J, Wang J, Liu R, Jiang Y, et al. 2016. Characterization of the Ca2+-responsive signaling pathway in regulating the expression and secretion of cellulases in Trichoderma reesei Rut-C30. Mol. Microbiol. 100: 560-575. 
  78. Tag A, Hicks J, Garifullina G, Ake Jr C, Phillips TD, Beremand M, et al. 2000. G-protein signalling mediates differential production of toxic secondary metabolites. Mol. Microbiol. 38: 658-665. 
  79. Bencina M, Panneman H, Ruijter GJG, Legisa M, Visser J. 1997. Characterization and overexpression of the Aspergillus niger gene encoding the cAMP-dependent protein kinase catalytic subunit. Microbiology (Reading, England) 143 ( Pt 4): 1211-1220. 
  80. Schuster A, Tisch D, Seidl-Seiboth V, Kubicek CP, Schmoll M. 2012. Roles of protein kinase A and adenylate cyclase in light-modulated cellulase regulation in Trichoderma reesei. Appl. Environ. Microbiol. 78: 2168-2178. 
  81. Yin X, Shin H-d, Li J, Du G, Liu L, Chen J. 2017. Comparative genomics and transcriptome analysis of Aspergillus niger and metabolic engineering for citrate production. Sci. Rep. 7: 41040. 
  82. van den Berg MA, Albang R, Albermann K, Badger JH, Daran J-M, M Driessen AJ, et al. 2008. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat. Biotechnol. 26: 1161-1168. 
  83. Zhao Q, Liu Q, Wang Q, Qin Y, Zhong Y, Gao L, Liu G, Qu Y. 2021. Disruption of the Trichoderma reesei gul1 gene stimulates hyphal branching and reduces broth viscosity in cellulase production. J. Ind. Microbiol. Biotechnol. 48: kuab012. 
  84. Chen Y, Wang J, Wang M, Han A, Zhao X, Wang W, Wei D. 2023. Engineering the metabolism and morphology of the filamentous fungus Trichoderma reesei for efficient L-malic acid production. Bioresour. Technol. 387: 129629. 
  85. Carrillo AJ, Cabrera IE, Spasojevic MJ, Schacht P, Stajich JE, Borkovich KA. 2020. Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa. BMC Genomics 21: 755. 
  86. Wang Y, Wang L, Wu F, Liu F, Wang Q, Zhang X, et al. 2018. A Consensus ochratoxin A biosynthetic pathway: Insights from the genome sequence of Aspergillus ochraceus and a comparative genomic analysis. Appl. Environ. Microbiol. 84: e01009-01018. 
  87. Mozsik L, Pohl C, Meyer V, Bovenberg RAL, Nygard Y, Driessen AJM. 2021. Modular synthetic biology toolkit for filamentous fungi. ACS Synt. Biol. 10: 2850-2861. 
  88. Jiang C, Lv G, Tu Y, Cheng X, Duan Y, Zeng B, et al. 2021. Applications of CRISPR/Cas9 in the synthesis of secondary metabolites in filamentous fungi. Front. Microbiol. 12: 638096. 
  89. Shao Y, Lu N, Wu Z, Cai C, Wang S, Zhang L-L, et al. 2018. Creating a functional single-chromosome yeast. Nature 560: 331-335. 
  90. Luo J, Sun X, Cormack BP, Boeke JD. 2018. Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast. Nature 560: 392-396. 
  91. Zheng X, Zheng P, Zhang K, Cairns TC, Meyer V, Sun J, et al. 2019. 5S rRNA Promoter for guide RNA expression enabled highly efficient CRISPR/Cas9 genome editing in Aspergillus niger. ACS Synt. Biol. 8: 1568-1574.