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Jo C, Zhang J, Tam JM, Church GM, Khalil AS, Segrè D, Tang TC. Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio 2023; 19:100560. [PMID: 36756210 PMCID: PMC9900623 DOI: 10.1016/j.mtbio.2023.100560] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023] Open
Abstract
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.
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Affiliation(s)
- Charles Jo
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Jing Zhang
- Biological Design Center, Boston University, Boston, MA, USA
- Graduate Program in Bioinformatics, Boston, MA, USA
| | - Jenny M. Tam
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ahmad S. Khalil
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Graduate Program in Bioinformatics, Boston, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
- Department of Physics, Boston University, Boston, MA, USA
| | - Tzu-Chieh Tang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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Wang Q, Zhong C, Xiao H. Genetic Engineering of Filamentous Fungi for Efficient Protein Expression and Secretion. Front Bioeng Biotechnol 2020; 8:293. [PMID: 32322579 PMCID: PMC7156587 DOI: 10.3389/fbioe.2020.00293] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/19/2020] [Indexed: 02/05/2023] Open
Abstract
Filamentous fungi are considered as unique cell factories for protein production due to the high efficiency of protein secretion and superior capability of post-translational modifications. In this review, we firstly introduce the secretory pathway in filamentous fungi. We next summarize the current state-of-the-art works regarding how various genetic engineering strategies are applied for enhancing protein expression and secretion in filamentous fungi. Finally, in a future perspective, we discuss the great potential of genome engineering for further improving protein expression and secretion in filamentous fungi.
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Affiliation(s)
- Qin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and Laboratory of Molecular Biochemical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Zhong
- Materials and Physical Biology Division, School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
- Materials Synthetic Biology Center, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Han Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and Laboratory of Molecular Biochemical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Qiao W, Tang S, Mi S, Jia X, Peng X, Han Y. Biochemical characterization of a novel thermostable GH11 xylanase with CBM6 domain from Caldicellulosiruptor kronotskyensis. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Lafond M, Guais O, Maestracci M, Bonnin E, Giardina T. Four GH11 xylanases from the xylanolytic fungus Talaromyces versatilis act differently on (arabino)xylans. Appl Microbiol Biotechnol 2014; 98:6339-52. [DOI: 10.1007/s00253-014-5606-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 12/12/2022]
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Fedorova TV, Chulkin AM, Vavilova EA, Maisuradze IG, Trofimov AA, Zorov IN, Khotchenkov VP, Polyakov KM, Benevolensky SV, Koroleva OV, Lamzin VS. Purification, biochemical characterization, and structure of recombinant endo-1,4-β-xylanase XylE. BIOCHEMISTRY (MOSCOW) 2012; 77:1190-8. [DOI: 10.1134/s0006297912100112] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
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Murphy C, Powlowski J, Wu M, Butler G, Tsang A. Curation of characterized glycoside hydrolases of fungal origin. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2011; 2011:bar020. [PMID: 21622642 PMCID: PMC3263737 DOI: 10.1093/database/bar020] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Fungi produce a wide range of extracellular enzymes to break down plant cell walls, which are composed mainly of cellulose, lignin and hemicellulose. Among them are the glycoside hydrolases (GH), the largest and most diverse family of enzymes active on these substrates. To facilitate research and development of enzymes for the conversion of cell-wall polysaccharides into fermentable sugars, we have manually curated a comprehensive set of characterized fungal glycoside hydrolases. Characterized glycoside hydrolases were retrieved from protein and enzyme databases, as well as literature repositories. A total of 453 characterized glycoside hydrolases have been cataloged. They come from 131 different fungal species, most of which belong to the phylum Ascomycota. These enzymes represent 46 different GH activities and cover 44 of the 115 CAZy GH families. In addition to enzyme source and enzyme family, available biochemical properties such as temperature and pH optima, specific activity, kinetic parameters and substrate specificities were recorded. To simplify comparative studies, enzyme and species abbreviations have been standardized, Gene Ontology terms assigned and reference to supporting evidence provided. The annotated genes have been organized in a searchable, online database called mycoCLAP (Characterized Lignocellulose-Active Proteins of fungal origin). It is anticipated that this manually curated collection of biochemically characterized fungal proteins will be used to enhance functional annotation of novel GH genes. Database URL: http://mycoCLAP.fungalgenomics.ca/.
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Affiliation(s)
- Caitlin Murphy
- Centre for Structural and Functional Genomics, Concordia University, Montreal QC H4B 1R6, Canada
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Maisuradze IG, Chulkin AM, Vavilova EA, Benevolenskii SV. Multigene families of endo-(1–4)-β-xylanases of Penicillium canescens. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411020128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sharma M, Chadha BS, Saini HS. Purification and characterization of two thermostable xylanases from Malbranchea flava active under alkaline conditions. BIORESOURCE TECHNOLOGY 2010; 101:8834-8842. [PMID: 20630749 DOI: 10.1016/j.biortech.2010.06.071] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 05/31/2010] [Accepted: 06/11/2010] [Indexed: 05/29/2023]
Abstract
Two xylanases, MFX I and MFX II, from the thermophilic fungus Malbranchea flava MTCC 4889 with molecular masses of 25.2 and 30kDa and pIs of 4.5 and 3.7, respectively were purified to homogeneity. The xylanases were optimally active at pH 9.0 and at 60 degrees C, exhibited a half-life of 4h at 60 degrees C, and showed distinct mode of action and product profiles when applied to birchwood, oat spelt, and larchwood xylan, and to wheat and rye arabinoxylan. The xylanases were most active on larchwood xylan with K(m) values of 1.25 and 3.7mg/ml. K(cat)/K(m) values suggested that the xylanases preferentially hydrolyzed rye arabinoxylan. LC-MS/MS (liquid chromatography/mass spectrometry) analysis of tryptic digests of MFX I and MFX II revealed similarity with known fungal xylanases and suggests that that they belonged to the GH 11 and 10 glycosyl hydrolase super families, respectively. These xylanases can potentially be used in enzyme-assisted bleaching of the pulp derived from agro-residues, as well as production of xylooligosaccharides for pre-biotic functional food applications.
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Affiliation(s)
- Manju Sharma
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India.
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Molecular cloning, gene expression analysis and structural modelling of the cellobiohydrolase I from Penicillium occitanis. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Cloning, expression and characterization of a novel acidic xylanase, XYL11B, from the acidophilic fungus Bispora sp. MEY-1. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2009.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Fusion of a family 1 carbohydrate binding module of Aspergillus niger to the Pycnoporus cinnabarinus laccase for efficient softwood kraft pulp biobleaching. J Biotechnol 2009; 142:220-6. [DOI: 10.1016/j.jbiotec.2009.04.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 04/11/2009] [Accepted: 04/26/2009] [Indexed: 11/15/2022]
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Chávez R, Bull P, Eyzaguirre J. The xylanolytic enzyme system from the genus Penicillium. J Biotechnol 2006; 123:413-33. [PMID: 16569456 DOI: 10.1016/j.jbiotec.2005.12.036] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2005] [Revised: 12/06/2005] [Accepted: 12/23/2005] [Indexed: 11/22/2022]
Abstract
In nature, there are numerous microorganisms that efficiently degrade xylan, a major component of lignocellulose. In particular, filamentous fungi have demonstrated a great capability for secreting a wide range of xylanases, being the genus Aspergillus and Trichoderma the most extensively studied and reviewed among the xylan-producing fungi. However, an important amount of information about the production and genetics of xylanases from fungi of the genus Penicillium has accumulated in recent years. A great number of Penicillia are active producers of xylanolytic enzymes, and the use of xylanases from these species has acquired growing importance in biotechnological applications. This review summarizes our current knowledge about the properties, genetics, expression and biotechnological potential of xylanases from the genus Penicillium.
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Affiliation(s)
- Renato Chávez
- Unidad de Biotecnología, Instituto de Investigaciones Agropecuarias (INIA), CRI-Carillanca, Temuco, Chile
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Aro N, Pakula T, Penttilä M. Transcriptional regulation of plant cell wall degradation by filamentous fungi. FEMS Microbiol Rev 2004; 29:719-39. [PMID: 16102600 DOI: 10.1016/j.femsre.2004.11.006] [Citation(s) in RCA: 286] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Revised: 10/29/2004] [Accepted: 11/01/2004] [Indexed: 11/22/2022] Open
Abstract
Plant cell wall consists mainly of the large biopolymers cellulose, hemicellulose, lignin and pectin. These biopolymers are degraded by many microorganisms, in particular filamentous fungi, with the aid of extracellular enzymes. Filamentous fungi have a key role in degradation of the most abundant biopolymers found in nature, cellulose and hemicelluloses, and therefore are essential for the maintenance of the global carbon cycle. The production of plant cell wall degrading enzymes, cellulases, hemicellulases, ligninases and pectinases, is regulated mainly at the transcriptional level in filamentous fungi. The genes are induced in the presence of the polymers or molecules derived from the polymers and repressed under growth conditions where the production of these enzymes is not necessary, such as on glucose. The expression of the genes encoding the enzymes is regulated by various environmental and cellular factors, some of which are common while others are more unique to either a certain fungus or a class of enzymes. This review summarises our current knowledge on the transcriptional regulation, focusing on the recently characterized transcription factors that regulate genes coding for enzymes involved in the breakdown of plant cell wall biopolymers.
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Affiliation(s)
- Nina Aro
- VTT Biotechnology, Espoo, Finland.
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Brutus A, Villard C, Durand A, Tahir T, Furniss C, Puigserver A, Juge N, Giardina T. The inhibition specificity of recombinant Penicillium funiculosum xylanase B towards wheat proteinaceous inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1701:121-8. [PMID: 15450181 DOI: 10.1016/j.bbapap.2004.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Revised: 06/14/2004] [Accepted: 06/24/2004] [Indexed: 11/23/2022]
Abstract
The filamentous fungus Penicillium funiculosum produces a mixture of modular and non-modular xylanases belonging to different glycoside hydrolase (GH) families. In the present study, we heterologously expressed the cDNA encoding GH11 xylanase B (XYNB) and studied the enzymatic properties of the recombinant enzyme. Expression in Escherichia coli led to the partial purification of a glutathione fusion protein from the soluble fraction whereas the recombinant protein produced in Pichia pastoris was successfully purified using a one-step chromatography. Despite O-glycosylation heterogeneity, the purified enzyme efficiently degraded low viscosity xylan [K(m)=40+/-3 g l(-1), V(max)=16.1+/-0.8 micromol xylose min(-1) and k(cat)=5405+/-150 s(-1) at pH 4.2 and 45 degrees C] and medium viscosity xylan [K(m)=34.5+/-3.2 g l(-1), V(max)=14.9+/-1.0 micromol xylose min(-1)k(cat)=4966+/-333 s(-1) at pH 4.2 and 45 degrees C]. XYNB was further tested for its ability to interact with wheat xylanase inhibitors. The xylanase activity of XYNB produced in P. pastoris was strongly inhibited by both XIP-I and TAXI-I in a competitive manner, with a K(i) of 89.7+/-8.5 and 2.9+/-0.3 nM, respectively, whereas no inhibition was detected with TAXI-II. Physical interaction of both TAXI-I and XIP-I with XYNB was observed using titration curves across a pH range 3-9.
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Affiliation(s)
- Alexandre Brutus
- Laboratoire de Biochimie et Biologie de la Nutrition, Institut Méditerranéen de Recherche en Nutrition, UMR Université Aix Marseille III-INRA 1111, Service 342, Faculté des Sciences et Techniques Saint-Jérôme, 13397 Marseille Cedex 20, France
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Abell BM, Hahn M, Holbrook LA, Moloney MM. Membrane topology and sequence requirements for oil body targeting of oleosin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 37:461-70. [PMID: 14756765 DOI: 10.1111/j.1365-313x.2003.01988.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Oleosin protein is targeted to oil bodies via the endoplasmic reticulum (ER) and consists of a lipid-submerged hydrophobic (H) domain that is flanked by cytosolic hydrophilic domains. We investigated the relationship between oleosin ER topology and its subsequent ability to target to oil bodies. Oleosin variants were created to yield differing ER membrane topologies and tagged with a reporter enzyme. Localisation was assessed by fractionation after transient expression in embryonic cells. Membrane-straddled topologies with N-terminal sequence in the ER lumen and C-terminal sequence in the cytosol were unable to target to oil bodies efficiently. Similarly, a translocated topology with only ER membrane and lumenal sequence was unable to target to oil bodies efficiently. Both topology variants accumulated proportionately higher in ER microsomal fractions, demonstrating a block in transferring from ER to oil bodies. The residual oil body accumulation for the inverted topology was shown to be because of partial adoption of native ER membrane topology, using a reporter variant, which becomes inactivated by ER-mediated glycosylation. In addition, the importance of H domain sequence for oil body targeting was assessed using variants that maintain native ER topology. The central proline knot motif (PKM) has previously been shown to be critical for oil body targeting, but here the arms of the H domain flanking this motif were shown to be interchangeable with only a moderate reduction in oil body targeting. We conclude that oil body targeting of oleosin depends on a specific ER membrane topology but does not require a specific sequence in the H domain flanking arms.
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Affiliation(s)
- Ben M Abell
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada T2N 1N4
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