1
|
Shestakova A, Fatkulin A, Surkova D, Osmolovskiy A, Popova E. First Insight into the Degradome of Aspergillus ochraceus: Novel Secreted Peptidases and Their Inhibitors. Int J Mol Sci 2024; 25:7121. [PMID: 39000228 PMCID: PMC11241649 DOI: 10.3390/ijms25137121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/07/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024] Open
Abstract
Aspergillus fungi constitute a pivotal element within ecosystems, serving as both contributors of biologically active compounds and harboring the potential to cause various diseases across living organisms. The organism's proteolytic enzyme complex, termed the degradome, acts as an intermediary in its dynamic interaction with the surrounding environment. Using techniques such as genome and transcriptome sequencing, alongside protein prediction methodologies, we identified putative extracellular peptidases within Aspergillus ochraceus VKM-F4104D. Following manual annotation procedures, a total of 11 aspartic, 2 cysteine, 2 glutamic, 21 serine, 1 threonine, and 21 metallopeptidases were attributed to the extracellular degradome of A. ochraceus VKM-F4104D. Among them are enzymes with promising applications in biotechnology, potential targets and agents for antifungal therapy, and microbial antagonism factors. Thus, additional functionalities of the extracellular degradome, extending beyond mere protein substrate digestion for nutritional purposes, were demonstrated.
Collapse
Affiliation(s)
- Anna Shestakova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
| | - Artem Fatkulin
- Laboratory of Molecular Physiology, HSE University, Moscow 101000, Russia
| | - Daria Surkova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
| | | | - Elizaveta Popova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
| |
Collapse
|
2
|
Sharan AA, Bellemare A, DiFalco M, Tsang A, Vuong TV, Edwards EA, Master ER. Functional screening pipeline to uncover laccase-like multicopper oxidase enzymes that transform industrial lignins. BIORESOURCE TECHNOLOGY 2024; 393:130084. [PMID: 38000639 DOI: 10.1016/j.biortech.2023.130084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/07/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023]
Abstract
Laccase-like multicopper oxidases are recognized for their potential to alter the reactivity of lignins for application in value-added products. Typically, model compounds are employed to discover such enzymes; however, they do not represent the complexity of industrial lignin substrates. In this work, a screening pipeline was developed to test enzymes simultaneously on model compounds and industrial lignins. A total of 12 lignin-active fungal multicopper oxidases were discovered, including 9 enzymes active under alkaline conditions (pH 11.0). Principal component analysis revealed the poor ability of model compounds to predict enzyme performance on industrial lignins. Additionally, sequence similarity analyses grouped these enzymes with Auxiliary Activity-1 sub-families with few previously characterized members, underscoring their taxonomic novelty. Correlation between the lignin-activity of these enzymes and their taxonomic origin, however, was not observed. These are critical insights to bridge the gap between enzyme discovery and application for industrial lignin valorization.
Collapse
Affiliation(s)
- Anupama A Sharan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Annie Bellemare
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Marcos DiFalco
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada; Department of Cell and Systems Biology, University of Toronto, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada; Department of Bioproducts and Biosystems, Aalto University, Finland.
| |
Collapse
|
3
|
Mathieu Y, Raji O, Bellemare A, Di Falco M, Nguyen TTM, Viborg AH, Tsang A, Master E, Brumer H. Functional characterization of fungal lytic polysaccharide monooxygenases for cellulose surface oxidation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:132. [PMID: 37679837 PMCID: PMC10486138 DOI: 10.1186/s13068-023-02383-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND Microbial lytic polysaccharide monooxygenases (LPMOs) cleave diverse biomass polysaccharides, including cellulose and hemicelluloses, by initial oxidation at C1 or C4 of glycan chains. Within the Carbohydrate-Active Enzymes (CAZy) classification, Auxiliary Activity Family 9 (AA9) comprises the first and largest group of fungal LPMOs, which are often also found in tandem with non-catalytic carbohydrate-binding modules (CBMs). LPMOs originally attracted attention for their ability to potentiate complete biomass deconstruction to monosaccharides. More recently, LPMOs have been applied for selective surface modification of insoluble cellulose and chitin. RESULTS To further explore the catalytic diversity of AA9 LPMOs, over 17,000 sequences were extracted from public databases, filtered, and used to construct a sequence similarity network (SSN) comprising 33 phylogenetically supported clusters. From these, 32 targets were produced successfully in the industrial filamentous fungus Aspergillus niger, 25 of which produced detectable LPMO activity. Detailed biochemical characterization of the eight most highly produced targets revealed individual C1, C4, and mixed C1/C4 regiospecificities of cellulose surface oxidation, different redox co-substrate preferences, and CBM targeting effects. Specifically, the presence of a CBM correlated with increased formation of soluble oxidized products and a more localized pattern of surface oxidation, as indicated by carbonyl-specific fluorescent labeling. On the other hand, LPMOs without native CBMs were associated with minimal release of soluble products and comparatively dispersed oxidation pattern. CONCLUSIONS This work provides insight into the structural and functional diversity of LPMOs, and highlights the need for further detailed characterization of individual enzymes to identify those best suited for cellulose saccharification versus surface functionalization toward biomaterials applications.
Collapse
Affiliation(s)
- Yann Mathieu
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Olanrewaju Raji
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Annie Bellemare
- Centre for Structural & Functional Genomics, Concordia University, 7141 Sherbrooke-West Street, Montreal, H4B 1R6, Canada
| | - Marcos Di Falco
- Centre for Structural & Functional Genomics, Concordia University, 7141 Sherbrooke-West Street, Montreal, H4B 1R6, Canada
| | - Thi Truc Minh Nguyen
- Centre for Structural & Functional Genomics, Concordia University, 7141 Sherbrooke-West Street, Montreal, H4B 1R6, Canada
| | - Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Adrian Tsang
- Centre for Structural & Functional Genomics, Concordia University, 7141 Sherbrooke-West Street, Montreal, H4B 1R6, Canada
| | - Emma Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada.
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Department of Botany, University of British Columbia, 3200 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
| |
Collapse
|
4
|
Identification of an l-Arabitol Transporter from Aspergillus niger. Biomolecules 2023; 13:biom13020188. [PMID: 36830558 PMCID: PMC9953744 DOI: 10.3390/biom13020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
l-arabitol is an intermediate of the pentose catabolic pathway in fungi but can also be used as a carbon source by many fungi, suggesting the presence of transporters for this polyol. In this study, an l-arabitol transporter, LatA, was identified in Aspergillus niger. Growth and expression profiles as well as sugar consumption analysis indicated that LatA only imports l-arabitol and is regulated by the arabinanolytic transcriptional activator AraR. Moreover, l-arabitol production from wheat bran was increased in a metabolically engineered A. niger mutant by the deletion of latA, indicating its potential for improving l-arabitol-producing cell factories. Phylogenetic analysis showed that homologs of LatA are widely conserved in fungi.
Collapse
|
5
|
Marinovíc M, Di Falco M, Aguilar Pontes MV, Gorzsás A, Tsang A, de Vries RP, Mäkelä MR, Hildén K. Comparative Analysis of Enzyme Production Patterns of Lignocellulose Degradation of Two White Rot Fungi: Obba rivulosa and Gelatoporia subvermispora. Biomolecules 2022; 12:biom12081017. [PMID: 35892327 PMCID: PMC9330253 DOI: 10.3390/biom12081017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
The unique ability of basidiomycete white rot fungi to degrade all components of plant cell walls makes them indispensable organisms in the global carbon cycle. In this study, we analyzed the proteomes of two closely related white rot fungi, Obba rivulosa and Gelatoporia subvermispora, during eight-week cultivation on solid spruce wood. Plant cell wall degrading carbohydrate-active enzymes (CAZymes) represented approximately 5% of the total proteins in both species. A core set of orthologous plant cell wall degrading CAZymes was shared between these species on spruce suggesting a conserved plant biomass degradation approach in this clade of basidiomycete fungi. However, differences in time-dependent production of plant cell wall degrading enzymes may be due to differences among initial growth rates of these species on solid spruce wood. The obtained results provide insight into specific enzymes and enzyme sets that are produced during the degradation of solid spruce wood in these fungi. These findings expand the knowledge on enzyme production in nature-mimicking conditions and may contribute to the exploitation of white rot fungi and their enzymes for biotechnological applications.
Collapse
Affiliation(s)
- Mila Marinovíc
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland; (M.M.); (M.R.M.)
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada; (M.D.F.); (A.T.)
| | - Maria Victoria Aguilar Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (M.V.A.P.); (R.P.d.V.)
| | - András Gorzsás
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden;
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada; (M.D.F.); (A.T.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (M.V.A.P.); (R.P.d.V.)
| | - Miia R. Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland; (M.M.); (M.R.M.)
| | - Kristiina Hildén
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland; (M.M.); (M.R.M.)
- Correspondence:
| |
Collapse
|
6
|
Miyazono KI, Kubota K, Takahashi K, Tanokura M. Crystal structure and substrate recognition mechanism of the prolyl endoprotease PEP from Aspergillus niger. Biochem Biophys Res Commun 2022; 591:76-81. [PMID: 34999257 DOI: 10.1016/j.bbrc.2021.12.114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 11/02/2022]
Abstract
Proteases are enzymes that are not only essential for life but also industrially important. Understanding the substrate recognition mechanisms of proteases is important to enhance the use of proteases. The fungus Aspergillus produces a wide variety of proteases, including PEP, which is a prolyl endoprotease from A. niger. Although PEP exhibits amino acid sequence similarity to the serine peptidase family S28 proteins (PRCP and DPP7) that recognize Pro-X bonds in the terminal regions of peptides, PEP recognizes Pro-X bonds not only in peptides but also in proteins. To reveal the structural basis of the prolyl endoprotease activity of PEP, we determined the structure of PEP by X-ray crystallography at a resolution of 1.75 Å. The PEP structure shows that PEP has a wide-open catalytic pocket compared to its homologs. The characteristic catalytic pocket structure of PEP is predicted to be important for the recognition of protein substrates.
Collapse
Affiliation(s)
- Ken-Ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Keiko Kubota
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan; Laboratory of Molecular Biochemistry, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi Hachioji, Tokyo, 192-0392, Japan
| | - Kenji Takahashi
- Laboratory of Molecular Biochemistry, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi Hachioji, Tokyo, 192-0392, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan.
| |
Collapse
|
7
|
Chen Y, Li P, He W, Liao L, Xia B, Jiang L, Liu Y. Analysis of microbial community and the characterization of Aspergillus flavus in Liuyang Douchi during fermentation. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
8
|
Kun RS, Garrigues S, Di Falco M, Tsang A, de Vries RP. Blocking utilization of major plant biomass polysaccharides leads Aspergillus niger towards utilization of minor components. Microb Biotechnol 2021; 14:1683-1698. [PMID: 34114741 PMCID: PMC8313289 DOI: 10.1111/1751-7915.13835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
Fungi produce a wide range of enzymes that allow them to grow on diverse plant biomass. Wheat bran is a low-cost substrate with high potential for biotechnological applications. It mainly contains cellulose and (arabino)xylan, as well as starch, proteins, lipids and lignin to a lesser extent. In this study, we dissected the regulatory network governing wheat bran degradation in Aspergillus niger to assess the relative contribution of the regulators to the utilization of this plant biomass substrate. Deletion of genes encoding transcription factors involved in (hemi-)cellulose utilization (XlnR, AraR, ClrA and ClrB) individually and in combination significantly reduced production of polysaccharide-degrading enzymes, but retained substantial growth on wheat bran. Proteomic analysis suggested the ability of A. niger to grow on other carbon components, such as starch, which was confirmed by the additional deletion of the amylolytic regulator AmyR. Growth was further reduced but not impaired, indicating that other minor components provide sufficient energy for residual growth, displaying the flexibility of A. niger, and likely other fungi, in carbon utilization. Better understanding of the complexity and flexibility of fungal regulatory networks will facilitate the generation of more efficient fungal cell factories that use plant biomass as a substrate.
Collapse
Affiliation(s)
- Roland S. Kun
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Sandra Garrigues
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B 1R6Canada
| | - Adrian Tsang
- Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B 1R6Canada
| | - Ronald P. de Vries
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| |
Collapse
|
9
|
Liu E, Segato F, Wilkins MR. Fed-batch production of Thermothelomyces thermophilus lignin peroxidase using a recombinant Aspergillus nidulans strain in stirred-tank bioreactor. BIORESOURCE TECHNOLOGY 2021; 325:124700. [PMID: 33461124 DOI: 10.1016/j.biortech.2021.124700] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Enzymatic lignin depolymerization is considered a favorable approach to utilize lignin due to the higher selectivity and less energy requirement when compared to thermochemical lignin valorization. Lignin peroxidase (LiP) is one of the key enzymes involved in lignin degradation and possesses high redox potential to oxidize non-phenolic structures and phenolic compounds in lignin. However, the production of LiP is mainly from white-rot fungi at small scales. It is critical to discover new LiP from other microorganisms and produce LiP at large scales. This study aims to produce a novel LiP originally from Thermothelomyces thermophiles using a recombinant Aspergillus nidulans strain. The LiP production medium was optimized, and different fed-batch strategies for LiP production were investigated to improve LiP activity, yield, and productivity. Results demonstrated that LiP production was enhanced by using multi-pulse fed-batch fermentation. A maximum LiP activity of 1,645 mU/L with a protein concentration of 0.26 g/L was achieved.
Collapse
Affiliation(s)
- Enshi Liu
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Fernando Segato
- Department of Biotechnology, University of São Paulo, Lorena, SP, Brazil
| | - Mark R Wilkins
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
| |
Collapse
|
10
|
Dong Z, Yang S, Lee BH. Bioinformatic mapping of a more precise Aspergillus niger degradome. Sci Rep 2021; 11:693. [PMID: 33436802 PMCID: PMC7804941 DOI: 10.1038/s41598-020-80028-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 11/21/2022] Open
Abstract
Aspergillus niger has the ability to produce a large variety of proteases, which are of particular importance for protein digestion, intracellular protein turnover, cell signaling, flavour development, extracellular matrix remodeling and microbial defense. However, the A. niger degradome (the full repertoire of peptidases encoded by the A. niger genome) available is not accurate and comprehensive. Herein, we have utilized annotations of A. niger proteases in AspGD, JGI, and version 12.2 MEROPS database to compile an index of at least 232 putative proteases that are distributed into the 71 families/subfamilies and 26 clans of the 6 known catalytic classes, which represents ~ 1.64% of the 14,165 putative A. niger protein content. The composition of the A. niger degradome comprises ~ 7.3% aspartic, ~ 2.2% glutamic, ~ 6.0% threonine, ~ 17.7% cysteine, ~ 31.0% serine, and ~ 35.8% metallopeptidases. One hundred and two proteases have been reassigned into the above six classes, while the active sites and/or metal-binding residues of 110 proteases were recharacterized. The probable physiological functions and active site architectures of these peptidases were also investigated. This work provides a more precise overview of the complete degradome of A. niger, which will no doubt constitute a valuable resource and starting point for further experimental studies on the biochemical characterization and physiological roles of these proteases.
Collapse
Affiliation(s)
- Zixing Dong
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Region of Mid-Line of South-To-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China.
| | - Shuangshuang Yang
- College of Physical Education, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Byong H Lee
- Department of Microbiology/Immunology, McGill University, Montreal, QC, Canada
| |
Collapse
|
11
|
Yang M, Zhu Z, Zhuang Z, Bai Y, Wang S, Ge F. Proteogenomic Characterization of the Pathogenic Fungus Aspergillus flavus Reveals Novel Genes Involved in Aflatoxin Production. Mol Cell Proteomics 2020; 20:100013. [PMID: 33568340 PMCID: PMC7950108 DOI: 10.1074/mcp.ra120.002144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/06/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022] Open
Abstract
Aspergillus flavus (A. flavus), a pathogenic fungus, can produce carcinogenic and toxic aflatoxins that are a serious agricultural and medical threat worldwide. Attempts to decipher the aflatoxin biosynthetic pathway have been hampered by the lack of a high-quality genome annotation for A. flavus. To address this gap, we performed a comprehensive proteogenomic analysis using high-accuracy mass spectrometry data for this pathogen. The resulting high-quality data set confirmed the translation of 8724 previously predicted genes and identified 732 novel proteins, 269 splice variants, 447 single amino acid variants, 188 revised genes. A subset of novel proteins was experimentally validated by RT-PCR and synthetic peptides. Further functional annotation suggested that a number of the identified novel proteins may play roles in aflatoxin biosynthesis and stress responses in A. flavus. This comprehensive strategy also identified a wide range of posttranslational modifications (PTMs), including 3461 modification sites from 1765 proteins. Functional analysis suggested the involvement of these modified proteins in the regulation of cellular metabolic and aflatoxin biosynthetic pathways. Together, we provided a high-quality annotation of A. flavus genome and revealed novel insights into the mechanisms of aflatoxin production and pathogenicity in this pathogen.
Collapse
Affiliation(s)
- Mingkun Yang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhuo Zhu
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenhong Zhuang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youhuang Bai
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shihua Wang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
| |
Collapse
|
12
|
Gorshkov V, Osipova E, Ponomareva M, Ponomarev S, Gogoleva N, Petrova O, Gogoleva O, Meshcherov A, Balkin A, Vetchinkina E, Potapov K, Gogolev Y, Korzun V. Rye Snow Mold-Associated Microdochium nivale Strains Inhabiting a Common Area: Variability in Genetics, Morphotype, Extracellular Enzymatic Activities, and Virulence. J Fungi (Basel) 2020; 6:E335. [PMID: 33287447 PMCID: PMC7761817 DOI: 10.3390/jof6040335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Snow mold is a severe plant disease caused by psychrophilic or psychrotolerant fungi, of which Microdochium species are the most harmful. A clear understanding of Microdochium biology has many gaps; the pathocomplex and its dynamic are poorly characterized, virulence factors are unknown, genome sequences are not available, and the criteria of plant snow mold resistance are not elucidated. Our study aimed to identify comprehensive characteristics of a local community of snow mold-causing Microdochium species colonizing a particular crop culture. By using the next-generation sequencing (NGS) technique, we characterized fungal and bacterial communities of pink snow mold-affected winter rye (Secale cereale) plants within a given geographical location shortly after snowmelt. Twenty-one strains of M. nivale were isolated, classified on the basis of internal transcribed spacer 2 (ITS2) region, and characterized by morphology, synthesis of extracellular enzymes, and virulence. Several types of extracellular enzymatic activities, the level of which had no correlations with the degree of virulence, were revealed for Microdochium species for the first time. Our study shows that genetically and phenotypically diverse M. nivale strains simultaneously colonize winter rye plants within a common area, and each strain is likely to utilize its own, unique strategy to cause the disease using "a personal" pattern of extracellular enzymes.
Collapse
Affiliation(s)
- Vladimir Gorshkov
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Elena Osipova
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Mira Ponomareva
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Sergey Ponomarev
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Natalia Gogoleva
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Olga Petrova
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Olga Gogoleva
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Azat Meshcherov
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Alexander Balkin
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Elena Vetchinkina
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, 410049 Saratov, Russia;
| | - Kim Potapov
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Yuri Gogolev
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Viktor Korzun
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
| |
Collapse
|
13
|
Liu E, Wilkins MR. Process optimization and scale-up production of fungal aryl alcohol oxidase from genetically modified Aspergillus nidulans in stirred-tank bioreactor. BIORESOURCE TECHNOLOGY 2020; 315:123792. [PMID: 32659422 DOI: 10.1016/j.biortech.2020.123792] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Microbial production of aryl alcohol oxidase (AAO) has attracted increasing attention due to the central role of AAO in enzymatic lignin depolymerization. However, large-scale production of AAO has not been reached because of the low yield and inefficient fermentation process. This study aims to optimize the process parameters and scale-up production of AAO using Aspergillus nidulans in a stirred-tank bioreactor. Effects of pH and dissolved oxygen on AAO production at bioreactor scale were particularly investigated. Results revealed that pH control significantly affected protein production and increasing dissolved oxygen level stimulated AAO production. The greatest AAO activity (1906 U/L) and protein concentration (1.19 g/L) were achieved in 48 h at 60% dissolved oxygen with pH controlled at 6.0. The yield and productivity (in 48 h) were 31.2 U/g maltose and 39.7 U/L/h, respectively. In addition, crude AAO was concentrated and partially purified by ultrafiltration and verified by protein identification.
Collapse
Affiliation(s)
- Enshi Liu
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Mark R Wilkins
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
| |
Collapse
|
14
|
Li C, Zhou J, Du G, Chen J, Takahashi S, Liu S. Developing Aspergillus niger as a cell factory for food enzyme production. Biotechnol Adv 2020; 44:107630. [PMID: 32919011 DOI: 10.1016/j.biotechadv.2020.107630] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/05/2020] [Accepted: 09/05/2020] [Indexed: 02/06/2023]
Abstract
Aspergillus niger has become one of the most important hosts for food enzyme production due to its unique food safety characteristics and excellent protein secretion systems. A series of food enzymes such as glucoamylase have been commercially produced by A. niger strains, making this species a suitable platform for the engineered of strains with improved enzyme production. However, difficulties in genetic manipulations and shortage of expression strategies limit the progress in this regard. Moreover, several mycotoxins have recently been detected in some A. niger strains, which raises the necessity for a regulatory approval process for food enzyme production. With robust strains, processing engineering strategies are also needed for producing the enzymes on a large scale, which is also challenging for A. niger, since its culture is aerobic, and non-Newtonian fluid properties are developed during submerged culture, making mixing and aeration very energy-intensive. In this article, the progress and challenges of developing A. niger for the production of food enzymes are reviewed, including its genetic manipulations, strategies for more efficient production of food enzymes, and elimination of mycotoxins for product safety.
Collapse
Affiliation(s)
- Cen Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Guocheng Du
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Song Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
15
|
Dilokpimol A, Peng M, Di Falco M, Chin A Woeng T, Hegi RMW, Granchi Z, Tsang A, Hildén KS, Mäkelä MR, de Vries RP. Penicillium subrubescens adapts its enzyme production to the composition of plant biomass. BIORESOURCE TECHNOLOGY 2020; 311:123477. [PMID: 32408196 DOI: 10.1016/j.biortech.2020.123477] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 06/11/2023]
Abstract
Penicillium subrubescens is able to degrade a broad range of plant biomass and it has an expanded set of Carbohydrate Active enzyme (CAZyme)-encoding genes in comparison to other Penicillium species. Here we used exoproteome and transcriptome analysis to demonstrate the versatile plant biomass degradation mechanism by P. subrubescens during growth on wheat bran and sugar beet pulp. On wheat bran P. subrubescens degraded xylan main chain and side residues from Day 2 of cultivation, whereas it started to degrade side chains of pectin in sugar beet pulp prior to attacking the main chain on Day 3. In addition, on Day 3 the cellulolytic enzymes were highly increased. Our results confirm that P. subrubescens adapts its enzyme production to the available plant biomass and is a promising new fungal cell factory for the production of CAZymes.
Collapse
Affiliation(s)
- Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, H4B 1R6 Montreal, Quebec, Canada
| | | | - Rosa M W Hegi
- GenomeScan B.V, Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | - Zoraide Granchi
- GenomeScan B.V, Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, H4B 1R6 Montreal, Quebec, Canada
| | - Kristiina S Hildén
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| |
Collapse
|
16
|
Lu Y, Tan X, Lv Y, Yang G, Chi Y, He Q. Physicochemical properties and microbial community dynamics during Chinese horse bean-chili-paste fermentation, revealed by culture-dependent and culture-independent approaches. Food Microbiol 2020; 85:103309. [PMID: 31500715 DOI: 10.1016/j.fm.2019.103309] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023]
Abstract
The production of Chinese horse bean-chili-paste (CHCP) involves three fermentation phases: chili-to-moromi fermentation (CF) phase, horse bean-to-meju fermentation (HF) phase and moromi-meju mixed fermentation (MF) phase. To understand the microbial dynamics among these three phases and the potential roles of viable microbes for fermentation, microbial community dynamics was investigated by using culture-dependent and culture-independent methods. Furthermore, the capacities of enzyme-producing of the isolates were determined. During the CF phase, reducing sugar content increased from 3.1% to 3.49%, while pH declined from 4.85 to 4.5. The protein content in the HF phase and MF phase reduced sharply from 22.23% to 10.29% and 4.39%-1.19%, respectively. Bacillus sp., Staphylococcus sp., Oceanobacillus sp., Candida sp., Zygosaccharomyces sp. and Aspergillus sp. dominated the CF phase, while Bacillus sp., Candida sp. and Zygosaccharomyces sp. were the dominant microorganisms in both the HF and MF phases. B. amyloliquefaciens, B. methylotrophicus, B. subtilis, B. licheniformis and A. oryzae possessed strong capacities of producing enzymes, i.e. α-amylase, cellulase and xylanase, acid protease and leucine aminopeptidase, and could make a great contribution to CHCP fermentation.
Collapse
Affiliation(s)
- Yunhao Lu
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China
| | - Xinyi Tan
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China
| | - Yuanping Lv
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China
| | - Guohua Yang
- Sichuan Dandan Pixian-douban Co., Ltd., Chengdu, 610065, PR China
| | - Yuanlong Chi
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China.
| | - Qiang He
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China.
| |
Collapse
|
17
|
Huang L, Dong L, Wang B, Pan L. The transcription factor PrtT and its target protease profiles in Aspergillus niger are negatively regulated by carbon sources. Biotechnol Lett 2020; 42:613-624. [PMID: 31970554 DOI: 10.1007/s10529-020-02806-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 01/13/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To survey genome-scale protease profiles regulated by the Aspergillus niger transcription factor PrtT and further controlled by carbon sources. RESULTS The PrtT disruption mutant (delprtT) and overexpression (OEprtT) strains were successfully generated and further confirmed by phenotypic and protease activity analysis. RNA-seq analysis of WT and mutants identified 32 differentially expressed protease genes, which mostly belonged to serine-type peptidases, aspartic-type endopeptidases, aminopeptidases and carboxypeptidases. Furthermore, based on the MEME predicted motif analysis of the PrtT promoter, EMSA and phenotypic and qRT-PCR analyses confirmed that the carbon metabolism regulator AmyR directly regulated the protease genes and their regulatory factor PrtT. CONCLUSION Thirty-two PrtT-regulated protease genes were identified by RNA-seq, and the secondary carbon source regulator AmyR was found to have a negative regulatory effect on the expression of PrtT and its target protease genes.
Collapse
Affiliation(s)
- Lianggang Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, No. 382, Waihuan East Rd, Guangzhou, 510006, China
| | - Liangbo Dong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, No. 382, Waihuan East Rd, Guangzhou, 510006, China
| | - Bin Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, No. 382, Waihuan East Rd, Guangzhou, 510006, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Li Pan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, No. 382, Waihuan East Rd, Guangzhou, 510006, China. .,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China.
| |
Collapse
|
18
|
Pandaranayaka EP, Frenkel O, Elad Y, Prusky D, Harel A. Network analysis exposes core functions in major lifestyles of fungal and oomycete plant pathogens. BMC Genomics 2019; 20:1020. [PMID: 31878885 PMCID: PMC6933724 DOI: 10.1186/s12864-019-6409-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Background Genomic studies demonstrate that components of virulence mechanisms in filamentous eukaryotic pathogens (FEPs, fungi and oomycetes) of plants are often highly conserved, or found in gene families that include secreted hydrolytic enzymes (e.g., cellulases and proteases) and secondary metabolites (e.g., toxins), central to the pathogenicity process. However, very few large-scale genomic comparisons have utilized complete proteomes from dozens of FEPs to reveal lifestyle-associated virulence mechanisms. Providing a powerful means for exploration, and the discovery of trends in large-scale datasets, network analysis has been used to identify core functions of the primordial cyanobacteria, and ancient evolutionary signatures in oxidoreductases. Results We used a sequence-similarity network to study components of virulence mechanisms of major pathogenic lifestyles (necrotroph (ic), N; biotroph (ic), B; hemibiotroph (ic), H) in complete pan-proteomes of 65 FEPs and 17 saprobes. Our comparative analysis highlights approximately 190 core functions found in 70% of the genomes of these pathogenic lifestyles. Core functions were found mainly in: transport (in H, N, B cores); carbohydrate metabolism, secondary metabolite synthesis, and protease (H and N cores); nucleic acid metabolism and signal transduction (B core); and amino acid metabolism (H core). Taken together, the necrotrophic core contains functions such as cell wall-associated degrading enzymes, toxin metabolism, and transport, which are likely to support their lifestyle of killing prior to feeding. The biotrophic stealth growth on living tissues is potentially controlled by a core of regulatory functions, such as: small G-protein family of GTPases, RNA modification, and cryptochrome-based light sensing. Regulatory mechanisms found in the hemibiotrophic core contain light- and CO2-sensing functions that could mediate important roles of this group, such as transition between lifestyles. Conclusions The selected set of enriched core functions identified in our work can facilitate future studies aimed at controlling FEPs. One interesting example would be to facilitate the identification of the pathogenic potential of samples analyzed by metagenomics. Finally, our analysis offers potential evolutionary scenarios, suggesting that an early-branching saprobe (identified in previous studies) has probably evolved a necrotrophic lifestyle as illustrated by the highest number of shared gene families between saprobes and necrotrophs.
Collapse
Affiliation(s)
- Eswari Pj Pandaranayaka
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Omer Frenkel
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Dov Prusky
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Arye Harel
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel.
| |
Collapse
|
19
|
Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens. Appl Environ Microbiol 2019; 85:AEM.01828-19. [PMID: 31585998 DOI: 10.1128/aem.01828-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/22/2019] [Indexed: 12/15/2022] Open
Abstract
The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for utilization of plant biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant biomass would benefit from derepressed or constitutively CAZyme-expressing strains.IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant biomass utilization in the white-rot fungus Dichomitus squalens This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.
Collapse
|
20
|
Mat'at'a M, Galádová H, Varečka L, Šimkovič M. The study of intracellular and secreted high-molecular-mass protease(s) of Trichoderma spp., and their responses to conidiation stimuli. Can J Microbiol 2019; 65:653-667. [PMID: 31059650 DOI: 10.1139/cjm-2018-0670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We continued our study of high-molecular-mass proteases (HMMPs) using several strains of the genus Trichoderma, and other filamentous fungi (Botrytis cinerea, Aspergillus niger, Fusarium culmorum, and Penicillium purpurogenum). We found that five Trichoderma strains secreted HMMPs into the media after induction with bovine serum albumin. Botrytis cinerea and F. culmorum secreted proteases in the absence of inducer, while A. niger or P. purpurogenum did not secrete proteolytic activity (PA). The activity of HMMPs secreted by or intracellularly located in Trichoderma spp. represents the predominant part of cellular PA, according to zymogram patterns. This observation allowed the study of HMMPs' physiological role(s) independent from the secretion. In studying conidiation, we found that illumination significantly stimulated PA in Trichoderma strains. In the T. atroviride IMI 206040 strain, we demonstrated that this stimulation is dependent on the BLR1 and BLR2 receptors. No stimulation of PA was observed when mechanical injury was used as an elicitor of conidiation. Compounds used as inhibitors or activators of conidiation exerted no congruent effects on both PA and conidiation. These results do not favour a direct role of HMMPs in conidiation. Probably, HMMP activity may be involved in the process of the activation of metabolism during vegetative growth, differentiation, and aging-related processes.
Collapse
Affiliation(s)
- Matej Mat'at'a
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovak Republic.,Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovak Republic
| | - Helena Galádová
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovak Republic.,Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovak Republic
| | - L'udovít Varečka
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovak Republic.,Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovak Republic
| | - Martin Šimkovič
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovak Republic.,Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovak Republic
| |
Collapse
|
21
|
Mäkelä M, DiFalco M, McDonnell E, Nguyen T, Wiebenga A, Hildén K, Peng M, Grigoriev I, Tsang A, de Vries R. Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli. Stud Mycol 2018; 91:79-99. [PMID: 30487660 PMCID: PMC6249967 DOI: 10.1016/j.simyco.2018.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse Aspergillus species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is A. clavatus where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section Nigri, A. aculeatus, A. nidulans and A. terreus, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time.
Collapse
Affiliation(s)
- M.R. Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - M. DiFalco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - E. McDonnell
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - T.T.M. Nguyen
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - A. Wiebenga
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - K. Hildén
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - M. Peng
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - I.V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94598, USA
| | - A. Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - R.P. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| |
Collapse
|
22
|
Genome mining for peptidases in heat-tolerant and mesophilic fungi and putative adaptations for thermostability. BMC Genomics 2018; 19:152. [PMID: 29463214 PMCID: PMC5819190 DOI: 10.1186/s12864-018-4549-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 02/13/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Peptidases (EC 3.4) consist of a large group of hydrolytic enzymes that catalyze the hydrolysis of proteins accounting for approximately 65% of the total worldwide enzyme production. Peptidases from thermophilic fungi have adaptations to high temperature that makes them adequate for biotechnological application. In the present study, we profiled the genomes of heat-tolerant fungi and phylogenetically related mesophilic species for genes encoding for peptidases and their putative adaptations for thermostability. RESULTS We generated an extensive catalogue of these enzymes ranging from 241 to 820 peptidase genes in the genomes of 23 fungi. Thermophilic species presented the smallest number of peptidases encoding genes in relation to mesophilic species, and the peptidases families with a greater number of genes were the most affected. We observed differences in peptidases in thermophilic species in comparison to mesophilic counterparts, at (i) the genome level: a great reduction in the number of peptidases encoding genes that harbored a higher number of copies; (ii) in the primary protein structure: shifts in proportion of single or groups of amino acids; and (iii) in the three-dimensional structure: reduction in the number of internal cavities. Similar results were reported for extremely thermophilic proteins, but here we show for the first time that several changes also occurred on the moderate thermophilic enzymes of fungi. In regards to the amino acids composition, peptidases from thermophilic species in relation to the mesophilic ones, contained a larger proportion of Ala, Glu, Gly, Pro, Arg and Val residues and a lower number of Cys, His, Ile, Lys, Met, Asn, Gln, Ser, Thr and Trp residues (P < 0.05). Moreover, we observed an increase in the proportion of hydrophobic and charged amino acids and a decrease in polar amino acids. CONCLUSIONS Although thermophilic fungi present less genes encoding for peptidases, these have adaptations that could play a role in thermal resistance from genome to protein structure level.
Collapse
|
23
|
Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger. PLoS One 2017; 12:e0189604. [PMID: 29281693 PMCID: PMC5744941 DOI: 10.1371/journal.pone.0189604] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/29/2017] [Indexed: 12/03/2022] Open
Abstract
Efficient deconstruction of plant biomass is a major barrier to the development of viable lignocellulosic biofuels. Pretreatment with ionic liquids reduces lignocellulose recalcitrance to enzymatic hydrolysis, increasing yields of sugars for conversion into biofuels. However, commercial cellulases are not compatible with many ionic liquids, necessitating extensive water washing of pretreated biomass prior to hydrolysis. To circumvent this issue, previous research has demonstrated that several thermophilic bacterial cellulases can efficiently deconstruct lignocellulose in the presence of the ionic liquid, 1-ethyl-3-methylimadizolium acetate. As promising as these enzymes are, they would need to be produced at high titer in an industrial enzyme production host before they could be considered a viable alternative to current commercial cellulases. Aspergillus niger has been used to produce high titers of secreted enzymes in industry and therefore, we assessed the potential of this organism to be used as an expression host for these ionic liquid-tolerant cellulases. We demonstrated that 29 of these cellulases were expressed at detectable levels in a wild-type strain of A. niger, indicating a basic level of compatibility and potential to be produced at high levels in a host engineered to produce high titers of enzymes. We then profiled one of these enzymes in detail, the β-glucosidase A5IL97, and compared versions expressed in both A. niger and Escherichia coli. This comparison revealed the enzymatic activity of A5IL97 purified from E. coli and A. niger is equivalent, suggesting that A. niger could be an excellent enzyme production host for enzymes originally characterized in E. coli, facilitating the transition from the laboratory to industry.
Collapse
|
24
|
Oida K, Einhorn L, Herrmann I, Panakova L, Resch Y, Vrtala S, Hofstetter G, Tanaka A, Matsuda H, Jensen-Jarolim E. Innate function of house dust mite allergens: robust enzymatic degradation of extracellular matrix at elevated pH. World Allergy Organ J 2017; 10:23. [PMID: 28702111 PMCID: PMC5496134 DOI: 10.1186/s40413-017-0154-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/25/2017] [Indexed: 11/16/2022] Open
Abstract
Background Exposure to the house dust mite Dermatophagoides pteronyssinus (D.p.) increases the risk for developing allergic diseases in humans and their best friends, the dogs. Here, we explored whether this allergenic mite via its enzymes may impact the cutaneous extracellular matrix (ECM), which critically determines epithelial barrier integrity both structurally and functionally. Methods Two extracts obtained from either dust-purified or cultured D.p. bodies were used in the present study. To assess the potential impact of D.p. on protein components of the ECM, proteolytic activity of the D.p. extracts were determined by casein and gelatin gel zymography, and their N-acetyl-β-hexosaminidase activity determined colorimetrically. In addition, IgE-dependent and innate degranulation potential of D.p. was examined in canine MPT-1 mast cells and neurite outgrowth assay using rat pheochromocytoma PC-12 cells. Results In gel zymography, both extracts digested the substrates casein and gelatin in a dose-dependent manner, especially at alkaline pH, and effective in a wide range of temperatures (30 °C−42 °C). In particular, a 25-kDa band corresponding to Der p 1, the major D.p. allergen for humans, was found enzymatically active in both casein and gelatin gels regardless of the presence of metal ions and of alkaline conditions. Besides protease activity, N-acetyl-β-hexosaminidase activity was detected in both extracts, suggesting that D.p. affects the cutaneous ECM through deteriorating both proteins and glycosaminoglycans. While both D.p. extracts induced IgE-dependent mast cell degranulation, much less innate effects on mast- and neuronal cells were observed. Conclusions Our data highlight that D.p. is a robust source of several distinct enzymes with protease- and N-acetyl-β-hexosaminidase activities. In alkaline milieu they can degrade components of the ECM. Therefore, D.p. may contribute to epithelial barrier disruption especially when the skin surface pH is elevated. Electronic supplementary material The online version of this article (doi:10.1186/s40413-017-0154-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kumiko Oida
- The interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.,Cooperative Major in Advanced Health Science, Graduate School of Bio-Applications and System Engineering, Tokyo University of Agriculture and Technology, Saiwai-cho 3-8-5, Fuchu, Tokyo 183-8509 Japan
| | - Lukas Einhorn
- The interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Ina Herrmann
- The interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.,Department for Companion Animals and Horses, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Lucia Panakova
- Department for Companion Animals and Horses, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Yvonne Resch
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Susanne Vrtala
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria.,Christian Doppler Laboratory for the Development of Allergen Chips, Medical University Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Gerlinde Hofstetter
- The interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Akane Tanaka
- Cooperative Major in Advanced Health Science, Graduate School of Bio-Applications and System Engineering, Tokyo University of Agriculture and Technology, Saiwai-cho 3-8-5, Fuchu, Tokyo 183-8509 Japan.,Laboratory of Comparative Animal Medicine Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology Division of Animal Life Science, Institute of Agriculture, Saiwai-cho 3-8-5, Fuchu, Tokyo 183-8509 Japan
| | - Hiroshi Matsuda
- Cooperative Major in Advanced Health Science, Graduate School of Bio-Applications and System Engineering, Tokyo University of Agriculture and Technology, Saiwai-cho 3-8-5, Fuchu, Tokyo 183-8509 Japan.,Laboratory of Veterinary Molecular Pathology and Therapeutics, Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-8-5, Fuchu, Tokyo 183-8509 Japan
| | - Erika Jensen-Jarolim
- The interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.,Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| |
Collapse
|
25
|
Rytioja J, Hildén K, Di Falco M, Zhou M, Aguilar-Pontes MV, Sietiö OM, Tsang A, de Vries RP, Mäkelä MR. The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses. Environ Microbiol 2017; 19:1237-1250. [PMID: 28028889 DOI: 10.1111/1462-2920.13652] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/16/2016] [Accepted: 12/18/2016] [Indexed: 12/27/2022]
Abstract
The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi, (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white-rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analyzed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good a match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant biomass types not present in its natural habitat.
Collapse
Affiliation(s)
- Johanna Rytioja
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Marcos Di Falco
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Miaomiao Zhou
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, 3584, CT, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, 3584, CT, The Netherlands
| | - Outi-Maaria Sietiö
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Ronald P de Vries
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, 3584, CT, The Netherlands
| | - Miia R Mäkelä
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
26
|
Mäkelä MR, Mansouri S, Wiebenga A, Rytioja J, de Vries RP, Hildén KS. Penicillium subrubescens is a promising alternative for Aspergillus niger in enzymatic plant biomass saccharification. N Biotechnol 2016; 33:834-841. [DOI: 10.1016/j.nbt.2016.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 07/01/2016] [Accepted: 07/21/2016] [Indexed: 10/21/2022]
|
27
|
Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8124636. [PMID: 27274991 PMCID: PMC4870676 DOI: 10.1155/2016/8124636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/06/2016] [Indexed: 11/17/2022]
Abstract
Aspergillus oryzae is widely used for the industrial production of enzymes. In A. oryzae metabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While the A. oryzae genome sequence is available, transporter annotation remains limited and thus the connectivity of metabolic networks is incomplete. In this study, we developed a metabolic annotation strategy to understand the relationship between the sequence, structure, and function for annotation of A. oryzae metabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in the A. oryzae genome encoded metabolic transporters. Under consensus integrative databases, 55 unambiguous metabolic transporter genes were distributed into channels and pores (7 genes), electrochemical potential-driven transporters (33 genes), and primary active transporters (15 genes). To reveal the transporter functional role, a combination of homology modeling and molecular dynamics simulation was implemented to assess the relationship between sequence to structure and structure to function. As in the energy metabolism of A. oryzae, the H+-ATPase encoded by the AO090005000842 gene was selected as a representative case study of multilevel linkage annotation. Our developed strategy can be used for enhancing metabolic network reconstruction.
Collapse
|
28
|
Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN. Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol 2016; 9:22-34. [PMID: 26275154 PMCID: PMC4720405 DOI: 10.1111/1751-7915.12309] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/26/2015] [Accepted: 07/02/2015] [Indexed: 12/01/2022] Open
Abstract
Recent reports have suggested that the establishment of industrially relevant enzyme collections from environmental genomes has become a routine procedure. Across the studies assessed, a mean number of approximately 44 active clones were obtained in an average size of approximately 53,000 clones tested using naïve screening protocols. This number could be significantly increased in shorter times when novel metagenome enzyme sequences obtained by direct sequencing are selected and subjected to high-throughput expression for subsequent production and characterization. The pre-screening of clone libraries by naïve screens followed by the pyrosequencing of the inserts allowed for a 106-fold increase in the success rate of identifying genes encoding enzymes of interest. However, a much longer time, usually on the order of years, is needed from the time of enzyme identification to the establishment of an industrial process. If the hit frequency for the identification of enzymes performing at high turnover rates under real application conditions could be increased while still covering a high natural diversity, the very expensive and time-consuming enzyme optimization phase would likely be significantly shortened. At this point, it is important to review the current knowledge about the success of fine-tuned naïve- and sequence-based screening protocols for enzyme selection and to describe the environments worldwide that have already been subjected to enzyme screen programmes through metagenomic tools. Here, we provide such estimations and suggest the current challenges and future actions needed before environmental enzymes can be successfully introduced into the market.
Collapse
Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Mónica Martínez-Martínez
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Wolfgang R Streit
- Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststraße 18, D-22609, Hamburg, Germany
| | - Olga V Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
| |
Collapse
|
29
|
Rytioja J, Hildén K, Mäkinen S, Vehmaanperä J, Hatakka A, Mäkelä MR. Saccharification of Lignocelluloses by Carbohydrate Active Enzymes of the White Rot Fungus Dichomitus squalens. PLoS One 2015; 10:e0145166. [PMID: 26660105 PMCID: PMC4682842 DOI: 10.1371/journal.pone.0145166] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/30/2015] [Indexed: 01/11/2023] Open
Abstract
White rot fungus Dichomitus squalens is an efficient lignocellulose degrading basidiomycete and a promising source for new plant cell wall polysaccharides depolymerizing enzymes. In this work, we focused on cellobiohydrolases (CBHs) of D. squalens. The native CBHI fraction of the fungus, consisting three isoenzymes, was purified and it maintained the activity for 60 min at 50°C, and was stable in acidic pH. Due to the lack of enzyme activity assay for detecting only CBHII activity, CBHII of D. squalens was produced recombinantly in an industrially important ascomycete host, Trichoderma reesei. CBH enzymes of D. squalens showed potential in hydrolysis of complex lignocellulose substrates sugar beet pulp and wheat bran, and microcrystalline cellulose, Avicel. Recombinant CBHII (rCel6A) of D. squalens hydrolysed all the studied plant biomasses. Compared to individual activities, synergistic effect between rCel6A and native CBHI fraction of D. squalens was significant in the hydrolysis of Avicel. Furthermore, the addition of laccase to the mixture of CBHI fraction and rCel6A significantly enhanced the amount of released reducing sugars from sugar beet pulp. Especially, synergy between individual enzymes is a crucial factor in the tailor-made enzyme mixtures needed for hydrolysis of different plant biomass feedstocks. Our data supports the importance of oxidoreductases in improved enzyme cocktails for lignocellulose saccharification.
Collapse
Affiliation(s)
- Johanna Rytioja
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | | | | | - Annele Hatakka
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Miia R. Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
- * E-mail:
| |
Collapse
|
30
|
Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization. Sci Rep 2015; 5:13592. [PMID: 26314379 PMCID: PMC4552001 DOI: 10.1038/srep13592] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/31/2015] [Indexed: 11/15/2022] Open
Abstract
Degradation of plant biomass to fermentable sugars is of critical importance for the use of plant materials for biofuels. Filamentous fungi are ubiquitous organisms and major plant biomass degraders. Single colonies of some fungal species can colonize massive areas as large as five soccer stadia. During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a major determinant of spatial gene expression in colonies of Aspergillus niger. We analyzed whole-genome gene expression in five concentric zones of 5-day-old colonies utilizing sugar beet pulp as a complex carbon source. Growth, protein production and secretion occurred throughout the colony. Genes involved in carbon catabolism were expressed uniformly from the centre to the periphery whereas genes encoding plant biomass degrading enzymes and nitrate utilization were expressed differentially across the colony. A combined adaptive response of carbon-catabolism and enzyme production to locally available monosaccharides was observed. Finally, our results demonstrate that A. niger employs different enzymatic tools to adapt its metabolism as it colonizes complex environments.
Collapse
|
31
|
Landowski CP, Huuskonen A, Wahl R, Westerholm-Parvinen A, Kanerva A, Hänninen AL, Salovuori N, Penttilä M, Natunen J, Ostermeier C, Helk B, Saarinen J, Saloheimo M. Enabling Low Cost Biopharmaceuticals: A Systematic Approach to Delete Proteases from a Well-Known Protein Production Host Trichoderma reesei. PLoS One 2015; 10:e0134723. [PMID: 26309247 PMCID: PMC4550459 DOI: 10.1371/journal.pone.0134723] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/13/2015] [Indexed: 11/22/2022] Open
Abstract
The filamentous fungus Trichoderma reesei has tremendous capability to secrete proteins. Therefore, it would be an excellent host for producing high levels of therapeutic proteins at low cost. Developing a filamentous fungus to produce sensitive therapeutic proteins requires that protease secretion is drastically reduced. We have identified 13 major secreted proteases that are related to degradation of therapeutic antibodies, interferon alpha 2b, and insulin like growth factor. The major proteases observed were aspartic, glutamic, subtilisin-like, and trypsin-like proteases. The seven most problematic proteases were sequentially removed from a strain to develop it for producing therapeutic proteins. After this the protease activity in the supernatant was dramatically reduced down to 4% of the original level based upon a casein substrate. When antibody was incubated in the six protease deletion strain supernatant, the heavy chain remained fully intact and no degradation products were observed. Interferon alpha 2b and insulin like growth factor were less stable in the same supernatant, but full length proteins remained when incubated overnight, in contrast to the original strain. As additional benefits, the multiple protease deletions have led to faster strain growth and higher levels of total protein in the culture supernatant.
Collapse
Affiliation(s)
| | - Anne Huuskonen
- VTT Technical Research Centre of Finland, Espoo, Finland
| | | | | | | | | | | | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
| | | | | | | | | | | |
Collapse
|
32
|
Benoit I, Culleton H, Zhou M, DiFalco M, Aguilar-Osorio G, Battaglia E, Bouzid O, Brouwer CPJM, El-Bushari HBO, Coutinho PM, Gruben BS, Hildén KS, Houbraken J, Barboza LAJ, Levasseur A, Majoor E, Mäkelä MR, Narang HM, Trejo-Aguilar B, van den Brink J, vanKuyk PA, Wiebenga A, McKie V, McCleary B, Tsang A, Henrissat B, de Vries RP. Closely related fungi employ diverse enzymatic strategies to degrade plant biomass. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:107. [PMID: 26236396 PMCID: PMC4522099 DOI: 10.1186/s13068-015-0285-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/09/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Plant biomass is the major substrate for the production of biofuels and biochemicals, as well as food, textiles and other products. It is also the major carbon source for many fungi and enzymes of these fungi are essential for the depolymerization of plant polysaccharides in industrial processes. This is a highly complex process that involves a large number of extracellular enzymes as well as non-hydrolytic proteins, whose production in fungi is controlled by a set of transcriptional regulators. Aspergillus species form one of the best studied fungal genera in this field, and several species are used for the production of commercial enzyme cocktails. RESULTS It is often assumed that related fungi use similar enzymatic approaches to degrade plant polysaccharides. In this study we have compared the genomic content and the enzymes produced by eight Aspergilli for the degradation of plant biomass. All tested Aspergilli have a similar genomic potential to degrade plant biomass, with the exception of A. clavatus that has a strongly reduced pectinolytic ability. Despite this similar genomic potential their approaches to degrade plant biomass differ markedly in the overall activities as well as the specific enzymes they employ. While many of the genes have orthologs in (nearly) all tested species, only very few of the corresponding enzymes are produced by all species during growth on wheat bran or sugar beet pulp. In addition, significant differences were observed between the enzyme sets produced on these feedstocks, largely correlating with their polysaccharide composition. CONCLUSIONS These data demonstrate that Aspergillus species and possibly also other related fungi employ significantly different approaches to degrade plant biomass. This makes sense from an ecological perspective where mixed populations of fungi together degrade plant biomass. The results of this study indicate that combining the approaches from different species could result in improved enzyme mixtures for industrial applications, in particular saccharification of plant biomass for biofuel production. Such an approach may result in a much better improvement of saccharification efficiency than adding specific enzymes to the mixture of a single fungus, which is currently the most common approach used in biotechnology.
Collapse
Affiliation(s)
- Isabelle Benoit
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Helena Culleton
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Megazyme International Ireland, IDA Business Park, Bray, Wicklow Ireland
| | - Miaomiao Zhou
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marcos DiFalco
- />Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Guillermo Aguilar-Osorio
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- />Department of Food Science and Biotechnology, Faculty of Chemistry, National University of México, UNAM, Cd. Universitaria, C.P. 04510 Mexico, DF Mexico
| | - Evy Battaglia
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ourdia Bouzid
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Carlo P J M Brouwer
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Hala B O El-Bushari
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Pedro M Coutinho
- />Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, 13288 Marseille, France
- />CNRS, UMR7257, Aix-Marseille University, 13288 Marseille, France
| | - Birgit S Gruben
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Kristiina S Hildén
- />Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Jos Houbraken
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Luis Alexis Jiménez Barboza
- />Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Anthony Levasseur
- />INRA, UMR1163 de Biotechnologie des Champignons Filamenteux, ESIL, Marseille, France
| | - Eline Majoor
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miia R Mäkelä
- />Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Hari-Mander Narang
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Blanca Trejo-Aguilar
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joost van den Brink
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Patricia A vanKuyk
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ad Wiebenga
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Vincent McKie
- />Megazyme International Ireland, IDA Business Park, Bray, Wicklow Ireland
| | - Barry McCleary
- />Megazyme International Ireland, IDA Business Park, Bray, Wicklow Ireland
| | - Adrian Tsang
- />Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Bernard Henrissat
- />Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, 13288 Marseille, France
- />INRA, USC 1408 AFMB, 13288 Marseille, France
- />Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ronald P de Vries
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|