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Miura D, Tsurigami R, Kato H, Wariishi H, Shimizu M. Pathway crosstalk between the central metabolic and heme biosynthetic pathways in Phanerochaete chrysosporium. Appl Microbiol Biotechnol 2024; 108:37. [PMID: 38183476 PMCID: PMC10771590 DOI: 10.1007/s00253-023-12846-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 01/08/2024]
Abstract
A comprehensive analysis to survey heme-binding proteins produced by the white-rot fungus Phanerochaete chrysosporium was achieved using a biotinylated heme-streptavidin beads system. Mitochondrial citrate synthase (PcCS), glyceraldehyde 3-phosphate dehydrogenase (PcGAPDH), and 2-Cys thioredoxin peroxidase (mammalian HBP23 homolog) were identified as putative heme-binding proteins. Among these, PcCS and PcGAPDH were further characterized using heterologously expressed recombinant proteins. Difference spectra of PcCS titrated with hemin exhibited an increase in the Soret absorbance at 414 nm, suggesting that the axial ligand of the heme is a His residue. The activity of PcCS was strongly inhibited by hemin with Ki oxaloacetate of 8.7 μM and Ki acetyl-CoA of 5.8 μM. Since the final step of heme biosynthesis occurred at the mitochondrial inner membrane, the inhibition of PcCS by heme is thought to be a physiological event. The inhibitory mode of the heme was similar to that of CoA analogues, suggesting that heme binds to PcCS at His347 at the AcCoA-CoA binding site, which was supported by the homology model of PcCS. PcGAPDH was also inhibited by heme, with a lower concentration than that for PcCS. This might be caused by the different location of these enzymes. From the integration of these phenomena, it was concluded that metabolic regulations by heme in the central metabolic and heme synthetic pathways occurred in the mitochondria and cytosol. This novel pathway crosstalk between the central metabolic and heme biosynthetic pathways, via a heme molecule, is important in regulating the metabolic balance (heme synthesis, ATP synthesis, flux balance of the tricarboxylic acid (TCA) cycle and cellular redox balance (NADPH production) during fungal aromatic degradation. KEY POINTS: • A comprehensive survey of heme-binding proteins in P. chrysosporium was achieved. • Several heme-binding proteins including CS and GAPDH were identified. • A novel metabolic regulation by heme in the central metabolic pathways was found.
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Affiliation(s)
- Daisuke Miura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
| | - Ryoga Tsurigami
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Hiroyuki Kato
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Hiroyuki Wariishi
- Faculty of Arts and Science, Kyushu University, Fukuoka, Fukuoka, 819-0395, Japan
| | - Motoyuki Shimizu
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan.
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2
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Si T, Wang A, Yan H, Kong L, Guan L, He C, Ma Y, Zhang H, Ma H. Progress in the Study of Natural Antimicrobial Active Substances in Pseudomonas aeruginosa. Molecules 2024; 29:4400. [PMID: 39339396 PMCID: PMC11434294 DOI: 10.3390/molecules29184400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/31/2024] [Accepted: 09/10/2024] [Indexed: 09/30/2024] Open
Abstract
The prevalence of antimicrobial resistance reduces the effectiveness of antimicrobial drugs in the prevention and treatment of infectious diseases caused by pathogens such as bacteria, fungi, and viruses. Microbial secondary metabolites have been recognized as important sources for new drug discovery and development, yielding a wide range of structurally novel and functionally diverse antimicrobial drugs for the treatment of a variety of diseases that are considered good producers of novel antimicrobial drugs. Bacteria produce a wide variety of antimicrobial compounds, and thus, antibiotics derived from natural products still dominate over purely synthetic antibiotics among the antimicrobial drugs developed and introduced over the last four decades. Among them, Pseudomonas aeruginosa secondary metabolites constitute a richly diverse source of antimicrobial substances with good antimicrobial activity. Therefore, they are regarded as an outstanding resource for finding novel bioactive compounds. The exploration of antimicrobial compounds among Pseudomonas aeruginosa metabolites plays an important role in drug development and biomedical research. Reports on the secondary metabolites of Pseudomonas aeruginosa, many of which are of pharmacological importance, hold great promise for the development of effective antimicrobial drugs against microbial infections by drug-resistant pathogens. In this review, we attempt to summarize published articles from the last twenty-five years (2000-2024) on antimicrobial secondary metabolites from Pseudomonas aeruginosa.
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Affiliation(s)
- Tianbo Si
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Anqi Wang
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Haowen Yan
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Lingcong Kong
- College of Veterinary Medicine, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Lili Guan
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Chengguang He
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Yiyi Ma
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Haipeng Zhang
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Hongxia Ma
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- College of Veterinary Medicine, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
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3
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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024; 17:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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Veličković M, Wu R, Gao Y, Thairu MW, Veličković D, Munoz N, Clendinen CS, Bilbao A, Chu RK, Lalli PM, Zemaitis K, Nicora CD, Kyle JE, Orton D, Williams S, Zhu Y, Zhao R, Monroe ME, Moore RJ, Webb-Robertson BJM, Bramer LM, Currie CR, Piehowski PD, Burnum-Johnson KE. Mapping microhabitats of lignocellulose decomposition by a microbial consortium. Nat Chem Biol 2024; 20:1033-1043. [PMID: 38302607 PMCID: PMC11288888 DOI: 10.1038/s41589-023-01536-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
The leaf-cutter ant fungal garden ecosystem is a naturally evolved model system for efficient plant biomass degradation. Degradation processes mediated by the symbiotic fungus Leucoagaricus gongylophorus are difficult to characterize due to dynamic metabolisms and spatial complexity of the system. Herein, we performed microscale imaging across 12-µm-thick adjacent sections of Atta cephalotes fungal gardens and applied a metabolome-informed proteome imaging approach to map lignin degradation. This approach combines two spatial multiomics mass spectrometry modalities that enabled us to visualize colocalized metabolites and proteins across and through the fungal garden. Spatially profiled metabolites revealed an accumulation of lignin-related products, outlining morphologically unique lignin microhabitats. Metaproteomic analyses of these microhabitats revealed carbohydrate-degrading enzymes, indicating a prominent fungal role in lignocellulose decomposition. Integration of metabolome-informed proteome imaging data provides a comprehensive view of underlying biological pathways to inform our understanding of metabolic fungal pathways in plant matter degradation within the micrometer-scale environment.
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Affiliation(s)
- Marija Veličković
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Margaret W Thairu
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Dušan Veličković
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nathalie Munoz
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chaevien S Clendinen
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Aivett Bilbao
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rosalie K Chu
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Priscila M Lalli
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kevin Zemaitis
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarai Williams
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ying Zhu
- Department of Microchemistry, Proteomics, Lipidomics, and Next Generation Sequencing, Genentech, San Francisco, CA, USA
| | - Rui Zhao
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Paul D Piehowski
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
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5
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Ilić N, Davidović S, Milić M, Lađarević J, Onjia A, Dimitrijević-Branković S, Mihajlovski K. Green biocatalyst for decolorization of azo dyes from industrial wastewater: Coriolopsis trogii 2SMKN laccase immobilized on recycled brewer's spent grain. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:32072-32090. [PMID: 38644428 DOI: 10.1007/s11356-024-33367-x] [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: 01/25/2024] [Accepted: 04/13/2024] [Indexed: 04/23/2024]
Abstract
This study presents an innovative approach for the reuse and recycling of waste material, brewer's spent grain (BSG) for creating a novel green biocatalyst. The same BSG was utilized in several consecutive steps: initially, it served as a substrate for the cultivation and production of laccase by a novel isolated fungal strain, Coriolopsis trogii 2SMKN, then, it was reused as a carrier for laccase immobilization, aiding in the process of azo dye decolorization and finally, reused as recycled BSG for the second successful laccase immobilization for six guaiacol oxidation, contributing to a zero-waste strategy. The novel fungal strain produced laccase with a maximum activity of 171.4 U/g after 6 days of solid-state fermentation using BSG as a substrate. The obtained laccase exhibited excellent performance in the decolorization of azo dyes, both as a free and immobilized, at high temperatures, without addition of harmful mediators, achieving maximum decolorization efficiencies of 99.0%, 71.2%, and 61.0% for Orange G (OG), Congo Red, and Eriochrome Black T (EBT), respectively. The immobilized laccase on BSG was successfully reused across five cycles of azo dye decolorization process. Notably, new green biocatalyst outperformed commercial laccase from Aspergillus spp. in the decolorization of OG and EBT. GC-MS and LC-MS revealed azo-dye degradation products and decomposition pathway. This analysis was complemented by antimicrobial and phytotoxicity tests, which confirmed the non-toxic nature of the degradation products, indicating the potential for safe environmental disposal.
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Affiliation(s)
- Nevena Ilić
- Innovation Centre of the Faculty of Technology and Metallurgy, Karnegijeva 4, Belgrade, 11120, Serbia
| | - Slađana Davidović
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, Belgrade, 11120, Serbia
| | - Marija Milić
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, Belgrade, 11120, Serbia
| | - Jelena Lađarević
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, Belgrade, 11120, Serbia
| | - Antonije Onjia
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, Belgrade, 11120, Serbia
| | | | - Katarina Mihajlovski
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, Belgrade, 11120, Serbia.
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Duran K, Kohlstedt M, van Erven G, Klostermann CE, America AHP, Bakx E, Baars JJP, Gorissen A, de Visser R, de Vries RP, Wittmann C, Comans RNJ, Kuyper TW, Kabel MA. From 13C-lignin to 13C-mycelium: Agaricus bisporus uses polymeric lignin as a carbon source. SCIENCE ADVANCES 2024; 10:eadl3419. [PMID: 38640242 PMCID: PMC11029805 DOI: 10.1126/sciadv.adl3419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/19/2024] [Indexed: 04/21/2024]
Abstract
Plant biomass conversion by saprotrophic fungi plays a pivotal role in terrestrial carbon (C) cycling. The general consensus is that fungi metabolize carbohydrates, while lignin is only degraded and mineralized to CO2. Recent research, however, demonstrated fungal conversion of 13C-monoaromatic compounds into proteinogenic amino acids. To unambiguously prove that polymeric lignin is not merely degraded, but also metabolized, carefully isolated 13C-labeled lignin served as substrate for Agaricus bisporus, the world's most consumed mushroom. The fungus formed a dense mycelial network, secreted lignin-active enzymes, depolymerized, and removed lignin. With a lignin carbon use efficiency of 0.14 (g/g) and fungal biomass enrichment in 13C, we demonstrate that A. bisporus assimilated and further metabolized lignin when offered as C-source. Amino acids were high in 13C-enrichment, while fungal-derived carbohydrates, fatty acids, and ergosterol showed traces of 13C. These results hint at lignin conversion via aromatic ring-cleaved intermediates to central metabolites, underlining lignin's metabolic value for fungi.
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Affiliation(s)
- Katharina Duran
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A 1.5, 66123 Saarbrücken, Germany
| | - Gijs van Erven
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
- Wageningen Food and Biobased Research, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
| | - Cynthia E. Klostermann
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
- Biobased Chemistry and Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen Netherlands
| | - Antoine H. P. America
- Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Edwin Bakx
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
| | - Johan J. P. Baars
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, Netherlands
- CNC Grondstoffen, Driekronenstraat 6, 6596 MA Milsbeek, Netherlands
| | - Antonie Gorissen
- IsoLife bv, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Ries de Visser
- IsoLife bv, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A 1.5, 66123 Saarbrücken, Germany
| | - Rob N. J. Comans
- Soil Chemistry and Chemical Soil Quality Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, Netherlands
| | - Thomas W. Kuyper
- Soil Biology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
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Chane AD, Košnář Z, Hřebečková T, Jozífek M, Doležal P, Tlustoš P. Persistent polycyclic aromatic hydrocarbons removal from sewage sludge-amended soil through phytoremediation combined with solid-state ligninolytic fungal cultures. Fungal Biol 2024; 128:1675-1683. [PMID: 38575240 DOI: 10.1016/j.funbio.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 04/06/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely present in the environment, causing increasing concern because of their impact on soil health, food safety and potential health risks. Four bioremediation strategies were examined to assess the dissipation of PAHs in agricultural soil amended with sewage sludge over a period of 120 days: soil-sludge natural attenuation (SS); phytoremediation using maize (Zea mays L.) (PSS); mycoremediation (MR) separately using three white-rot fungi (Pleurotus ostreatus, Phanerochaete chrysosporium and Irpex lacteus); and plant-assisted mycoremediation (PMR) using a combination of maize and fungi. In the time frame of the experiment, mycoremediation using P. chrysosporium (MR-PH) exhibited a significantly higher (P < 0.05) degradation of total PAHs compared to the SS and PSS treatments, achieving a degradation rate of 52 %. Both the SS and PSS treatments demonstrated a lower degradation rate of total PAHs, with removal rates of 18 % and 32 %, respectively. The PMR treatments showed the highest removal rates of total PAHs at the end of the study, with degradation rates of 48-60 %. In the shoots of maize, only low- and medium-molecular-weight PAHs were found in both the PSS and PMR treatments. The calculated translocation and bioconversion factors always showed values < 1. The analysed enzymatic activities were higher in the PMR treatments compared to other treatments, which can be positively related to the higher degradation of PAHs in the soil.
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Affiliation(s)
- Abraham Demelash Chane
- Department of Agro-Environmental Chemistry and Plant Nutrition, Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praha-Suchdol, Czech Republic
| | - Zdeněk Košnář
- Department of Agro-Environmental Chemistry and Plant Nutrition, Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praha-Suchdol, Czech Republic.
| | - Tereza Hřebečková
- Department of Agro-Environmental Chemistry and Plant Nutrition, Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praha-Suchdol, Czech Republic
| | - Miroslav Jozífek
- Department of Horticulture, Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praha-Suchdol, Czech Republic
| | - Petr Doležal
- Department of Agro-Environmental Chemistry and Plant Nutrition, Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praha-Suchdol, Czech Republic
| | - Pavel Tlustoš
- Department of Agro-Environmental Chemistry and Plant Nutrition, Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praha-Suchdol, Czech Republic
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8
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Gadd GM, Fomina M, Pinzari F. Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation. Microbiol Mol Biol Rev 2024; 88:e0020022. [PMID: 38179930 PMCID: PMC10966957 DOI: 10.1128/mmbr.00200-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/11/2023] [Indexed: 01/06/2024] Open
Abstract
SUMMARYFungi are ubiquitous and important biosphere inhabitants, and their abilities to decompose, degrade, and otherwise transform a massive range of organic and inorganic substances, including plant organic matter, rocks, and minerals, underpin their major significance as biodeteriogens in the built environment and of cultural heritage. Fungi are often the most obvious agents of cultural heritage biodeterioration with effects ranging from discoloration, staining, and biofouling to destruction of building components, historical artifacts, and artwork. Sporulation, morphological adaptations, and the explorative penetrative lifestyle of filamentous fungi enable efficient dispersal and colonization of solid substrates, while many species are able to withstand environmental stress factors such as desiccation, ultra-violet radiation, salinity, and potentially toxic organic and inorganic substances. Many can grow under nutrient-limited conditions, and many produce resistant cell forms that can survive through long periods of adverse conditions. The fungal lifestyle and chemoorganotrophic metabolism therefore enable adaptation and success in the frequently encountered extremophilic conditions that are associated with indoor and outdoor cultural heritage. Apart from free-living fungi, lichens are a fungal growth form and ubiquitous pioneer colonizers and biodeteriogens of outdoor materials, especially stone- and mineral-based building components. This article surveys the roles and significance of fungi in the biodeterioration of cultural heritage, with reference to the mechanisms involved and in relation to the range of substances encountered, as well as the methods by which fungal biodeterioration can be assessed and combated, and how certain fungal processes may be utilized in bioprotection.
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Affiliation(s)
- Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, College of Chemical Engineering and Environment, China University of Petroleum, Beijing, China
| | - Marina Fomina
- Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- National Reserve “Sophia of Kyiv”, Kyiv, Ukraine
| | - Flavia Pinzari
- Institute for Biological Systems (ISB), Council of National Research of Italy (CNR), Monterotondo (RM), Italy
- Natural History Museum, London, United Kingdom
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9
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Kato H, Takahashi Y, Suzuki H, Ohashi K, Kawashima R, Nakamura K, Sakai K, Hori C, Takasuka TE, Kato M, Shimizu M. Identification and characterization of methoxy- and dimethoxyhydroquinone 1,2-dioxygenase from Phanerochaete chrysosporium. Appl Environ Microbiol 2024; 90:e0175323. [PMID: 38259078 PMCID: PMC10880611 DOI: 10.1128/aem.01753-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
White-rot fungi, such as Phanerochaete chrysosporium, are the most efficient degraders of lignin, a major component of plant biomass. Enzymes produced by these fungi, such as lignin peroxidases and manganese peroxidases, break down lignin polymers into various aromatic compounds based on guaiacyl, syringyl, and hydroxyphenyl units. These intermediates are further degraded, and the aromatic ring is cleaved by 1,2,4-trihydroxybenzene dioxygenases. This study aimed to characterize homogentisate dioxygenase (HGD)-like proteins from P. chrysosporium that are strongly induced by the G-unit fragment of vanillin. We overexpressed two homologous recombinant HGDs, PcHGD1 and PcHGD2, in Escherichia coli. Both PcHGD1 and PcHGD2 catalyzed the ring cleavage in methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ). The two enzymes had the highest catalytic efficiency (kcat/Km) for MHQ, and therefore, we named PcHGD1 and PcHGD2 as MHQ dioxygenases 1 and 2 (PcMHQD1 and PcMHQD2), respectively, from P. chrysosporium. This is the first study to identify and characterize MHQ and DMHQ dioxygenase activities in members of the HGD superfamily. These findings highlight the unique and broad substrate spectra of PcHGDs, rendering them attractive candidates for biotechnological applications.IMPORTANCEThis study aimed to elucidate the properties of enzymes responsible for degrading lignin, a dominant natural polymer in terrestrial lignocellulosic biomass. We focused on two homogentisate dioxygenase (HGD) homologs from the white-rot fungus, P. chrysosporium, and investigated their roles in the degradation of lignin-derived aromatic compounds. In the P. chrysosporium genome database, PcMHQD1 and PcMHQD2 were annotated as HGDs that could cleave the aromatic rings of methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ) with a preference for MHQ. These findings suggest that MHQD1 and/or MHQD2 play important roles in the degradation of lignin-derived aromatic compounds by P. chrysosporium. The preference of PcMHQDs for MHQ and DMHQ not only highlights their potential for biotechnological applications but also underscores their critical role in understanding lignin degradation by a representative of white-rot fungus, P. chrysosporium.
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Affiliation(s)
- Hiroyuki Kato
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | | | | | - Keisuke Ohashi
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | | | - Koki Nakamura
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Kiyota Sakai
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Chiaki Hori
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | | | - Masashi Kato
- Faculty of Agriculture, Meijo University, Nagoya, Japan
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10
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Nakazawa T, Kawauchi M, Otsuka Y, Han J, Koshi D, Schiphof K, Ramírez L, Pisabarro AG, Honda Y. Pleurotus ostreatus as a model mushroom in genetics, cell biology, and material sciences. Appl Microbiol Biotechnol 2024; 108:217. [PMID: 38372792 PMCID: PMC10876731 DOI: 10.1007/s00253-024-13034-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/11/2024] [Accepted: 01/25/2024] [Indexed: 02/20/2024]
Abstract
Pleurotus ostreatus, also known as the oyster mushroom, is a popular edible mushroom cultivated worldwide. This review aims to survey recent progress in the molecular genetics of this fungus and demonstrate its potential as a model mushroom for future research. The development of modern molecular genetic techniques and genome sequencing technologies has resulted in breakthroughs in mushroom science. With efficient transformation protocols and multiple selection markers, a powerful toolbox, including techniques such as gene knockout and genome editing, has been developed, and numerous new findings are accumulating in P. ostreatus. These include molecular mechanisms of wood component degradation, sexual development, protein secretion systems, and cell wall structure. Furthermore, these techniques enable the identification of new horizons in enzymology, biochemistry, cell biology, and material science through protein engineering, fluorescence microscopy, and molecular breeding. KEY POINTS: • Various genetic techniques are available in Pleurotus ostreatus. • P. ostreatus can be used as an alternative model mushroom in genetic analyses. • New frontiers in mushroom science are being developed using the fungus.
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Affiliation(s)
- Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Moriyuki Kawauchi
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yuitsu Otsuka
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Junxian Han
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Daishiro Koshi
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Kim Schiphof
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006, Pamplona, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006, Pamplona, Spain
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan.
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11
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Zheng L, Wang R, Fei Y, Pan Y, Zhou P, Shen R, Lan P. Fungal Secretomics Through iTRAQ-Based Analysis. Methods Mol Biol 2024; 2820:139-153. [PMID: 38941021 DOI: 10.1007/978-1-0716-3910-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Our understanding of how fungi respond and adapt to external environments can be increased by the comprehensive data sets of fungal-secreted proteins. Fungi produce a variety of secreted proteins, and environmental conditions can easily influence the fungal secretome. However, the low abundance of secreted proteins and their post-translational modifications make protein extraction more challenging. Hence, the enrichment of secreted proteins is a crucial procedure for secretome analysis. This chapter illustrates a protocol for iTRAQ-based quantitative secretome analysis describing the example of fungi exposed to different environmental conditions. The fungal-secreted proteins can be extracted by combining ultrafiltration and TCA-acetone precipitation. Subsequently, the secreted proteins can be identified and quantified by the iTRAQ-based quantitative proteomics approach.
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Affiliation(s)
- Lu Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ruonan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuchen Fei
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yilin Pan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peijun Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
- University of Chinese Academy of Sciences, Nanjing, China.
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12
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Mazzola A, Kuhar F, Greslebin AG. Progression Over Time of Nutritional Content and Antioxidant Activity of Grains Fermented with the Medicinal Mushrooms Pleurotus ostreatus and Ganoderma sessile (Agaricomycetes). Int J Med Mushrooms 2024; 26:55-67. [PMID: 39171631 DOI: 10.1615/intjmedmushrooms.2024054939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Solid-state fermentation of cereals with edible fungi is a promising strategy for producing functional flours. Hypothetically, the nutritional and functional properties of these flours could be modulated by manipulating substrate composition, fungal species, and incubation conditions. This article reports the variation over time in nutritional, polyphenol, and triterpene contents, as well as the antioxidant activity of rice and wheat fermented with Ganoderma sessile and Pleurotus ostreatus. Solid-state fermentation significantly improved the antioxidant power of the substrates which seemed to be highly correlated with the increase of the phenolic compounds. This increase peaked in the second to third week and decreased after this point. Triterpene content also increased, especially in substrates fermented with G. sessile. Substrates fermented with G. sessile showed higher values than those fermented with P. ostreatus in all compounds, which could be a result of a higher growth rate. Fermented wheat showed higher values than fermented rice in all measured compounds except reducing sugars which can be related to a slower progress in the fermentation due to the more complex structure of the wheat grain. Our results reinforce the importance of substrate and strain selection for product modulation to meet the industry's growing needs.
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Affiliation(s)
- Antonella Mazzola
- Laboratorio de Bioprospección en Investigación Aplicada en Plantas y Hongos (LaBIAPH), FCNyCS, Universidad Nacional de la Patagonia (UNPSJB), Esquel, Chubut, Argentina; Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (Agencia I+D+i), Argentina
| | - Francisco Kuhar
- Instituto Multidisciplinario de Biología Vegetal, Córdoba, Argentina
| | - Alina G Greslebin
- National University of Patagonia (UNPSJB) and CONICET, Argentina Argentina
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13
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Yarden O, Zhang J, Marcus D, Changwal C, Mabjeesh SJ, Lipzen A, Zhang Y, Savage E, Ng V, Grigoriev IV, Hadar Y. Altered Expression of Two Small Secreted Proteins ( ssp4 and ssp6) Affects the Degradation of a Natural Lignocellulosic Substrate by Pleurotus ostreatus. Int J Mol Sci 2023; 24:16828. [PMID: 38069150 PMCID: PMC10705924 DOI: 10.3390/ijms242316828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Pleurotus ostreatus is a white-rot fungus that can degrade lignin in a preferential manner using a variety of extracellular enzymes, including manganese and versatile peroxidases (encoded by the vp1-3 and mnp1-6 genes, respectively). This fungus also secretes a family of structurally related small secreted proteins (SSPs) encoded by the ssp1-6 genes. Using RNA sequencing (RNA-seq), we determined that ssp4 and ssp6 are the predominant members of this gene family that were expressed by P. ostreatus during the first three weeks of growth on wheat straw. Downregulation of ssp4 in a strain harboring an ssp RNAi construct (KDssp1) was then confirmed, which, along with an increase in ssp6 transcript levels, coincided with reduced lignin degradation and the downregulation of vp2 and mnp1. In contrast, we observed an increase in the expression of genes related to pectin and side-chain hemicellulose degradation, which was accompanied by an increase in extracellular pectin-degrading capacity. Genome-wide comparisons between the KDssp1 and the wild-type strains demonstrated that ssp silencing conferred accumulated changes in gene expression at the advanced cultivation stages in an adaptive rather than an inductive mode of transcriptional response. Based on co-expression networking, crucial gene modules were identified and linked to the ssp knockdown genotype at different cultivation times. Based on these data, as well as previous studies, we propose that P. ostreatus SSPs have potential roles in modulating the lignocellulolytic and pectinolytic systems, as well as a variety of fundamental biological processes related to fungal growth and development.
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Affiliation(s)
- Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (D.M.); (C.C.); (Y.H.)
| | - Jiwei Zhang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA;
| | - Dor Marcus
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (D.M.); (C.C.); (Y.H.)
| | - Chunoti Changwal
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (D.M.); (C.C.); (Y.H.)
| | - Sameer J. Mabjeesh
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel;
| | - Anna Lipzen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (Y.Z.); (E.S.); (V.N.); (I.V.G.)
| | - Yu Zhang
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (Y.Z.); (E.S.); (V.N.); (I.V.G.)
| | - Emily Savage
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (Y.Z.); (E.S.); (V.N.); (I.V.G.)
| | - Vivian Ng
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (Y.Z.); (E.S.); (V.N.); (I.V.G.)
| | - Igor V. Grigoriev
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (Y.Z.); (E.S.); (V.N.); (I.V.G.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (D.M.); (C.C.); (Y.H.)
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14
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Bautista-Zamudio PA, Flórez-Restrepo MA, López-Legarda X, Monroy-Giraldo LC, Segura-Sánchez F. Biodegradation of plastics by white-rot fungi: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165950. [PMID: 37536592 DOI: 10.1016/j.scitotenv.2023.165950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/18/2023] [Accepted: 07/30/2023] [Indexed: 08/05/2023]
Abstract
Plastic pollution is one of the most environmental problems in the last two centuries, because of their excessive usage and their rapidly increasing production, which overcome the ability of natural degradation. Moreover, this problem become an escalating environmental issue caused by inadequate disposal, ineffective or nonexistent waste collection methods, and a lack of appropriate measures to deal with the problem, such as incineration and landfilling. Consequently, plastic wastes have become so ubiquitous and have accumulated in the environment impacting ecosystems and wildlife. The above, enhances the urgent need to explore alternative approaches that can effectively reduce waste without causing harsh environmental consequences. For example, white-rot fungi are a promising alternative to deal with the problem. These fungi produce ligninolytic enzymes able to break down the molecular structures of plastics, making them more bioavailable and allowing their degradation process, thereby mitigating waste accumulation. Over the years, several research studies have focused on the utilization of white-rot fungi to degrade plastics. This review presents a summary of plastic degradation biochemistry by white-rot fungi and the function of their ligninolytic enzymes. It also includes a collection of different research studies involving white-rot fungi to degrade plastic, their enzymes, the techniques used and the obtained results. Also, this highlights the significance of pre-treatments and the study of plastic blends with natural fibers or metallic ions, which have shown higher levels of degradation. Finally, it raises the limitations of the biotechnological processes and the prospects for future studies.
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Affiliation(s)
- Paula Andrea Bautista-Zamudio
- Grupo Biopolimer, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 No. 52 - 21, Medellín 050010, Colombia
| | - María Alejandra Flórez-Restrepo
- Grupo Biopolimer, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 No. 52 - 21, Medellín 050010, Colombia
| | - Xiomara López-Legarda
- Grupo Biopolimer, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 No. 52 - 21, Medellín 050010, Colombia.
| | - Leidy Carolina Monroy-Giraldo
- Grupo Biopolimer, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 No. 52 - 21, Medellín 050010, Colombia
| | - Freimar Segura-Sánchez
- Grupo Biopolimer, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 No. 52 - 21, Medellín 050010, Colombia
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15
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Kurniawan B, Bankeeree W, Yanatatsaneejit P, Prasongsuk S. Antiproliferative activity and apoptosis‑inducing effects of Trametes polyzona polysaccharides against human breast cancer cells. Biomed Rep 2023; 19:83. [PMID: 37881601 PMCID: PMC10594067 DOI: 10.3892/br.2023.1665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/29/2023] [Indexed: 10/27/2023] Open
Abstract
Fungal polysaccharides have garnered interest due to their biological activities in terms of anticancer properties and antioxidant activity. The present study aimed to evaluate the anticancer properties and antioxidant activity of a newly isolated white-rot fungus, Trametes polyzona CU07 from Thailand. Crude T. polyzona polysaccharides (CTPPs) were extracted from mycelia using hot water. The chemical properties, including total carbohydrates, molecular weight and protein content, and Fourier-transform infrared spectroscopy analysis, were then investigated. The antioxidant activity was determined against the radicals 2,2-diphenyl-1-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS). The anticancer properties were evaluated in MCF-7 breast cancer (BC) cells, whereas the 293 cell line was used as a control. The inhibitory effects of CTPPs on viability were determined by MTT assay, followed by BrdU incorporation assay to assess cell proliferation. The induction of apoptosis was determined by flow cytometry. CTPPs were considered polysaccharide-protein conjugates, which had molecular weights in the range of 0.3-22,528 kDa. They contained ~50 and 37% carbohydrate and protein, respectively, with glucose as the main monosaccharide component. Notably, CTPPs had high antioxidant activity against ABTS, and had a significant inhibitory effect on the MCF-7 cell line with a half-maximal inhibitory concentration value of 0.58 mg/ml. However, they exhibited little effect on the 293 cell line. The BrdU incorporation assay demonstrated that CTPPs inhibited proliferation by ~20% compared with that in untreated cells. CTPPs also induced early- and late-stage apoptosis of MCF-7 cells. These results indicated that the CTPPs may exhibit potential antiproliferative and antioxidant activity, and apoptosis-inducing effects against human BC cells.
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Affiliation(s)
- Budi Kurniawan
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Human Genetics Research Group and Plant Breeding Laboratory, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wichanee Bankeeree
- Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattamawadee Yanatatsaneejit
- Human Genetics Research Group and Plant Breeding Laboratory, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sehanat Prasongsuk
- Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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16
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Kózka B, Sośnicka A, Nałęcz-Jawecki G, Drobniewska A, Turło J, Giebułtowicz J. Various species of Basidiomycota fungi reveal different abilities to degrade pharmaceuticals and also different pathways of degradation. CHEMOSPHERE 2023; 338:139481. [PMID: 37454990 DOI: 10.1016/j.chemosphere.2023.139481] [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: 10/21/2022] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
The presence of pharmaceuticals (PhACs) in the aquatic environment is an emerging problem worldwide. PhACs reach surface water via the effluents of wastewater treatment plants (WWTPs). WWTPs, although able to remove organic pollutants, do not always remove PhACs. Currently, in the treatment of sewage with the activated sludge method, numerous microorganisms are used, mostly bacteria. Nevertheless, these microorganisms are not resistant to many drug contaminants, and some may also pose a risk to human health. White-rot fungi (WRF), which degrade a wide spectrum of environmental pollutants, may be used as an alternative to microorganisms. However, little data exists comparing the removal of various PhACs by different WRF. In this study, we aimed to determine the ability of three WRF Basidiomycota species, Armillaria mellea, Phanerochaete chrysosporium, and Pleurotus ostreatus, to remove PhACs from various therapeutic groups over the course of 1 h-4 days. Additionally, we identified the fungal metabolites of PhACs, proposed the degradation pathways, and assessed the toxicity of the post-culture media. All selected WRF removed PhACs, but the degree of removal depended on WRF species and PhACs type. Antidepressants and immunosuppressants were removed most efficiently by P. ostreatus, cardiovascular drugs and sulfamethoxazole by A. mellea, and erythromycin by P. chrysosporium. The vast differences observed highlight the need for more intensive testing of different WRF species to select the best species for removing pharmaceuticals of interest. The structure of metabolites generated during degradation strongly depended on WRF species, but the most frequent xenobiotic transformations were oxidation and dealkylation. The obtained results gave insight into the substrate specificity of selected WRF while also providing a broad extension of the knowledge of pharmaceutical degradation by A. mellea.
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Affiliation(s)
- B Kózka
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Chemistry, Poland
| | - A Sośnicka
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Technology and Pharmaceutical Biotechnology, Poland
| | - G Nałęcz-Jawecki
- Medical University of Warsaw, Faculty of Pharmacy, Department of Environmental Health Sciences, Poland
| | - A Drobniewska
- Medical University of Warsaw, Faculty of Pharmacy, Department of Environmental Health Sciences, Poland
| | - J Turło
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Technology and Pharmaceutical Biotechnology, Poland
| | - J Giebułtowicz
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Chemistry, Poland.
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17
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Moiseenko KV, Glazunova OA, Savinova OS, Fedorova TV. Exoproteomic Study and Transcriptional Responses of Laccase and Ligninolytic Peroxidase Genes of White-Rot Fungus Trametes hirsuta LE-BIN 072 Grown in the Presence of Monolignol-Related Phenolic Compounds. Int J Mol Sci 2023; 24:13115. [PMID: 37685920 PMCID: PMC10487439 DOI: 10.3390/ijms241713115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Being an abundant renewable source of aromatic compounds, lignin is an important component of future bio-based economy. Currently, biotechnological processing of lignin through low molecular weight compounds is one of the conceptually promising ways for its valorization. To obtain lignin fragments suitable for further inclusion into microbial metabolism, it is proposed to use a ligninolytic system of white-rot fungi, which mainly comprises laccases and peroxidases. However, laccase and peroxidase genes are almost always represented by many non-allelic copies that form multigene families within the genome of white-rot fungi, and the contributions of exact family members to the overall process of lignin degradation has not yet been determined. In this article, the response of the Trametes hirsuta LE-BIN 072 ligninolytic system to the presence of various monolignol-related phenolic compounds (veratryl alcohol, p-coumaric acid, vanillic acid, and syringic acid) in culture media was monitored at the level of gene transcription and protein secretion. By showing which isozymes contribute to the overall functioning of the ligninolytic system of the T. hirsuta LE-BIN 072, the data obtained in this study will greatly contribute to the possible application of this fungus and its ligninolytic enzymes in lignin depolymerization processes.
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Affiliation(s)
| | - Olga A. Glazunova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (K.V.M.); (O.S.S.); (T.V.F.)
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18
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Duran K, Magnin J, America AH, Peng M, Hilgers R, de Vries RP, Baars JJ, van Berkel WJ, Kuyper TW, Kabel MA. The secretome of Agaricus bisporus: Temporal dynamics of plant polysaccharides and lignin degradation. iScience 2023; 26:107087. [PMID: 37426348 PMCID: PMC10329178 DOI: 10.1016/j.isci.2023.107087] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Despite substantial lignocellulose conversion during mycelial growth, previous transcriptome and proteome studies have not yet revealed how secretomes from the edible mushroom Agaricus bisporus develop and whether they modify lignin models in vitro. To clarify these aspects, A. bisporus secretomes collected throughout a 15-day industrial substrate production and from axenic lab-cultures were subjected to proteomics, and tested on polysaccharides and lignin models. Secretomes (day 6-15) comprised A. bisporus endo-acting and substituent-removing glycoside hydrolases, whereas β-xylosidase and glucosidase activities gradually decreased. Laccases appeared from day 6 onwards. From day 10 onwards, many oxidoreductases were found, with numerous multicopper oxidases (MCO), aryl alcohol oxidases (AAO), glyoxal oxidases (GLOX), a manganese peroxidase (MnP), and unspecific peroxygenases (UPO). Secretomes modified dimeric lignin models, thereby catalyzing syringylglycerol-β-guaiacyl ether (SBG) cleavage, guaiacylglycerol-β-guaiacyl ether (GBG) polymerization, and non-phenolic veratrylglycerol-β-guaiacyl ether (VBG) oxidation. We explored A. bisporus secretomes and insights obtained can help to better understand biomass valorization.
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Affiliation(s)
- Katharina Duran
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Joris Magnin
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Antoine H.P. America
- Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Roelant Hilgers
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Johan J.P. Baars
- CNC Grondstoffen, Driekronenstraat 6, 6596 MA Milsbeek, the Netherlands
| | - Willem J.H. van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Thomas W. Kuyper
- Soil Biology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, the Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
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19
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Okal EJ, Heng G, Magige EA, Khan S, Wu S, Ge Z, Zhang T, Mortimer PE, Xu J. Insights into the mechanisms involved in the fungal degradation of plastics. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115202. [PMID: 37390726 DOI: 10.1016/j.ecoenv.2023.115202] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Fungi are considered among the most efficient microbial degraders of plastics, as they produce salient enzymes and can survive on recalcitrant compounds with limited nutrients. In recent years, studies have reported numerous species of fungi that can degrade different types of plastics, yet there remain many gaps in our understanding of the processes involved in biodegradation. In addition, many unknowns need to be resolved regarding the fungal enzymes responsible for plastic fragmentation and the regulatory mechanisms which fungi use to hydrolyse, assimilate and mineralize synthetic plastics. This review aims to detail the main methods used in plastic hydrolysis by fungi, key enzymatic and molecular mechanisms, chemical agents that enhance the enzymatic breakdown of plastics, and viable industrial applications. Considering that polymers such as lignin, bioplastics, phenolics, and other petroleum-based compounds exhibit closely related characteristics in terms of hydrophobicity and structure, and are degraded by similar fungal enzymes as plastics, we have reasoned that genes that have been reported to regulate the biodegradation of these compounds or their homologs could equally be involved in the regulation of plastic degrading enzymes in fungi. Thus, this review highlights and provides insight into some of the most likely regulatory mechanisms by which fungi degrade plastics, target enzymes, genes, and transcription factors involved in the process, as well as key limitations to industrial upscaling of plastic biodegradation and biological approaches that can be employed to overcome these challenges.
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Affiliation(s)
- Eyalira Jacob Okal
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Gui Heng
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
| | - Ephie A Magige
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Sehroon Khan
- Department of Biotechnology, Faculty of Natural Sciences, University of Science and Technology Bannu, 28100 Bannu, Khyber Pakhtunkhwa, Pakistan
| | - Shixi Wu
- Science and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, Hubei, China
| | - Zhiqiang Ge
- Science and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, Hubei, China
| | - Tianfu Zhang
- Science and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, Hubei, China
| | - Peter E Mortimer
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
| | - Jianchu Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
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20
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Zikeli F, Vettraino AM, Biscontri M, Bergamasco S, Palocci C, Humar M, Romagnoli M. Lignin Nanoparticles with Entrapped Thymus spp. Essential Oils for the Control of Wood-Rot Fungi. Polymers (Basel) 2023; 15:2713. [PMID: 37376359 DOI: 10.3390/polym15122713] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
After decades of utilization of fossil-based and environmentally hazardous compounds for wood preservation against fungal attack, there is a strong need to substitute those compounds with bio-based bioactive solutions, such as essential oils. In this work, lignin nanoparticles containing four essential oils from thyme species (Thymus capitatus, Coridothymus capitatus, T. vulgaris, and T. vulgaris Demeter) were applied as biocides in in vitro experiments to test their anti-fungal effect against two white-rot fungi (Trametes versicolor and Pleurotus ostreatus) and two brown-rot fungi (Poria monticola and Gloeophyllum trabeum). Entrapment of essential oils provided a delayed release over a time frame of 7 days from the lignin carrier matrix and resulted in lower minimum inhibitory concentrations of the essential oils against the brown-rot fungi (0.30-0.60 mg/mL), while for the white-rot fungi, identical concentrations were determined compared with free essential oils (0.05-0.30 mg/mL). Fourier Transform infrared (FTIR) spectroscopy was used to assess the fungal cell wall changes in the presence of essential oils in the growth medium. The results regarding brown-rot fungi present a promising approach for a more effective and sustainable utilization of essential oils against this class of wood-rot fungi. In the case of white-rot fungi, lignin nanoparticles, as essential oils delivery vehicles, still need optimization in their efficacy.
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Affiliation(s)
- Florian Zikeli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Anna Maria Vettraino
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Margherita Biscontri
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Sara Bergamasco
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Cleofe Palocci
- Department of Chemistry, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
- Research Center for Applied Sciences to the Safeguard of Environment and Cultural Heritage (CIABC), Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Miha Humar
- Department of Wood Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Manuela Romagnoli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
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21
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Peng M, Bervoets S, Chin-A-Woeng T, Granchi Z, Hildén K, Mäkelä MR, de Vries RP. The transcriptomic response of two basidiomycete fungi to plant biomass is modulated by temperature to a different extent. Microbiol Res 2023; 270:127333. [PMID: 36804127 DOI: 10.1016/j.micres.2023.127333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Many fungi show a strong preference for specific habitats and growth conditions. Investigating the molecular mechanisms of fungal adaptation to varying environmental conditions is of great interest to biodiversity research and is important for many industrial applications. In this study, we compared the transcriptome profiles of two previously genome-sequenced white-rot wood-decay fungi, Trametes pubescens and Phlebia centrifuga, during their growth on two common plant biomass substrates (wheat straw and spruce) at two temperatures (15 °C and 25 °C). The results showed that both fungi partially tailored their molecular responses to different types of carbon sources, differentially expressing genes encoding polysaccharide degrading enzymes, transporters, proteases and monooxygenases. Notably, more lignin modification related AA2 genes and cellulose degradation related AA9 genes were differentially expressed in the tested conditions of T. pubescens than P. centrifuga. In addition, we detected more remarkable transcriptome changes to different growth temperature in P. centrifuga than in T. pubescens, which reflected their different ability to adapt to the temperature fluctuations. In P. centrifuga, differentially expressed genes (DEGs) related to temperature response mainly encode protein kinases, trehalose metabolism, carbon metabolic enzymes and glycoside hydrolases, while the main temperature-related DEGs identified in T. pubescens are only the carbon metabolic enzymes and glycoside hydrolases. Our study revealed both conserved and species-specific transcriptome changes during fungal adaptation to a changing environment, improving our understanding of the molecular mechanisms underlying fungal plant biomass conversion at varying temperatures.
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Affiliation(s)
- Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Sander Bervoets
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, the Netherlands
| | | | - Zoraide Granchi
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, the Netherlands
| | - Kristiina 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
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22
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Hirakawa MP, Rodriguez A, Tran-Gyamfi MB, Light YK, Martinez S, Diamond-Pott H, Simmons BA, Sale KL. Phenothiazines Rapidly Induce Laccase Expression and Lignin-Degrading Properties in the White-Rot Fungus Phlebia radiata. J Fungi (Basel) 2023; 9:jof9030371. [PMID: 36983539 PMCID: PMC10053029 DOI: 10.3390/jof9030371] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
Phlebia radiata is a widespread white-rot basidiomycete fungus with significance in diverse biotechnological applications due to its ability to degrade aromatic compounds, xenobiotics, and lignin using an assortment of oxidative enzymes including laccase. In this work, a chemical screen with 480 conditions was conducted to identify chemical inducers of laccase expression in P. radiata. Among the chemicals tested, phenothiazines were observed to induce laccase activity in P. radiata, with promethazine being the strongest laccase inducer of the phenothiazine-derived compounds examined. Secretomes produced by promethazine-treated P. radiata exhibited increased laccase protein abundance, increased enzymatic activity, and an enhanced ability to degrade phenolic model lignin compounds. Transcriptomics analyses revealed that promethazine rapidly induced the expression of genes encoding lignin-degrading enzymes, including laccase and various oxidoreductases, showing that the increased laccase activity was due to increased laccase gene expression. Finally, the generality of promethazine as an inducer of laccases in fungi was demonstrated by showing that promethazine treatment also increased laccase activity in other relevant fungal species with known lignin conversion capabilities including Trametes versicolor and Pleurotus ostreatus.
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Affiliation(s)
- Matthew P. Hirakawa
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94550, USA
- Correspondence: (M.P.H.); (K.L.S.)
| | - Alberto Rodriguez
- Biomaterials and Biomanufacturing Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Mary B. Tran-Gyamfi
- Bioresource and Environmental Security Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Yooli K. Light
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Salvador Martinez
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Henry Diamond-Pott
- Bioresource and Environmental Security Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Blake A. Simmons
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Kenneth L. Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Computational Biology and Biophysics Department, Sandia National Laboratories, Livermore, CA 94550, USA
- Correspondence: (M.P.H.); (K.L.S.)
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23
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Tsers I, Marenina E, Meshcherov A, Petrova O, Gogoleva O, Tkachenko A, Gogoleva N, Gogolev Y, Potapenko E, Muraeva O, Ponomareva M, Korzun V, Gorshkov V. First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale. IMA Fungus 2023; 14:2. [PMID: 36627722 PMCID: PMC9830731 DOI: 10.1186/s43008-022-00107-0] [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: 08/20/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
Pink snow mold, caused by a phytopathogenic and psychrotolerant fungus, Microdochium nivale, is a severe disease of winter cereals and grasses that predominantly occurs under snow cover or shortly after its melt. Snow mold has significantly progressed during the past decade, often reaching epiphytotic levels in northern countries and resulting in dramatic yield losses. In addition, M. nivale gradually adapts to a warmer climate, spreading to less snowy territories and causing different types of plant diseases throughout the growing period. Despite its great economic importance, M. nivale is poorly investigated; its genome has not been sequenced and its crucial virulence determinants have not been identified or even predicted. In our study, we applied a hybrid assembly based on Oxford Nanopore and Illumina reads to obtain the first genome sequence of M. nivale. 11,973 genes (including 11,789 protein-encoding genes) have been revealed in the genome assembly. To better understand the genetic potential of M. nivale and to obtain a convenient reference for transcriptomic studies on this species, the identified genes were annotated and split into hierarchical three-level functional categories. A file with functionally classified M. nivale genes is presented in our study for general use. M. nivale gene products that best meet the criteria for virulence factors have been identified. The genetic potential to synthesize human-dangerous mycotoxins (fumonisin, ochratoxin B, aflatoxin, and gliotoxin) has been revealed for M. nivale. The transcriptome analysis combined with the assays for extracellular enzymatic activities (conventional virulence factors of many phytopathogens) was carried out to assess the effect of host plant (rye) metabolites on the M. nivale phenotype. In addition to disclosing plant-metabolite-upregulated M. nivale functional gene groups (including those related to host plant protein destruction and amino acid metabolism, xenobiotic detoxication (including phytoalexins benzoxazinoids), cellulose destruction (cellulose monooxygenases), iron transport, etc.), the performed analysis pointed to a crucial role of host plant lipid destruction and fungal lipid metabolism modulation in plant-M. nivale interactions.
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Affiliation(s)
- Ivan Tsers
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Ekaterina Marenina
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Azat Meshcherov
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Olga Petrova
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Olga Gogoleva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Alexander Tkachenko
- grid.35915.3b0000 0001 0413 4629Laboratory of Computer Technologies, ITMO University, Saint Petersburg, Russia 197101
| | - Natalia Gogoleva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Yuri Gogolev
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Evgenii Potapenko
- grid.18098.380000 0004 1937 0562Institute of Evolution, University of Haifa, 3498838 Haifa, Israel ,grid.18098.380000 0004 1937 0562Department of Evolutionary and Environmental Biology, University of Haifa, 3498838 Haifa, Israel
| | - Olga Muraeva
- grid.512700.1Bioinformatics Institute, Saint Petersburg, Russia 197342
| | - Mira Ponomareva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Viktor Korzun
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111 ,grid.425691.dKWS SAAT SE & Co. KGaA, 37555 Einbeck, Germany
| | - Vladimir Gorshkov
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
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24
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Metabolomics Highlights Different Life History Strategies of White and Brown Rot Wood-Degrading Fungi. mSphere 2022; 7:e0054522. [PMID: 36468887 PMCID: PMC9769625 DOI: 10.1128/msphere.00545-22] [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] [Indexed: 12/10/2022] Open
Abstract
White and brown rot fungi efficiently deconstruct lignocellulose in wood, Earth's largest pool of aboveground biotic carbon and an important natural resource. Despite its vital importance, little is known about the metabolomic signatures among fungal species and nutritional modes (rot types). In this study, we used GC-MS metabolomics in solid wood substrates (in planta) to compare brown rot fungi (Rhodonia placenta and Gloeophylum trabeum) and white rot fungi (Trametes versicolor and Pleurotus ostreatus) at two decay stages (earlier and later), finding identifiable patterns for brown rot fungi at later decay stages. These patterns occurred in highly reducing environments that were not observed in white rot fungi. Metabolomes measured among the two white rot fungi were notably different, but we found a potential biomarker compound, galactitol, that was characteristic to white rot taxa. In addition, we found that white rot fungi were more efficient at catabolizing phenolic compounds that were originally present in wood. Collectively, white rot fungi were characterized by measured sugar release relative to higher carbohydrate solubilization by brown rot fungi, a distinction in soluble sugar availability that might shape success in the face of "cheater" competitors. This need to protect excess free sugars may explain the differentially high brown rot fungal production of pyranones and furanones, likely linked to an expansion of polyketide synthase genes. IMPORTANCE Despite the ecological and economic importance of wood-degrading fungi, little is known about the array of metabolites that fungi produce during wood decomposition. This study provides an in-depth insight into the wood decomposition process by analyzing and comparing the changes of >100 compounds produced by fungi with metabolic distinct nutritional modes (white and brown rot fungi) at different decay stages. We found a unique pattern of metabolites that correlated well with brown rot (carbohydrate selective mode) in later decay. These compounds were in line with some of the physiochemical and genetic features previously seen in these fungi such as a faster sugar release, lower pH, and the expansion of polyketide-synthase genes compared to white rot fungi (lignin-degrading mode). This study provides spatiotemporally resolved mechanism insights as well as critical groundwork that will be valuable for studies in basic biology and ecology, as well as applied biomass deconstruction and bioremediation.
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25
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Savinova OS, Shabaev AV, Glazunova OA, Moiseenko KV, Fedorova TV. Benzyl Butyl Phthalate and Diisobutyl Phthalate Biodegradation by White-rot Fungus Trametes hirsuta. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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26
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Shabaev AV, Moiseenko KV, Glazunova OA, Savinova OS, Fedorova TV. Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi. Int J Mol Sci 2022; 23:ijms231810322. [PMID: 36142233 PMCID: PMC9499651 DOI: 10.3390/ijms231810322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
White-rot basidiomycete fungi are a unique group of organisms that evolved an unprecedented arsenal of extracellular enzymes for an efficient degradation of all components of wood such as cellulose, hemicelluloses and lignin. The exoproteomes of white-rot fungi represent a natural enzymatic toolbox for white biotechnology. Currently, only exoproteomes of a narrow taxonomic group of white-rot fungi—fungi belonging to the Polyporales order—are extensively studied. In this article, two white-rot fungi, Peniophora lycii LE-BIN 2142 from the Russulales order and Trametes hirsuta LE-BIN 072 from the Polyporales order, were compared and contrasted in terms of their enzymatic machinery used for degradation of different types of wood substrates—alder, birch and pine sawdust. Our findings suggested that the studied fungi use extremely different enzymatic systems for the degradation of carbohydrates and lignin. While T. hirsuta LE-BIN 072 behaved as a typical white-rot fungus, P. lycii LE-BIN 2142 demonstrated substantial peculiarities. Instead of using cellulolytic and hemicellulolytic hydrolytic enzymes, P. lycii LE-BIN 2142 primarily relies on oxidative polysaccharide-degrading enzymes such as LPMO and GMC oxidoreductase. Moreover, exoproteomes of P. lycii LE-BIN 2142 completely lacked ligninolytic peroxidases, a well-known marker of white-rot fungi, but instead contained several laccase isozymes and previously uncharacterized FAD-binding domain-containing proteins.
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27
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Tsivileva OM, Koftin OV, Evseeva NV. Coumarins as Fungal Metabolites with Potential Medicinal Properties. Antibiotics (Basel) 2022; 11:1156. [PMID: 36139936 PMCID: PMC9495007 DOI: 10.3390/antibiotics11091156] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Coumarins are a structurally varied set of 2H-chromen-2-one compounds categorized also as members of the benzopyrone group of secondary metabolites. Coumarin derivatives attract interest owing to their wide practical application and the unique reactivity of fused benzene and pyrone ring systems in molecular structure. Coumarins have their own specific fingerprints as antiviral, antimicrobial, antioxidant, anti-inflammatory, antiadipogenic, cytotoxic, apoptosis, antitumor, antitubercular, and cytotoxicity agents. Natural products have played an essential role in filling the pharmaceutical pipeline for thousands of years. Biological effects of natural coumarins have laid the basis of low-toxic and highly effective drugs. Presently, more than 1300 coumarins have been identified in plants, bacteria, and fungi. Fungi as cultivated microbes have provided many of the nature-inspired syntheses of chemically diverse drugs. Endophytic fungi bioactivities attract interest, with applications in fields as diverse as cancer and neuronal injury or degeneration, microbial and parasitic infections, and others. Fungal mycelia produce several classes of bioactive molecules, including a wide group of coumarins. Of promise are further studies of conditions and products of the natural and synthetic coumarins' biotransformation by the fungal cultures, aimed at solving the urgent problem of searching for materials for biomedical engineering. The present review evaluates the fungal coumarins, their structure-related peculiarities, and their future therapeutic potential. Special emphasis has been placed on the coumarins successfully bioprospected from fungi, whereas an industry demand for the same coumarins earlier found in plants has faced hurdles. Considerable attention has also been paid to some aspects of the molecular mechanisms underlying the coumarins' biological activity. The compounds are selected and grouped according to their cytotoxic, anticancer, antibacterial, antifungal, and miscellaneous effects.
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Affiliation(s)
- Olga M. Tsivileva
- Laboratory of Microbiology, Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov 410049, Russia
| | - Oleg V. Koftin
- Department of Biochemistry, V.I. Razumovsky Saratov State Medical University, 112 ul. Bol’shaya Kazach’ya, Saratov 410012, Russia
| | - Nina V. Evseeva
- Laboratory of Immunochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov 410049, Russia
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