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Krusong K, Ismail A, Wangpaiboon K, Pongsawasdi P. Production of Large-Ring Cyclodextrins by Amylomaltases. Molecules 2022; 27:molecules27041446. [PMID: 35209232 PMCID: PMC8875642 DOI: 10.3390/molecules27041446] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/10/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Amylomaltase is a well-known glucan transferase that can produce large ring cyclodextrins (LR-CDs) or so-called cycloamyloses via cyclization reaction. Amylomaltases have been found in several microorganisms and their optimum temperatures are generally around 60–70 °C for thermostable amylomaltases and 30–45 °C for the enzymes from mesophilic bacteria and plants. The optimum pHs for mesophilic amylomaltases are around pH 6.0–7.0, while the thermostable amylomaltases are generally active at more acidic conditions. Size of LR-CDs depends on the source of amylomaltases and the reaction conditions including pH, temperature, incubation time, and substrate. For example, in the case of amylomaltase from Corynebacterium glutamicum, LR-CD productions at alkaline pH or at a long incubation time favored products with a low degree of polymerization. In this review, we explore the synthesis of LR-CDs by amylomaltases, structural information of amylomaltases, as well as current applications of LR-CDs and amylomaltases.
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Affiliation(s)
- Kuakarun Krusong
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phyathai Rd., Patumwan, Bangkok 10330, Thailand; (A.I.); (K.W.)
- Correspondence: ; Tel.: + 66-(0)2-218-5413
| | - Abbas Ismail
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phyathai Rd., Patumwan, Bangkok 10330, Thailand; (A.I.); (K.W.)
| | - Karan Wangpaiboon
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phyathai Rd., Patumwan, Bangkok 10330, Thailand; (A.I.); (K.W.)
| | - Piamsook Pongsawasdi
- Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phyathai Rd., Patumwan, Bangkok 10330, Thailand;
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2
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Polak J, Grąz M, Wlizło K, Szałapata K, Kapral-Piotrowska J, Paduch R, Jarosz-Wilkołazka A. Bioactive Properties of a Novel Antibacterial Dye Obtained from Laccase-Mediated Oxidation of 8-Anilino-1-naphthalenesulfonic Acid. Molecules 2022; 27:molecules27020487. [PMID: 35056804 PMCID: PMC8780785 DOI: 10.3390/molecules27020487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022]
Abstract
Fungal laccase obtained from a Cerrena unicolor strain was used as an effective biocatalyst for the transformation of 8-anilino-1-naphthalenesulfonic acid into a green-coloured antibacterial compound, which can be considered as both an antimicrobial agent and a textile dye, simultaneously. The process of biosynthesis was performed in buffered solutions containing methanol as a co-solvent, allowing better solubilisation of substrate. The transformation process was optimised in terms of the buffer pH value, laccase activity, and concentrations of the substrate and co-solvent. The crude product obtained exhibited low cytotoxicity, antibacterial properties against Staphylococcus aureus and Staphylococcus epidermidis, and antioxidant properties. Moreover, the synthesised green-coloured compound proved non-allergenic and demonstrated a high efficiency of dyeing wool fibres.
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Affiliation(s)
- Jolanta Polak
- Department of Biochemistry and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-031 Lublin, Poland; (M.G.); (K.S.); (A.J.-W.)
- Correspondence: or
| | - Marcin Grąz
- Department of Biochemistry and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-031 Lublin, Poland; (M.G.); (K.S.); (A.J.-W.)
| | - Kamila Wlizło
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-031 Lublin, Poland;
| | - Katarzyna Szałapata
- Department of Biochemistry and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-031 Lublin, Poland; (M.G.); (K.S.); (A.J.-W.)
| | - Justyna Kapral-Piotrowska
- Department of Functional Anatomy and Cytobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-031 Lublin, Poland;
| | - Roman Paduch
- Department of Virology and Immunology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-031 Lublin, Poland;
| | - Anna Jarosz-Wilkołazka
- Department of Biochemistry and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-031 Lublin, Poland; (M.G.); (K.S.); (A.J.-W.)
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3
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Dou Y, Yang Y, Mund NK, Wei Y, Liu Y, Wei L, Wang Y, Du P, Zhou Y, Liesche J, Huang L, Fang H, Zhao C, Li J, Wei Y, Chen S. Comparative Analysis of Herbaceous and Woody Cell Wall Digestibility by Pathogenic Fungi. Molecules 2021; 26:molecules26237220. [PMID: 34885803 PMCID: PMC8659149 DOI: 10.3390/molecules26237220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/21/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Fungal pathogens have evolved combinations of plant cell-wall-degrading enzymes (PCWDEs) to deconstruct host plant cell walls (PCWs). An understanding of this process is hoped to create a basis for improving plant biomass conversion efficiency into sustainable biofuels and bioproducts. Here, an approach integrating enzyme activity assay, biomass pretreatment, field emission scanning electron microscopy (FESEM), and genomic analysis of PCWDEs were applied to examine digestibility or degradability of selected woody and herbaceous biomass by pathogenic fungi. Preferred hydrolysis of apple tree branch, rapeseed straw, or wheat straw were observed by the apple-tree-specific pathogen Valsa mali, the rapeseed pathogen Sclerotinia sclerotiorum, and the wheat pathogen Rhizoctonia cerealis, respectively. Delignification by peracetic acid (PAA) pretreatment increased PCW digestibility, and the increase was generally more profound with non-host than host PCW substrates. Hemicellulase pretreatment slightly reduced or had no effect on hemicellulose content in the PCW substrates tested; however, the pretreatment significantly changed hydrolytic preferences of the selected pathogens, indicating a role of hemicellulose branching in PCW digestibility. Cellulose organization appears to also impact digestibility of host PCWs, as reflected by differences in cellulose microfibril organization in woody and herbaceous PCWs and variation in cellulose-binding domain organization in cellulases of pathogenic fungi, which is known to influence enzyme access to cellulose. Taken together, this study highlighted the importance of chemical structure of both hemicelluloses and cellulose in host PCW digestibility by fungal pathogens.
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Affiliation(s)
- Yanhua Dou
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yan Yang
- College of Chemistry and Chemical Engineering, Shanxi Datong University, Datong 037009, China;
| | - Nitesh Kumar Mund
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yanping Wei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yisong Liu
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Linfang Wei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yifan Wang
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Panpan Du
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yunheng Zhou
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Johannes Liesche
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Lili Huang
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Hao Fang
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chen Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jisheng Li
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yahong Wei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Northwest A&F University, Yangling, Xianyang 712100, China
- Correspondence: (Y.W.); (S.C.); Tel.: +86-029-87091021 (S.C.)
| | - Shaolin Chen
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Northwest A&F University, Yangling, Xianyang 712100, China
- Correspondence: (Y.W.); (S.C.); Tel.: +86-029-87091021 (S.C.)
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4
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Diwan D, Usmani Z, Sharma M, Nelson JW, Thakur VK, Christie G, Molina G, Gupta VK. Thrombolytic Enzymes of Microbial Origin: A Review. Int J Mol Sci 2021; 22:10468. [PMID: 34638809 PMCID: PMC8508633 DOI: 10.3390/ijms221910468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/10/2023] Open
Abstract
Enzyme therapies are attracting significant attention as thrombolytic drugs during the current scenario owing to their great affinity, specificity, catalytic activity, and stability. Among various sources, the application of microbial-derived thrombolytic and fibrinolytic enzymes to prevent and treat vascular occlusion is promising due to their advantageous cost-benefit ratio and large-scale production. Thrombotic complications such as stroke, myocardial infarction, pulmonary embolism, deep venous thrombosis, and peripheral occlusive diseases resulting from blood vessel blockage are the major cause of poor prognosis and mortality. Given the ability of microbial thrombolytic enzymes to dissolve blood clots and prevent any adverse effects, their use as a potential thrombolytic therapy has attracted great interest. A better understanding of the hemostasis and fibrinolytic system may aid in improving the efficacy and safety of this treatment approach over classical thrombolytic agents. Here, we concisely discuss the physiological mechanism of thrombus formation, thrombo-, and fibrinolysis, thrombolytic and fibrinolytic agents isolated from bacteria, fungi, and algae along with their mode of action and the potential application of microbial enzymes in thrombosis therapy.
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Affiliation(s)
- Deepti Diwan
- Department of Neurosurgery, Washington University School of Medicine, Saint Louis, MO 63110, USA; (D.D.); (J.W.N.)
| | - Zeba Usmani
- Department of Applied Biology, University of Science & Technology, Techno City, Killing Road, Baridua 9th Mile 793101, Meghalaya, India; (Z.U.); (M.S.)
| | - Minaxi Sharma
- Department of Applied Biology, University of Science & Technology, Techno City, Killing Road, Baridua 9th Mile 793101, Meghalaya, India; (Z.U.); (M.S.)
| | - James W. Nelson
- Department of Neurosurgery, Washington University School of Medicine, Saint Louis, MO 63110, USA; (D.D.); (J.W.N.)
| | - Vijay Kumar Thakur
- Biorefining and Advanced Materials Research Center, SRUC, Edinburgh EH9 3JG, UK;
- School of Engineering, University of Petroleum & Energy Studies (UPES), Dehradun 248007, Uttarakhand, India
| | - Graham Christie
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge CB2 1TN, UK;
| | - Gustavo Molina
- Laboratory of Bioflavors and Bioactive Compounds, Department of Food Science, Faculty of Food Engineering, State University of Campinas, R. Monteiro Lobato, 80, Campinas, São Paulo 13083-862, Brazil;
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Edinburgh EH9 3JG, UK;
- Centre for Safe and Improved Food, SRUC, Edinburgh EH9 3JG, UK
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5
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Watanabe Y, Spangenberg GC, Shinozuka H. Fungus-originated glucanase and monooxygenase genes in creeping bent grass (Agrostis stolonifera L.). PLoS One 2021; 16:e0257173. [PMID: 34506557 PMCID: PMC8432771 DOI: 10.1371/journal.pone.0257173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/24/2021] [Indexed: 11/24/2022] Open
Abstract
Recent studies have revealed presence of fungus-originated genes in genomes of cool-season grasses, suggesting occurrence of multiple ancestral gene transfer events between the two distant lineages. The current article describes identification of glucanase-like and monooxygenase-like genes from creeping bent grass, as lateral gene transfer candidates. An in silico analysis suggested presence of the glucanase-like gene in Agrostis, Deyeuxia, and Polypogon genera, but not in other species belonging to the clade 1 of the Poeae tribe. Similarly, the monooxygenase-like gene was confined to Agrostis and Deyeuxia genera. A consistent result was obtained from PCR-based screening. The glucanase-like gene was revealed to be ubiquitously expressed in young seedlings of creeping bent grass. Although expression of the monooxygenase-like gene was suggested in plant tissues, the levels were considerably lower than those of the glucanase-like gene. A phylogenetic analysis revealed close relationships of the two genes between the corresponding genes in fungal endophyte species of the Epichloë genus, suggesting that the genes originated from the Epichloë lineage.
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Affiliation(s)
- Yugo Watanabe
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Hiroshi Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
- * E-mail:
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6
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Abstract
The use of potent fungal mixed cultures is a promising technique for the biodegradation of crude oil. Four isolates of fungi, namely, Alternaria alternata (AA-1), Aspergillus flavus (AF-3), Aspergillus terreus (AT-7), and Trichoderma harzianum (TH-5), were isolated from date palm soil in Saudi Arabia. The mixed fungal of the four isolates have a powerful tool for biodegradation up to 73.6% of crude oil (1%, w/v) in 14 days. The fungal consortium no. 15 containing the four isolates (1:1:1:1) performed significantly better as a biodegradation agent than other consortium in a variety of environmental factors containing crude oil concentration, incubation temperature, initial pH, biodegradation time and the salinity of the medium. The fungal consortium showed better performance in the biodegradation of normal alkanes (n-alkanes) than that of the polycyclic aromatic hydrocarbons (PAHs); the biodegradation efficiency of normal alkanes of the fungal consortium (67.1%) was clearly high than that of the PAHs (56.8%).
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Affiliation(s)
- Abeer R. M. Abd El-Aziz
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- * E-mail:
| | - Monira R. Al-Othman
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sameh M. Hisham
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shereen M. Shehata
- Pharmaceutical Chemistry Department, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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7
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Jezewski A, Alden KM, Esan TE, DeBouver ND, Abendroth J, Bullen JC, Calhoun BM, Potts KT, Murante DM, Hagen TJ, Fox D, Krysan DJ. Structural Characterization of the Reaction and Substrate Specificity Mechanisms of Pathogenic Fungal Acetyl-CoA Synthetases. ACS Chem Biol 2021; 16:1587-1599. [PMID: 34369755 PMCID: PMC8383264 DOI: 10.1021/acschembio.1c00484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Acetyl CoA synthetases (ACSs) are Acyl-CoA/NRPS/Luciferase (ANL) superfamily enzymes that couple acetate with CoA to generate acetyl CoA, a key component of central carbon metabolism in eukaryotes and prokaryotes. Normal mammalian cells are not dependent on ACSs, while tumor cells, fungi, and parasites rely on acetate as a precursor for acetyl CoA. Consequently, ACSs have emerged as a potential drug target. As part of a program to develop antifungal ACS inhibitors, we characterized fungal ACSs from five diverse human fungal pathogens using biochemical and structural studies. ACSs catalyze a two-step reaction involving adenylation of acetate followed by thioesterification with CoA. Our structural studies captured each step of these two half-reactions including the acetyl-adenylate intermediate of the first half-reaction in both the adenylation conformation and the thioesterification conformation and thus provide a detailed picture of the reaction mechanism. We also used a systematic series of increasingly larger alkyl adenosine esters as chemical probes to characterize the structural basis of the exquisite ACS specificity for acetate over larger carboxylic acid substrates. Consistent with previous biochemical and genetic data for other enzymes, structures of fungal ACSs with these probes bound show that a key tryptophan residue limits the size of the alkyl binding site and forces larger alkyl chains to adopt high energy conformers, disfavoring their efficient binding. Together, our analysis provides highly detailed structural models for both the reaction mechanism and substrate specificity that should be useful in designing selective inhibitors of eukaryotic ACSs as potential anticancer, antifungal, and antiparasitic drugs.
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Affiliation(s)
- Andrew
J. Jezewski
- Department
of Pediatrics Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, United States
| | - Katy M. Alden
- Department
of Pediatrics Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, United States
| | - Taiwo E. Esan
- Department
of Chemistry and Biochemistry, Northern
Illinois University, DeKalb, Illinois 60115, United States
| | - Nicholas D. DeBouver
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Jan Abendroth
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Jameson C. Bullen
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Brandy M. Calhoun
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Kristy T. Potts
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Beryllium
Discovery Corp., 7869
NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Daniel M. Murante
- Department
of Pediatrics Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, United States
| | - Timothy J. Hagen
- Department
of Chemistry and Biochemistry, Northern
Illinois University, DeKalb, Illinois 60115, United States
| | - David Fox
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Beryllium
Discovery Corp., 7869
NE Day Road West, Bainbridge Island, Washington 98110, United States
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Damian J. Krysan
- Department
of Pediatrics Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, United States
- Microbiology/Immunology,
Carver College of Medicine, University of
Iowa, Iowa City, Iowa 52242, United States
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8
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Šuchová K, Puchart V, Spodsberg N, Mørkeberg Krogh KBR, Biely P. Catalytic Diversity of GH30 Xylanases. Molecules 2021; 26:molecules26154528. [PMID: 34361682 PMCID: PMC8347883 DOI: 10.3390/molecules26154528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/16/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Catalytic properties of GH30 xylanases belonging to subfamilies 7 and 8 were compared on glucuronoxylan, modified glucuronoxylans, arabinoxylan, rhodymenan, and xylotetraose. Most of the tested bacterial GH30-8 enzymes are specific glucuronoxylanases (EC 3.2.1.136) requiring for action the presence of free carboxyl group of MeGlcA side residues. These enzymes were not active on arabinoxylan, rhodymenan and xylotetraose, and conversion of MeGlcA to its methyl ester or its reduction to MeGlc led to a remarkable drop in their specific activity. However, some GH30-8 members are nonspecific xylanases effectively hydrolyzing all tested substrates. In terms of catalytic activities, the GH30-7 subfamily is much more diverse. In addition to specific glucuronoxylanases, the GH30-7 subfamily contains nonspecific endoxylanases and predominantly exo-acting enzymes. The activity of GH30-7 specific glucuronoxylanases also depend on the presence of the MeGlcA carboxyl, but not so strictly as in bacterial enzymes. The modification of the carboxyl group of glucuronoxylan had only weak effect on the action of predominantly exo-acting enzymes, as well as nonspecific xylanases. Rhodymenan and xylotetraose were the best substrates for exo-acting enzymes, while arabinoxylan represented hardly degradable substrate for almost all tested GH30-7 enzymes. The results expand current knowledge on the catalytic properties of this relatively novel group of xylanases.
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Affiliation(s)
- Katarína Šuchová
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia; (V.P.); (P.B.)
- Correspondence: ; Tel.: +421-25-941-0229
| | - Vladimír Puchart
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia; (V.P.); (P.B.)
| | - Nikolaj Spodsberg
- Novozymes A/S, Krogshøjvej 36, 2880 Bagsværd, Denmark; (N.S.); (K.B.R.M.K.)
| | | | - Peter Biely
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia; (V.P.); (P.B.)
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9
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Zitare UA, Habib MH, Rozeboom H, Mascotti ML, Todorovic S, Fraaije MW. Mutational and structural analysis of an ancestral fungal dye-decolorizing peroxidase. FEBS J 2021; 288:3602-3618. [PMID: 33369202 PMCID: PMC8248431 DOI: 10.1111/febs.15687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/31/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) constitute a superfamily of heme-containing peroxidases that are related neither to animal nor to plant peroxidase families. These are divided into four classes (types A, B, C, and D) based on sequence features. The active site of DyPs contains two highly conserved distal ligands, an aspartate and an arginine, the roles of which are still controversial. These ligands have mainly been studied in class A-C bacterial DyPs, largely because no effective recombinant expression systems have been developed for the fungal (D-type) DyPs. In this work, we employ ancestral sequence reconstruction (ASR) to resurrect a D-type DyP ancestor, AncDyPD-b1. Expression of AncDyPD-b1 in Escherichia coli results in large amounts of a heme-containing soluble protein and allows for the first mutagenesis study on the two distal ligands of a fungal DyP. UV-Vis and resonance Raman (RR) spectroscopic analyses, in combination with steady-state kinetics and the crystal structure, reveal fine pH-dependent details about the heme active site structure and show that both the aspartate (D222) and the arginine (R390) are crucial for hydrogen peroxide reduction. Moreover, the data indicate that these two residues play important but mechanistically different roles on the intraprotein long-range electron transfer process. DATABASE: Structural data are available in the PDB database under the accession number 7ANV.
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Affiliation(s)
- Ulises A. Zitare
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE)Departamento de Química Inorgánica, Analítica y Química FísicaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires and CONICETArgentina
| | - Mohamed H. Habib
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- Department of Microbiology and ImmunologyFaculty of PharmacyCairo UniversityEgypt
| | | | - Maria L. Mascotti
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- IMIBIO‐SL CONICETFacultad de Química Bioquímica y FarmaciaUniversidad Nacional de San LuisArgentina
| | - Smilja Todorovic
- Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
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10
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Dautt-Castro M, Rosendo-Vargas M, Casas-Flores S. The Small GTPases in Fungal Signaling Conservation and Function. Cells 2021; 10:cells10051039. [PMID: 33924947 PMCID: PMC8146680 DOI: 10.3390/cells10051039] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Monomeric GTPases, which belong to the Ras superfamily, are small proteins involved in many biological processes. They are fine-tuned regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Several families have been identified in organisms from different kingdoms. Overall, the most studied families are Ras, Rho, Rab, Ran, Arf, and Miro. Recently, a new family named Big Ras GTPases was reported. As a general rule, the proteins of all families have five characteristic motifs (G1–G5), and some specific features for each family have been described. Here, we present an exhaustive analysis of these small GTPase families in fungi, using 56 different genomes belonging to different phyla. For this purpose, we used distinct approaches such as phylogenetics and sequences analysis. The main functions described for monomeric GTPases in fungi include morphogenesis, secondary metabolism, vesicle trafficking, and virulence, which are discussed here. Their participation during fungus–plant interactions is reviewed as well.
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11
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Supuran CT, Capasso C. A Highlight on the Inhibition of Fungal Carbonic Anhydrases as Drug Targets for the Antifungal Armamentarium. Int J Mol Sci 2021; 22:4324. [PMID: 33919261 PMCID: PMC8122340 DOI: 10.3390/ijms22094324] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
Carbon dioxide (CO2), a vital molecule of the carbon cycle, is a critical component in living organisms' metabolism, performing functions that lead to the building of compounds fundamental for the life cycle. In all living organisms, the CO2/bicarbonate (HCO3-) balancing is governed by a superfamily of enzymes, known as carbonic anhydrases (CAs, EC 4.2.1.1). CAs catalyze the pivotal physiological reaction, consisting of the reversible hydration of the CO2 to HCO3- and protons. Opportunistic and pathogenic fungi can sense the environmental CO2 levels, which influence their virulence or environmental subsistence traits. The fungal CO2-sensing is directly stimulated by HCO3- produced in a CA-dependent manner, which directly activates adenylyl cyclase (AC) involved in the fungal spore formation. The interference with CA activity may impair fungal growth and virulence, making this approach interesting for designing antifungal drugs with a novel mechanism of action: the inhibition of CAs linked to the CO2/HCO3-/pH chemosensing and signaling. This review reports that sulfonamides and their bioisosteres as well as inorganic anions can inhibit in vitro the β- and α-CAs from the fungi, suggesting how CAs may be considered as a novel "pathogen protein" target of many opportunistic, pathogenic fungi.
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Affiliation(s)
- Claudiu T. Supuran
- Section of Pharmaceutical and Nutraceutical Sciences, Department of Neurofarba, University of Florence, Via U. Schiff 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
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12
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Losada-Garcia N, Jimenez-Alesanco A, Velazquez-Campoy A, Abian O, Palomo JM. Enzyme/Nanocopper Hybrid Nanozymes: Modulating Enzyme-like Activity by the Protein Structure for Biosensing and Tumor Catalytic Therapy. ACS Appl Mater Interfaces 2021; 13:5111-5124. [PMID: 33472360 PMCID: PMC8486171 DOI: 10.1021/acsami.0c20501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/12/2021] [Indexed: 05/30/2023]
Abstract
Artificial enzymes with modulated enzyme-mimicking activities of natural systems represent a challenge in catalytic applications. Here, we show the creation of artificial Cu metalloenzymes based on the generation of Cu nanoparticles in an enzyme matrix. Different enzymes were used, and the structural differences between the enzymes especially influenced the controlled the size of the nanoparticles and the environment that surrounds them. Herein, we demonstrated that the oxidase-like catalytic activity of these copper nanozymes was rationally modulated by enzyme used as a scaffold, with a special role in the nanoparticle size and their environment. In this sense, these nanocopper hybrids have confirmed the ability to mimic a unique enzymatic activity completely different from the natural activity of the enzyme used as a scaffold, such as tyrosinase-like activity or as Fenton catalyst, which has extremely higher stability than natural mushroom tyrosinase. More interestingly, the oxidoreductase-like activity of nanocopper hybrids was cooperatively modulated with the synergistic effect between the enzyme and the nanoparticles improving the catalase activity (no peroxidase activity). Additionally, a novel dual (metallic and enzymatic activity) of the nanozyme made the highly improved catechol-like activity interesting for the design of 3,4-dihydroxy-l-phenylalanine (l-DOPA) biosensor for detection of tyrosinase. These hybrids also showed cytotoxic activity against different tumor cells, interesting in biocatalytic tumor therapy.
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Affiliation(s)
- Noelia Losada-Garcia
- Department
of Biocatalysis, Institute of Catalysis
(CSIC), c/Marie curie 2, Cantoblanco Campus UAM, 28049 Madrid, Spain
| | - Ana Jimenez-Alesanco
- Instituto
de Biocomputación y Física de Sistemas Complejos, Joint
Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Fundación
ARAID, Gobierno de Aragón, 50018 Zaragoza, Spain
- Instituto
de Biocomputación y Física de Sistemas Complejos, Joint
Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Fundación
Instituto de Investigación Sanitaria de Aragón (IIS
Aragón), 50009 Zaragoza, Spain
- Centro
de Investigación Biomédica en Red en el Área
Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento
de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Olga Abian
- Instituto
de Biocomputación y Física de Sistemas Complejos, Joint
Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Fundación
Instituto de Investigación Sanitaria de Aragón (IIS
Aragón), 50009 Zaragoza, Spain
- Centro
de Investigación Biomédica en Red en el Área
Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento
de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto
Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
| | - Jose M. Palomo
- Department
of Biocatalysis, Institute of Catalysis
(CSIC), c/Marie curie 2, Cantoblanco Campus UAM, 28049 Madrid, Spain
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13
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Yin J, Li F, Zhou Y, Mou M, Lu Y, Chen K, Xue J, Luo Y, Fu J, He X, Gao J, Zeng S, Yu L, Zhu F. INTEDE: interactome of drug-metabolizing enzymes. Nucleic Acids Res 2021; 49:D1233-D1243. [PMID: 33045737 PMCID: PMC7779056 DOI: 10.1093/nar/gkaa755] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/19/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022] Open
Abstract
Drug-metabolizing enzymes (DMEs) are critical determinant of drug safety and efficacy, and the interactome of DMEs has attracted extensive attention. There are 3 major interaction types in an interactome: microbiome-DME interaction (MICBIO), xenobiotics-DME interaction (XEOTIC) and host protein-DME interaction (HOSPPI). The interaction data of each type are essential for drug metabolism, and the collective consideration of multiple types has implication for the future practice of precision medicine. However, no database was designed to systematically provide the data of all types of DME interactions. Here, a database of the Interactome of Drug-Metabolizing Enzymes (INTEDE) was therefore constructed to offer these interaction data. First, 1047 unique DMEs (448 host and 599 microbial) were confirmed, for the first time, using their metabolizing drugs. Second, for these newly confirmed DMEs, all types of their interactions (3359 MICBIOs between 225 microbial species and 185 DMEs; 47 778 XEOTICs between 4150 xenobiotics and 501 DMEs; 7849 HOSPPIs between 565 human proteins and 566 DMEs) were comprehensively collected and then provided, which enabled the crosstalk analysis among multiple types. Because of the huge amount of accumulated data, the INTEDE made it possible to generalize key features for revealing disease etiology and optimizing clinical treatment. INTEDE is freely accessible at: https://idrblab.org/intede/.
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Affiliation(s)
- Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhou
- The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yinjing Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kangli Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jia Xue
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xu He
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Lushan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
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14
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Frandsen KEH, Haon M, Grisel S, Henrissat B, Lo Leggio L, Berrin JG. Identification of the molecular determinants driving the substrate specificity of fungal lytic polysaccharide monooxygenases (LPMOs). J Biol Chem 2021; 296:100086. [PMID: 33199373 PMCID: PMC7949027 DOI: 10.1074/jbc.ra120.015545] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 01/30/2023] Open
Abstract
Understanding enzymatic breakdown of plant biomass is crucial to develop nature-inspired biotechnological processes. Lytic polysaccharide monooxygenases (LPMOs) are microbial enzymes secreted by fungal saprotrophs involved in carbon recycling. LPMOs modify biomass by oxidatively cleaving polysaccharides, thereby enhancing the efficiency of glycoside hydrolases. Fungal AA9 LPMOs are active on cellulose, but some members also display activity on hemicelluloses and/or oligosaccharides. Although the active site subsites are well defined for a few model LPMOs, the molecular determinants driving broad substrate specificity are still not easily predictable. Based on bioinformatic clustering and sequence alignments, we selected seven fungal AA9 LPMOs that differ in the amino-acid residues constituting their subsites. Investigation of their substrate specificities revealed that all these LPMOs are active on cellulose and cello-oligosaccharides, as well as plant cell wall-derived hemicellulosic polysaccharides, and carry out C4 oxidative cleavage. The product profiles from cello-oligosaccharide degradation suggest that the subtle differences in amino-acid sequence within the substrate-binding loop regions lead to different preferred binding modes. Our functional analyses allowed us to probe the molecular determinants of substrate binding within two AA9 LPMO subclusters. Many wood-degrading fungal species rich in AA9 genes have at least one AA9 enzyme with structural loop features that allow recognition of short β-(1,4)-linked glucan chains. Time-course monitoring of these AA9 LPMOs on cello-oligosaccharides also provides a useful model system for mechanistic studies of LPMO catalysis. These results are valuable for the understanding of LPMO contribution to wood decaying process in nature and for the development of sustainable biorefineries.
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Affiliation(s)
- Kristian E H Frandsen
- INRAE, Aix-Marseille University, Polytech Marseille, UMR1163 BBF, Marseille, France; Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Mireille Haon
- INRAE, Aix-Marseille University, Polytech Marseille, UMR1163 BBF, Marseille, France
| | - Sacha Grisel
- INRAE, Aix-Marseille University, Polytech Marseille, UMR1163 BBF, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France; INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Jean-Guy Berrin
- INRAE, Aix-Marseille University, Polytech Marseille, UMR1163 BBF, Marseille, France.
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15
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Farian E, Cholewa G, Cholewa A, Matczuk M, Angelina WF. The effect of fruit on the extracellular enzyme profiles of fungi. Ann Agric Environ Med 2020; 27:562-567. [PMID: 33356061 DOI: 10.26444/aaem/127557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
INTRODUCTION In recent years, the number of diseases caused by fungal pathogens has increased significantly. Many species of fungi are pathogenic for plants, causing a threat to food production and to humans, and are among the causes of chronic diseases. OBJECTIVE The aim of the study is to determine the enzyme profiles of fungi, depending on the different types of fruit with which they have contact, and to determine the differences in these profiles in relation to the substrate on which they are grown. MATERIAL AND METHODS Six strains of fungi identified as Cladosporium sphaerospermum, Fusarium poae, Alternaria alternata, Penicillium expansum, Penicillium verucosum and Acremonium strictum, isolated from fruits, were selected and analyzed for enzymatic profiles. The enzymatic activity was assessed using the API ZYM test (bioMerieux, France). RESULTS In the majority of the 6 fungal strains isolated from fruits, enzymes belonging to glycol-hydrolases were the most active. The exception was Acremonium strictum, where phosphatases dominated. Among most fungal isolates, the enzymes β- glucosidase and N-acetyl-β-glucosaminidase showed the highest activity. The highest β-glucosidase activities were found in Cladosporium sphaerospermum and Penicillium expansum. On the other hand, lipase, α-fucosidase and α-chymotrypsin showed the least activity. The least activity of these enzymes or their complete absence was observed in Fusarium poae, Alternaria alternata, Penicillium expansum and Acremonium strictum. CONCLUSIONS The activity of hydrolytic enzymes in the isolated fungi depended on the addition of fruit and the type of medium. Individual fruits can increase or decrease the activity of the enzymes. Fungi present in fruit have pathogenic properties and can be possible risk factors for fungal infections.
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Affiliation(s)
- Ewelina Farian
- Department of Biological Health Hazards and Parasitology, Institute of Rural Health, Lublin, Poland
| | - Grażyna Cholewa
- Department of Biological Health Hazards and Parasitology, Institute of Rural Health, Lublin, Poland
| | - Alicja Cholewa
- Department of Biological Health Hazards and Parasitology, Institute of Rural Health, Lublin, Poland
| | - Magdalena Matczuk
- Department of Biological Health Hazards and Parasitology, Institute of Rural Health, Lublin, Poland
| | - Wójcik-Fatla Angelina
- Department of Biological Health Hazards and Parasitology, Institute of Rural Health, Lublin, Poland
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16
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Pilolli R, De Angelis M, Lamonaca A, De Angelis E, Rizzello CG, Siragusa S, Gadaleta A, Mamone G, Monaci L. Prototype Gluten-Free Breads from Processed Durum Wheat: Use of Monovarietal Flours and Implications for Gluten Detoxification Strategies. Nutrients 2020; 12:E3824. [PMID: 33327648 PMCID: PMC7765144 DOI: 10.3390/nu12123824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022] Open
Abstract
In this investigation, we reported the production of prototype breads from the processed flours of three specific Triticum turgidum wheat genotypes that were selected in our previous investigation for their potential low toxic/immunogenic activity for celiac disease (CD) patients. The flours were subjected to sourdough fermentation with a mixture of selected Lactobacillus strains, and in presence of fungal endoproteases. The breads were characterized by R5 competitive enzyme linked immunosorbent assay in order to quantify the residual gluten, and the differential efficacy in gluten degradation was assessed. In particular, two of them were classified as gluten-free (<20 ppm) and very low-gluten content (<100 ppm) breads, respectively, whereas the third monovarietal prototype retained a gluten content that was well above the safety threshold prescribed for direct consumption by CD patients. In order to investigate such a genotype-dependent efficiency of the detoxification method applied, an advanced proteomic characterization by high-resolution tandem mass spectrometry was performed. Notably, to the best of our knowledge, this is the first proteomic investigation which benefitted, for protein identification, from the full sequencing of the Triticum turgidum ssp. durum genome. The differences of the proteins' primary structures affecting their susceptibility to hydrolysis were investigated. As a confirmation of the previous immunoassay-based results, two out of the three breads made with the processed flours presented an exhaustive degradation of the epitopic sequences that are relevant for CD immune stimulatory activity. The list of the detected epitopes was analyzed and critically discussed in light of their susceptibility to the detoxification strategy applied. Finally, in-vitro experiments of human gastroduodenal digestion were carried out in order to assess, in-silico, the toxicity risk of the prototype breads under investigation for direct consumption by CD patients. This approach allowed us to confirm the total degradation of the epitopic sequences upon gastro-duodenal digestion.
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Affiliation(s)
- Rosa Pilolli
- Institute of Sciences of Food Production, CNR-ISPA, 70126 Bari, Italy; (A.L.); (E.D.A.); (L.M.)
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy; (M.D.A.); (C.G.R.); (S.S.)
| | - Antonella Lamonaca
- Institute of Sciences of Food Production, CNR-ISPA, 70126 Bari, Italy; (A.L.); (E.D.A.); (L.M.)
| | - Elisabetta De Angelis
- Institute of Sciences of Food Production, CNR-ISPA, 70126 Bari, Italy; (A.L.); (E.D.A.); (L.M.)
| | - Carlo Giuseppe Rizzello
- Department of Soil, Plant and Food Science, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy; (M.D.A.); (C.G.R.); (S.S.)
| | - Sonya Siragusa
- Department of Soil, Plant and Food Science, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy; (M.D.A.); (C.G.R.); (S.S.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Sciences, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy;
| | | | - Linda Monaci
- Institute of Sciences of Food Production, CNR-ISPA, 70126 Bari, Italy; (A.L.); (E.D.A.); (L.M.)
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17
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Grabarczyk M, Mączka W, Żołnierczyk AK, Wińska K. Transformations of Monoterpenes with the p-Menthane Skeleton in the Enzymatic System of Bacteria, Fungi and Insects. Molecules 2020; 25:E4840. [PMID: 33092264 PMCID: PMC7587936 DOI: 10.3390/molecules25204840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 12/02/2022] Open
Abstract
The main objective of this article was to present the possibilities of using the enzymatic system of microorganisms and insects to transform small molecules, such as monoterpenes. The most important advantage of this type of reaction is the possibility of obtaining derivatives that are not possible to obtain with standard methods of organic synthesis or are very expensive to obtain. The interest of industrial centers focuses mainly on obtaining particles of high optical purity, which have the desired biological properties. The cost of obtaining such a compound and the elimination of toxic or undesirable chemical waste is important. Enzymatic reactions based on enzymes alone or whole microorganisms enable obtaining products with a specific structure and purity in accordance with the rules of Green Chemistry.
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Affiliation(s)
- Małgorzata Grabarczyk
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland;
| | - Wanda Mączka
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland;
| | | | - Katarzyna Wińska
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland;
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18
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Saldarriaga-Hernández S, Velasco-Ayala C, Leal-Isla Flores P, de Jesús Rostro-Alanis M, Parra-Saldivar R, Iqbal HMN, Carrillo-Nieves D. Biotransformation of lignocellulosic biomass into industrially relevant products with the aid of fungi-derived lignocellulolytic enzymes. Int J Biol Macromol 2020; 161:1099-1116. [PMID: 32526298 DOI: 10.1016/j.ijbiomac.2020.06.047] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023]
Abstract
Lignocellulosic material has drawn significant attention among the scientific community due to its year-round availability as a renewable resource for industrial consumption. Being an economic substrate alternative, various industries are reevaluating processes to incorporate derived compounds from these materials. Varieties of fungi and bacteria have the ability to depolymerize lignocellulosic biomass by synthesizing degrading enzymes. Owing to catalytic activity stability and high yields of conversion, lignocellulolytic enzymes derived from fungi currently have a high spectrum of industrial applications. Moreover, these materials are cost effective, eco-friendly and nontoxic while having a low energy input. Techno-economic analysis for current enzyme production technologies indicates that synthetic production is not commercially viable. Instead, the economic projection of the use of naturally-produced ligninolytic enzymes is promising. This approach may improve the economic feasibility of the process by lowering substrate expenses and increasing lignocellulosic by-product's added value. The present review will discuss the classification and enzymatic degradation pathways of lignocellulolytic biomass as well as the potential and current industrial applications of the involved fungal enzymes.
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Affiliation(s)
- Sara Saldarriaga-Hernández
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Carolina Velasco-Ayala
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Paulina Leal-Isla Flores
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Magdalena de Jesús Rostro-Alanis
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Roberto Parra-Saldivar
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Danay Carrillo-Nieves
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramón Corona 2514, Nuevo México, Zapopan C.P. 45138, Jalisco, Mexico.
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Nieto-Domínguez M, Fernández de Toro B, de Eugenio LI, Santana AG, Bejarano-Muñoz L, Armstrong Z, Méndez-Líter JA, Asensio JL, Prieto A, Withers SG, Cañada FJ, Martínez MJ. Thioglycoligase derived from fungal GH3 β-xylosidase is a multi-glycoligase with broad acceptor tolerance. Nat Commun 2020; 11:4864. [PMID: 32978392 PMCID: PMC7519651 DOI: 10.1038/s41467-020-18667-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/02/2020] [Indexed: 11/09/2022] Open
Abstract
The synthesis of customized glycoconjugates constitutes a major goal for biocatalysis. To this end, engineered glycosidases have received great attention and, among them, thioglycoligases have proved useful to connect carbohydrates to non-sugar acceptors. However, hitherto the scope of these biocatalysts was considered limited to strong nucleophilic acceptors. Based on the particularities of the GH3 glycosidase family active site, we hypothesized that converting a suitable member into a thioglycoligase could boost the acceptor range. Herein we show the engineering of an acidophilic fungal β-xylosidase into a thioglycoligase with broad acceptor promiscuity. The mutant enzyme displays the ability to form O-, N-, S- and Se- glycosides together with sugar esters and phosphoesters with conversion yields from moderate to high. Analyses also indicate that the pKa of the target compound was the main factor to determine its suitability as glycosylation acceptor. These results expand on the glycoconjugate portfolio attainable through biocatalysis.
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Affiliation(s)
- Manuel Nieto-Domínguez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Beatriz Fernández de Toro
- NMR and Molecular Recognition Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Laura I de Eugenio
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Andrés G Santana
- Glycochemistry and Molecular recognition group, Instituto de Química Orgánica General (CSIC), C/Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Lara Bejarano-Muñoz
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Zach Armstrong
- Department of Chemistry, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada
| | - Juan Antonio Méndez-Líter
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular recognition group, Instituto de Química Orgánica General (CSIC), C/Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Alicia Prieto
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Stephen G Withers
- Department of Chemistry, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada
| | - Francisco Javier Cañada
- NMR and Molecular Recognition Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - María Jesús Martínez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain.
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20
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Abstract
Phytic acid stores 60-90% of the inorganic phosphorus in legumes, oil seeds, and cereals, making it inaccessible for metabolic processes in living systems. In addition, given its negative charge, phytic acid complexes with divalent cations, starch, and proteins. Inorganic phosphorous can be released from phytic acid upon the action of phytases. Phytases are phosphatases produced by animals, plants, and microorganisms, notably Aspergillus niger, and are employed as animal feed additive, in chemical industry and for ethanol production. Given the industrial relevance of phytases produced by filamentous fungi, this work discusses the functional characterization of fungal phytase-coding genes/proteins, highlighting the physicochemical parameters that govern the enzymatic activity, the development of phytase super-producing strains, and key features for industrial applications.
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Affiliation(s)
- Thamy Lívia Ribeiro Corrêa
- Department of Microbiology/BIOAGRO, Federal University of Viçosa, Av. Peter Henry Rolfs s/n, Vicosa, MG, 36570-000, Brazil.
| | - Elza Fernandes de Araújo
- Department of Microbiology/BIOAGRO, Federal University of Viçosa, Av. Peter Henry Rolfs s/n, Vicosa, MG, 36570-000, Brazil
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Abstract
Lipases are very versatile enzymes, and produced the attention of the several industrial processes. Lipase can be achieved from several sources, animal, vegetable, and microbiological. The uses of microbial lipase market is estimated to be USD 425.0 Million in 2018 and it is projected to reach USD 590.2 Million by 2023, growing at a CAGR of 6.8% from 2018. Microbial lipases (EC 3.1.1.3) catalyze the hydrolysis of long chain triglycerides. The microbial origins of lipase enzymes are logically dynamic and proficient also have an extensive range of industrial uses with the manufacturing of altered molecules. The unique lipase (triacylglycerol acyl hydrolase) enzymes catalyzed the hydrolysis, esterification and alcoholysis reactions. Immobilization has made the use of microbial lipases accomplish its best performance and hence suitable for several reactions and need to enhance aroma to the immobilization processes. Immobilized enzymes depend on the immobilization technique and the carrier type. The choice of the carrier concerns usually the biocompatibility, chemical and thermal stability, and insolubility under reaction conditions, capability of easy rejuvenation and reusability, as well as cost proficiency. Bacillus spp., Achromobacter spp., Alcaligenes spp., Arthrobacter spp., Pseudomonos spp., of bacteria and Penicillium spp., Fusarium spp., Aspergillus spp., of fungi are screened large scale for lipase production. Lipases as multipurpose biological catalyst has given a favorable vision in meeting the needs for several industries such as biodiesel, foods and drinks, leather, textile, detergents, pharmaceuticals and medicals. This review represents a discussion on microbial sources of lipases, immobilization methods increased productivity at market profitability and reduce logistical liability on the environment and user.
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Affiliation(s)
- Prem Chandra
- Food Microbiology & Toxicology, Department of Microbiology, School for Biomedical and Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, Uttar Pradesh 226025 India
| | - Enespa
- Department of Plant Pathology, School for Agriculture, SMPDC, University of Lucknow, Lucknow, 226007 U.P. India
| | - Ranjan Singh
- Department of Environmental Science, School for Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, U.P. India
| | - Pankaj Kumar Arora
- Department of Microbiology, School for Biomedical and Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, U.P. India
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Mathew GM, Madhavan A, Arun KB, Sindhu R, Binod P, Singhania RR, Sukumaran RK, Pandey A. Thermophilic Chitinases: Structural, Functional and Engineering Attributes for Industrial Applications. Appl Biochem Biotechnol 2020; 193:142-164. [PMID: 32827066 DOI: 10.1007/s12010-020-03416-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
Chitin is the second most widely found natural polymer next to cellulose. Chitinases degrade the insoluble chitin to bioactive chitooligomers and monomers for various industrial applications. Based on their function, these enzymes act as biocontrol agents against pathogenic fungi and invasive pests compared with conventional chemical fungicides and insecticides. They have other functional roles in shellfish waste management, fungal protoplast generation, and Single-Cell Protein production. Among the chitinases, thermophilic and thermostable chitinases are gaining popularity in recent years, as they can withstand high temperatures and maintain the enzyme stability for longer periods. Not all chitinases are thermostable; hence, tailor-made thermophilic chitinases are designed to enhance their thermostability by direct evolution, genetic engineering involving mutagenesis, and proteomics approach. Although research has been done extensively on cloning and expression of thermophilic chitinase genes, there are only few papers discussing on the mechanism of chitin degradation using thermophiles. The current review discusses the sources of thermophilic chitinases, improvement of protein stability by gene manipulation, metagenomics approaches, chitin degradation mechanism in thermophiles, and their prospective applications for industrial, agricultural, and pharmaceutical purposes.
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Affiliation(s)
- Gincy M Mathew
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - K B Arun
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | | | - Rajeev K Sukumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR - Indian Institute of Toxicology Research, Lucknow, 226 001, India.
- Frontier Research Lab, Yonsei University, Seoul, South Korea.
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24
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Gomez-Fernandez BJ, Risso VA, Rueda A, Sanchez-Ruiz JM, Alcalde M. Ancestral Resurrection and Directed Evolution of Fungal Mesozoic Laccases. Appl Environ Microbiol 2020; 86:e00778-20. [PMID: 32414792 PMCID: PMC7357490 DOI: 10.1128/aem.00778-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Ancestral sequence reconstruction and resurrection provides useful information for protein engineering, yet its alliance with directed evolution has been little explored. In this study, we have resurrected several ancestral nodes of fungal laccases dating back ∼500 to 250 million years. Unlike modern laccases, the resurrected Mesozoic laccases were readily secreted by yeast, with similar kinetic parameters, a broader stability, and distinct pH activity profiles. The resurrected Agaricomycetes laccase carried 136 ancestral mutations, a molecular testimony to its origin, and it was subjected to directed evolution in order to improve the rate of 1,3-cyclopentanedione oxidation, a β-diketone initiator commonly used in vinyl polymerization reactions.IMPORTANCE The broad variety of biotechnological uses of fungal laccases is beyond doubt (food, textiles, pulp and paper, pharma, biofuels, cosmetics, and bioremediation), and protein engineering (in particular, directed evolution) has become the key driver for adaptation of these enzymes to harsh industrial conditions. Usually, the first requirement for directed laccase evolution is heterologous expression, which presents an important hurdle and often a time-consuming process. In this work, we resurrected a fungal Mesozoic laccase node which showed strikingly high heterologous expression and pH stability. As a proof of concept that the ancestral laccase is a suitable blueprint for engineering, we performed a quick directed evolution campaign geared to the oxidation of the β-diketone 1,3-cyclopentanedione, a poor laccase substrate that is used in the polymerization of vinyl monomers.
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Affiliation(s)
- Bernardo J Gomez-Fernandez
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry, CSIC, Madrid, Spain
- EvoEnzyme, S.L., Madrid, Spain
| | - Valeria A Risso
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Andres Rueda
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Quebec, Canada
| | - Jose M Sanchez-Ruiz
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry, CSIC, Madrid, Spain
- EvoEnzyme, S.L., Madrid, Spain
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Chikkerur J, Samanta AK, Kolte AP, Dhali A, Roy S. Production of Short Chain Fructo-oligosaccharides from Inulin of Chicory Root Using Fungal Endoinulinase. Appl Biochem Biotechnol 2020; 191:695-715. [PMID: 31845198 DOI: 10.1007/s12010-019-03215-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/05/2019] [Indexed: 11/28/2022]
Abstract
Short chain fructo-oligosaccharides (SC-FOS) are the potential prebiotics possessing diverse applications in both food and feed industries. The present study was aimed to extract inulin from chicory roots followed by its conversion into SC-FOS applying endoinulinase from Aspergillus fumigatus. The inulin was extracted from chicory roots through boiling in hot water, followed by precipitation with ethanol at room temperature or freezing condition. Maximum yield (42%) of inulin was obtained with three volumes of chilled absolute ethanol at room temperature. HPLC analysis of enzymatic hydrolysate detected kestose (GF2), nystose (GF3), and other FOS having higher degree of polymerization (DP). Maximum GF2 (5.79 mg/ml) was detected at temperature 50 °C, pH 5.5 with 2 U of enzyme dose after 6 h of hydrolysis; while maximum GF3 (4.33 mg/ml) was recorded at 60 °C, 5.5 pH with 0.5 U enzyme dose after 2 h of hydrolysis. Nevertheless, complete hydrolysis of inulin was noticed with 99% total oligosaccharide yield at 55 °C, 5.5 pH with 0.5 U enzyme dose after 4 h of hydrolysis with negligible amount of mono- and di-saccharides. The present finding demonstrated the process for higher yield of inulin from chicory roots followed by its conversion into SC-FOS applying fungal endoinulinase.
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Affiliation(s)
- Jayaram Chikkerur
- ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Hosur road, Bengaluru, Karnataka, 560030, India
- Department of Microbiology, School of Sciences, Jain University, Bengaluru, Karnataka, 560011, India
| | - Ashis Kumar Samanta
- ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Hosur road, Bengaluru, Karnataka, 560030, India.
- SAARC Agriculture Centre, BARC Complex, Farmgate, Dhaka, 1215, Bangladesh.
| | - Atul P Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Hosur road, Bengaluru, Karnataka, 560030, India
| | - Arindam Dhali
- ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Hosur road, Bengaluru, Karnataka, 560030, India
| | - Sohini Roy
- ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Hosur road, Bengaluru, Karnataka, 560030, India
- Department of Microbiology, School of Sciences, Jain University, Bengaluru, Karnataka, 560011, India
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Babot ED, Aranda C, Del Rı O JC, Ullrich R, Kiebist J, Scheibner K, Hofrichter M, Martı Nez AT, Gutiérrez A. Selective Oxygenation of Ionones and Damascones by Fungal Peroxygenases. J Agric Food Chem 2020; 68:5375-5383. [PMID: 32292026 DOI: 10.1021/acs.jafc.0c01019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Apocarotenoids are among the most highly valued fragrance constituents, being also appreciated as synthetic building blocks. This work shows the ability of unspecific peroxygenases (UPOs, EC1.11.2.1) from several fungi, some of them being described recently, to catalyze the oxyfunctionalization of α- and β-ionones and α- and β-damascones. Enzymatic reactions yielded oxygenated products such as hydroxy, oxo, carboxy, and epoxy derivatives that are interesting compounds for the flavor and fragrance and pharmaceutical industries. Although variable regioselectivity was observed depending on the substrate and enzyme, oxygenation was preferentially produced at the allylic position in the ring, being especially evident in the reaction with α-ionone, forming 3-hydroxy-α-ionone and/or 3-oxo-α-ionone. Noteworthy were the reactions with damascones, in the course of which some UPOs oxygenated the terminal position of the side chain, forming oxygenated derivatives (i.e., the corresponding alcohol, aldehyde, and carboxylic acid) at C-10, which were predominant in the Agrocybe aegerita UPO reactions, and first reported here.
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Affiliation(s)
- Esteban D Babot
- Instituto de Recursos Naturales y Agrobiologı́a de Sevilla, CSIC, Av. Reina Mercedes 10, E-41012 Seville, Spain
| | - Carmen Aranda
- Instituto de Recursos Naturales y Agrobiologı́a de Sevilla, CSIC, Av. Reina Mercedes 10, E-41012 Seville, Spain
| | - José C Del Rı O
- Instituto de Recursos Naturales y Agrobiologı́a de Sevilla, CSIC, Av. Reina Mercedes 10, E-41012 Seville, Spain
| | - René Ullrich
- Department of Bio- and Environmental Sciences, TU Dresden, International Institute Zittau, Markt 23, 02763 Zittau, Germany
| | - Jan Kiebist
- JenaBios GmbH, Löbstedter Str. 80, 07749 Jena, Germany
| | | | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, TU Dresden, International Institute Zittau, Markt 23, 02763 Zittau, Germany
| | - Angel T Martı Nez
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiologı́a de Sevilla, CSIC, Av. Reina Mercedes 10, E-41012 Seville, Spain
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Rodríguez-Sifuentes L, Marszalek JE, Chuck-Hernández C, Serna-Saldívar SO. Legumes Protease Inhibitors as Biopesticides and Their Defense Mechanisms against Biotic Factors. Int J Mol Sci 2020; 21:E3322. [PMID: 32397104 PMCID: PMC7246880 DOI: 10.3390/ijms21093322] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 11/29/2022] Open
Abstract
Legumes are affected by biotic factors such as insects, molds, bacteria, and viruses. These plants can produce many different molecules in response to the attack of phytopathogens. Protease inhibitors (PIs) are proteins produced by legumes that inhibit the protease activity of phytopathogens. PIs are known to reduce nutrient availability, which diminishes pathogen growth and can lead to the death of the pathogen. PIs are classified according to the specificity of the mechanistic activity of the proteolytic enzymes, with serine and cysteine protease inhibitors being studied the most. Previous investigations have reported the efficacy of these highly stable proteins against diverse biotic factors and the concomitant protective effects in crops, representing a possible replacement of toxic agrochemicals that harm the environment.
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Affiliation(s)
- Lucio Rodríguez-Sifuentes
- Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Carretera Torreón-Matamoros Km 7.5, Torreón Coahuila 27104, Mexico; (L.R.-S.); (J.E.M.)
| | - Jolanta Elzbieta Marszalek
- Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Carretera Torreón-Matamoros Km 7.5, Torreón Coahuila 27104, Mexico; (L.R.-S.); (J.E.M.)
| | - Cristina Chuck-Hernández
- Tecnológico de Monterrey, School of Engineering and Sciences, Eugenio Garza Sada 2501, Col. Tecnológico, Monterrey Nuevo León 64849, Mexico;
| | - Sergio O. Serna-Saldívar
- Tecnológico de Monterrey, School of Engineering and Sciences, Eugenio Garza Sada 2501, Col. Tecnológico, Monterrey Nuevo León 64849, Mexico;
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Oliw EH, Hamberg M. Charge migration fragmentation in the negative ion mode of cyclopentenone and cyclopentanone intermediates in the biosynthesis of jasmonates. Rapid Commun Mass Spectrom 2020; 34:e8665. [PMID: 31734961 DOI: 10.1002/rcm.8665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/04/2019] [Accepted: 11/14/2019] [Indexed: 05/26/2023]
Abstract
RATIONALE Jasmonates are formed from 12-oxo-10,15(Z)-phytodienoic acid (12-OPDA) in plants and also from 12-oxo-10-phytoenoic acid (12-OPEA) in fungi. Collision-induced dissociation (CID) of [M-H]- generates characteristic product anions at m/z 165 [C11 H17 O]- . Our goal was to investigate the structure and mode of formation of this anion by CID of 12-OPDA, 12-OPEA, and 12-oxophytonoic acid (12-OPA). METHODS We investigated the CID of the [M-H]- , [M-H-CO2 ]- , and [M-H-H2 O]- anions using electrospray ionization and MS/MS analysis of 12-OPDA, 12-OPEA, and 12-OPA, and compared the results with the data obtained with the corresponding compounds labeled with 2 H at C-6 and C-7 and with structural and side chain analogs. RESULTS CID of [6,6,7,7-2 H4 ]12-OPEA and [6,6-2 H2 ]12-OPDA ([M-H]- and [M-H-CO2 ]- ) showed that one or two 2 H atoms were transferred to anions at m/z 165 as judged by the signal intensities of m/z 165 + 1 or 165 + 2, respectively. CID of [6,6-2 H2 ]- and [6,6,7,7-2 H4 ]-12-OPA ([M-H]- and [M-H-CO2 ]- ) yielded the loss of H2 from the cyclopentanone and displayed the transfer of one 2 H atom in analogy to 12-OPEA. In contrast, CID of [6,6,7,7-2 H4 ]12-OPEA and [6,6,7,7-2 H4 ]12-OPA [M-H-H2 O]- demonstrated the transfer of two 2 H atoms (m/z 165 + 2). All spectra obtained by CID of [6,6,7,7-2 H4 ]12-OPDA and [6,6,7,7-2 H4 ]12-oxo-9(13),15(Z)-phytodienoic acid showed that one or two additional 2 H atoms could be transferred to this anion at m/z 167 of [6,6-2 H2 ]12-OPDA due to isotope scrambling. CONCLUSIONS CID of 12-OPDA and 12-OPEA generates cyclopentanone enolate anions at m/z 165 by charge-driven hydride transfer as a common mechanism and by bond cleavage between C-7 and C-8 of the carboxyl side chains with either gain or loss of a hydrogen atom.
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Affiliation(s)
- Ernst H Oliw
- Division of Biochemical Pharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Mats Hamberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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Abstract
The class of fungal indole alkaloids containing the bicyclo[2.2.2]diazaoctane ring is comprised of diverse molecules that display a range of biological activities. While much interest has been garnered due to their therapeutic potential, this class of molecules also displays unique chemical functionality, making them intriguing synthetic targets. Many elegant and intricate total syntheses have been developed to generate these alkaloids, but the selectivity required to produce them in high yield presents great barriers. Alternatively, if we can understand the molecular mechanisms behind how fungi make these complex molecules, we can leverage the power of nature to perform these chemical transformations. Here, we describe the various studies regarding the evolutionary development of enzymes involved in fungal indole alkaloid biosynthesis.
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Affiliation(s)
- Amy E. Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States
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Barrett K, Jensen K, Meyer AS, Frisvad JC, Lange L. Fungal secretome profile categorization of CAZymes by function and family corresponds to fungal phylogeny and taxonomy: Example Aspergillus and Penicillium. Sci Rep 2020; 10:5158. [PMID: 32198418 PMCID: PMC7083838 DOI: 10.1038/s41598-020-61907-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/28/2020] [Indexed: 01/02/2023] Open
Abstract
Fungi secrete an array of carbohydrate-active enzymes (CAZymes), reflecting their specialized habitat-related substrate utilization. Despite its importance for fitness, enzyme secretome composition is not used in fungal classification, since an overarching relationship between CAZyme profiles and fungal phylogeny/taxonomy has not been established. For 465 Ascomycota and Basidiomycota genomes, we predicted CAZyme-secretomes, using a new peptide-based annotation method, Conserved-Unique-Peptide-Patterns, enabling functional prediction directly from sequence. We categorized each enzyme according to CAZy-family and predicted molecular function, hereby obtaining a list of "EC-Function;CAZy-Family" observations. These "Function;Family"-based secretome profiles were compared, using a Yule-dissimilarity scoring algorithm, giving equal consideration to the presence and absence of individual observations. Assessment of "Function;Family" enzyme profile relatedness (EPR) across 465 genomes partitioned Ascomycota from Basidiomycota placing Aspergillus and Penicillium among the Ascomycota. Analogously, we calculated CAZyme "Function;Family" profile-similarities among 95 Aspergillus and Penicillium species to form an alignment-free, EPR-based dendrogram. This revealed a stunning congruence between EPR categorization and phylogenetic/taxonomic grouping of the Aspergilli and Penicillia. Our analysis suggests EPR grouping of fungi to be defined both by "shared presence" and "shared absence" of CAZyme "Function;Family" observations. This finding indicates that CAZymes-secretome evolution is an integral part of fungal speciation, supporting integration of cladogenesis and anagenesis.
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Affiliation(s)
- Kristian Barrett
- Department for Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Kristian Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Anne S Meyer
- Department for Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Jens C Frisvad
- Department for Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800, Lyngby, Denmark.
| | - Lene Lange
- LLa Bioeconomy, Research & Advisory, Karensgade 5, DK-2500, Valby, Denmark
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Liu SH, Tsai SL, Guo PY, Lin CW. Inducing laccase activity in white rot fungi using copper ions and improving the efficiency of azo dye treatment with electricity generation using microbial fuel cells. Chemosphere 2020; 243:125304. [PMID: 31715296 DOI: 10.1016/j.chemosphere.2019.125304] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/17/2019] [Accepted: 11/03/2019] [Indexed: 05/25/2023]
Abstract
This work presents a white rot fungus-microbial fuel cell (WRF-MFC) that uses WRF that is grown at its cathode. Adding Cu2+ to the fungi-containing solid medium stimulated WRF-secreting laccase, which catalyzed the redox reaction in the MFC and thereby promoting the generation of electricity. Adding 12.5 mg L-1 Cu2+ to a G. lucidum-containing medium provided the greatest laccase stimulation and increased the laccase activity by a factor of 1.6. Adding 12.5 mg L-1 Cu2+ to the WRF chamber of WRF-MFC increased its decolorization of Acid Orange 7 (AO-7) and increased its power density to 223 mW m-2, which was 1.77 times that of an MFC without WRF. The enhancement of decolorization and electricity generation improved the performance of the WRF-MFC, indicating that a laccase-catalyzed cathode has great potential effectiveness in microbial fuel cells.
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Affiliation(s)
- Shu-Hui Liu
- Department of Safety, Health and Environmental Engineering, National Yunlin University of Science and Technology, Douliu, Yunlin, 64002, Taiwan, ROC
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, No.43, Keelung Rd., Sec.4, Da-An Dist., Taipei, 10607, Taiwan, ROC
| | - Pei-Yu Guo
- Department of Safety, Health and Environmental Engineering, National Yunlin University of Science and Technology, Douliu, Yunlin, 64002, Taiwan, ROC
| | - Chi-Wen Lin
- Department of Safety, Health and Environmental Engineering, National Yunlin University of Science and Technology, Douliu, Yunlin, 64002, Taiwan, ROC; National Yunlin University of Science and Technology, Feng Tay Distinguished Professor, Taiwan, ROC.
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Baćmaga M, Wyszkowska J, Kucharski J. Response of soil microorganisms and enzymes to the foliar application of Helicur 250 EW fungicide on Horderum vulgare L. Chemosphere 2020; 242:125163. [PMID: 31677518 DOI: 10.1016/j.chemosphere.2019.125163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/17/2019] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
Abstract
The use of fungicides bears the risk of many undesirable outcomes that are manifested in, among other things, changes in the structure and activity of microorganisms. This study aimed at determining the effect of a Helicur 250 EW preparation, used to protect crops against fungal diseases, on the microbiological and biochemical activity of soil and on the development of Horderum vulgare L. The fungicide was sprayed on leaves of spring barley in the following doses (per active substance, i.e. tebuconazole, TEB): 0.046, 0.093, 0.139, 1.395, and 2.790 mg TEB plant-1. The following indices were analyzed in the study: index of microorganisms resistance (RS) to the effects of fungicide, microorganisms colony development index (CD), microorganisms ecophysiological diversity index (EP), genetic diversity of bacteria, enzymatic activity, and effect of the fungicide on spring barley development (IFH). The most susceptible to the effects of the fungicide turned out to be fungi. The metagenomic analysis demonstrated that the bacterial community differed in terms of structure and percentage contribution in the soil exposed to the fungicide from the control soil even at the Phylum level. However, Proteobacteria appeared to be the prevailing taxon in both soils. Bacillus arabhattai, B. soli, and B. simplex occurred exclusively in the control soil, whereas Ramlibacter tataounensis, Azospirillum palatum, and Kaistobacter terrae - exclusively in the soil contaminated with the fungicide. Helicur 250 EW suppressed activities of all soil enzymes except for arylsulfatase. In addition, it proved to be a strong inhibitor of spring barley growth and development.
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Affiliation(s)
- Małgorzata Baćmaga
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland
| | - Jadwiga Wyszkowska
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland.
| | - Jan Kucharski
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland
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33
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Zhang R. Functional characterization of cellulose-degrading AA9 lytic polysaccharide monooxygenases and their potential exploitation. Appl Microbiol Biotechnol 2020; 104:3229-3243. [PMID: 32076777 DOI: 10.1007/s00253-020-10467-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 12/25/2019] [Accepted: 02/12/2020] [Indexed: 01/05/2023]
Abstract
Cellulose-degrading auxiliary activity family 9 (AA9) lytic polysaccharide monooxygenases (LPMOs) are known to be widely distributed among filamentous fungi and participate in the degradation of lignocellulose via the oxidative cleavage of celluloses, cello-oligosaccharides, or hemicelluloses. AA9 LPMOs have been reported to have extensive interactions with not only cellulases but also oxidases. The addition of AA9 LPMOs can greatly reduce the amount of cellulase needed for saccharification and increase the yield of glucose. The discovery of AA9 LPMOs has greatly changed our understanding of how fungi degrade cellulose. In this review, apart from summarizing the recent discoveries related to their catalytic reaction, functional diversity, and practical applications, the stability, expression system, and protein engineering of AA9 LPMOs are reviewed for the first time. This review may provide a reference value to further broaden the substrate range of AA9 LPMOs, expand the scope of their practical applications, and realize their customization for industrial utilization.Key Points• The stability and expression system of AA9 LPMOs are reviewed for the first time.• The protein engineering of AA9 LPMOs is systematically summarized for the first time.• The latest research results on the catalytic mechanism of AA9 LPMOs are summarized.• The application of AA9 LPMOs and their relationship with other enzymes are reviewed.
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Affiliation(s)
- Ruiqin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China.
- Department of Bioengineering, Huainan Normal University, No. 278 Xueyuannan Road, Huainan, 232038, China.
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Janusz G, Pawlik A, Świderska-Burek U, Polak J, Sulej J, Jarosz-Wilkołazka A, Paszczyński A. Laccase Properties, Physiological Functions, and Evolution. Int J Mol Sci 2020; 21:ijms21030966. [PMID: 32024019 PMCID: PMC7036934 DOI: 10.3390/ijms21030966] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 01/16/2023] Open
Abstract
Discovered in 1883, laccase is one of the first enzymes ever described. Now, after almost 140 years of research, it seems that this copper-containing protein with a number of unique catalytic properties is widely distributed across all kingdoms of life. Laccase belongs to the superfamily of multicopper oxidases (MCOs)—a group of enzymes comprising many proteins with different substrate specificities and diverse biological functions. The presence of cupredoxin-like domains allows all MCOs to reduce oxygen to water without producing harmful byproducts. This review describes structural characteristics and plausible evolution of laccase in different taxonomic groups. The remarkable catalytic abilities and broad substrate specificity of laccases are described in relation to other copper-containing MCOs. Through an exhaustive analysis of laccase roles in different taxa, we find that this enzyme evolved to serve an important, common, and protective function in living systems.
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Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 Street, 20-033 Lublin, Poland; (A.P.); (J.P.); (J.S.); (A.J.-W.)
- Correspondence: ; Tel.: +48-81-537-5521
| | - Anna Pawlik
- Department of Biochemistry and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 Street, 20-033 Lublin, Poland; (A.P.); (J.P.); (J.S.); (A.J.-W.)
| | - Urszula Świderska-Burek
- Department of Botany, Mycology and Ecology, Maria Curie-Skłodowska University, Akademicka 19 Street, 20-033 Lublin, Poland;
| | - Jolanta Polak
- Department of Biochemistry and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 Street, 20-033 Lublin, Poland; (A.P.); (J.P.); (J.S.); (A.J.-W.)
| | - Justyna Sulej
- Department of Biochemistry and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 Street, 20-033 Lublin, Poland; (A.P.); (J.P.); (J.S.); (A.J.-W.)
| | - Anna Jarosz-Wilkołazka
- Department of Biochemistry and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 Street, 20-033 Lublin, Poland; (A.P.); (J.P.); (J.S.); (A.J.-W.)
| | - Andrzej Paszczyński
- Professor Emeritus, School of Food Science, University of Idaho, Moscow, ID 83844, USA;
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35
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Doraiswamy N, Sarathi M, Pennathur G. Improvement in biochemical characteristics of cross-linked enzyme aggregates (CLEAs) with magnetic nanoparticles as support matrix. Methods Enzymol 2020; 630:133-158. [PMID: 31931983 DOI: 10.1016/bs.mie.2019.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Recent developments in novel carriers for enzyme immobilization have led to improvement in the stability and cost-effectiveness of the biocatalysts for their enhanced suitability in the industrial applications. Cross-linked enzyme aggregates (CLEAs), a recent technique developed in the carrier-free type of enzyme immobilization is a simple and straightforward method. Moreover, the magnetic property and the higher surface-to-volume ratio of the maghemite nanoparticles have also been utilized in the present immobilization technique as magnetic nanoparticle-supported CLEAs (Mgnp-CLEAs). The stability studies of the free and immobilized enzyme revealed the Mgnp-CLEAs to have enhanced enzyme stability with an increase in the reusability cycle. The physical characterization of the nanoparticles and immobilized enzymes by the Scanning Electron Microscopy (SEM), Fourier-Transform Infrared spectroscopy (FT-IR) and X-ray diffraction analysis (XRD) showed the successful immobilization of the enzyme for its improved stability.
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Affiliation(s)
| | | | - Gautam Pennathur
- Centre for Biotechnology, Anna University, Chennai, Tamil Nadu, India; AU-KBC Research Centre, Anna University, Chennai, Tamil Nadu, India.
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36
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Abstract
In this chapter we describe different strategies for enzyme immobilization in biomimetic silica nanoparticles. Synthesis of this type of support is performed under mild and biocompatible conditions and has been proven suitable for the immobilization and stabilization of a range of enzymes and enzymatic systems in nanostructured particles. Immobilization occurs by entrapment while the silica matrix is formed via catalysis of a polyamine molecule and the presence of silicic acid. Parameters such as enzyme, polyamine molecule, or source of Si concentration have been tailored in order to maximize enzymatic loads, stabilities, and specific activities of the catalysts. We provide different approaches for the immobilization and co-immobilization of enzymes that could be potentially extensible to other biocatalysts.
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Affiliation(s)
- Erienne Jackson
- Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Montevideo, Uruguay
| | - Sonali Correa
- Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Montevideo, Uruguay
| | - Lorena Betancor
- Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Montevideo, Uruguay.
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37
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McKenna DD, Shin S, Ahrens D, Balke M, Beza-Beza C, Clarke DJ, Donath A, Escalona HE, Friedrich F, Letsch H, Liu S, Maddison D, Mayer C, Misof B, Murin PJ, Niehuis O, Peters RS, Podsiadlowski L, Pohl H, Scully ED, Yan EV, Zhou X, Ślipiński A, Beutel RG. The evolution and genomic basis of beetle diversity. Proc Natl Acad Sci U S A 2019; 116:24729-24737. [PMID: 31740605 PMCID: PMC6900523 DOI: 10.1073/pnas.1909655116] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The order Coleoptera (beetles) is arguably the most speciose group of animals, but the evolutionary history of beetles, including the impacts of plant feeding (herbivory) on beetle diversification, remain poorly understood. We inferred the phylogeny of beetles using 4,818 genes for 146 species, estimated timing and rates of beetle diversification using 89 genes for 521 species representing all major lineages and traced the evolution of beetle genes enabling symbiont-independent digestion of lignocellulose using 154 genomes or transcriptomes. Phylogenomic analyses of these uniquely comprehensive datasets resolved previously controversial beetle relationships, dated the origin of Coleoptera to the Carboniferous, and supported the codiversification of beetles and angiosperms. Moreover, plant cell wall-degrading enzymes (PCWDEs) obtained from bacteria and fungi via horizontal gene transfers may have been key to the Mesozoic diversification of herbivorous beetles-remarkably, both major independent origins of specialized herbivory in beetles coincide with the first appearances of an arsenal of PCWDEs encoded in their genomes. Furthermore, corresponding (Jurassic) diversification rate increases suggest that these novel genes triggered adaptive radiations that resulted in nearly half of all living beetle species. We propose that PCWDEs enabled efficient digestion of plant tissues, including lignocellulose in cell walls, facilitating the evolution of uniquely specialized plant-feeding habits, such as leaf mining and stem and wood boring. Beetle diversity thus appears to have resulted from multiple factors, including low extinction rates over a long evolutionary history, codiversification with angiosperms, and adaptive radiations of specialized herbivorous beetles following convergent horizontal transfers of microbial genes encoding PCWDEs.
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Affiliation(s)
- Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152;
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152
| | - Seunggwan Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152
| | - Dirk Ahrens
- Center for Taxonomy and Evolutionary Research, Arthropoda Department, Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Michael Balke
- Bavarian State Collection of Zoology, Bavarian Natural History Collections, 81247 Munich, Germany
| | - Cristian Beza-Beza
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152
| | - Dave J Clarke
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Hermes E Escalona
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
- Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
- Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, 79104 Freiburg, Germany
| | - Frank Friedrich
- Institute of Zoology, University of Hamburg, D-20146 Hamburg, Germany
| | - Harald Letsch
- Department of Botany and Biodiversity Research, University of Wien, Wien 1030, Austria
| | - Shanlin Liu
- China National GeneBank, BGI-Shenzhen, 518083 Guangdong, People's Republic of China
| | - David Maddison
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Peyton J Murin
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, 79104 Freiburg, Germany
| | - Ralph S Peters
- Center for Taxonomy and Evolutionary Research, Arthropoda Department, Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Hans Pohl
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, D-07743 Jena, Germany
| | - Erin D Scully
- Center for Grain and Animal Health, Stored Product Insect and Engineering Research Unit, Agricultural Research Service, US Department of Agriculture, Manhattan, KS 66502
| | - Evgeny V Yan
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, D-07743 Jena, Germany
- Borissiak Paleontological Institute, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Adam Ślipiński
- Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, D-07743 Jena, Germany
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Okuda-Shimazaki J, Yoshida H, Sode K. FAD dependent glucose dehydrogenases - Discovery and engineering of representative glucose sensing enzymes. Bioelectrochemistry 2019; 132:107414. [PMID: 31838457 DOI: 10.1016/j.bioelechem.2019.107414] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/24/2019] [Accepted: 11/10/2019] [Indexed: 11/17/2022]
Abstract
The history of the development of glucose sensors goes hand-in-hand with the history of the discovery and the engineering of glucose-sensing enzymes. Glucose oxidase (GOx) has been used for glucose sensing since the development of the first electrochemical glucose sensor. The principle utilizing oxygen as the electron acceptor is designated as the first-generation electrochemical enzyme sensors. With increasing demand for hand-held and cost-effective devices for the "self-monitoring of blood glucose (SMBG)", second-generation electrochemical sensor strips employing electron mediators have become the most popular platform. To overcome the inherent drawback of GOx, namely, the use of oxygen as the electron acceptor, various glucose dehydrogenases (GDHs) have been utilized in second-generation principle-based sensors. Among the various enzymes employed in glucose sensors, GDHs harboring FAD as the redox cofactor, FADGDHs, especially those derived from fungi, fFADGDHs, are currently the most popular enzymes in the sensor strips of second-generation SMBG sensors. In addition, the third-generation principle, employing direct electron transfer (DET), is considered the most elegant approach and is ideal for use in electrochemical enzyme sensors. However, glucose oxidoreductases capable of DET are limited. One of the most prominent GDHs capable of DET is a bacteria-derived FADGDH complex (bFADGDH). bFADGDH has three distinct subunits; the FAD harboring the catalytic subunit, the small subunit, and the electron-transfer subunit, which makes bFADGDH capable of DET. In this review, we focused on the two representative glucose sensing enzymes, fFADGDHs and bFADGDHs, by presenting their discovery, sources, and protein and enzyme properties, and the current engineering strategies to improve their potential in sensor applications.
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Affiliation(s)
- Junko Okuda-Shimazaki
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA.
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Arregui L, Ayala M, Gómez-Gil X, Gutiérrez-Soto G, Hernández-Luna CE, Herrera de los Santos M, Levin L, Rojo-Domínguez A, Romero-Martínez D, Saparrat MCN, Trujillo-Roldán MA, Valdez-Cruz NA. Laccases: structure, function, and potential application in water bioremediation. Microb Cell Fact 2019; 18:200. [PMID: 31727078 PMCID: PMC6854816 DOI: 10.1186/s12934-019-1248-0] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/31/2019] [Indexed: 11/11/2022] Open
Abstract
The global rise in urbanization and industrial activity has led to the production and incorporation of foreign contaminant molecules into ecosystems, distorting them and impacting human and animal health. Physical, chemical, and biological strategies have been adopted to eliminate these contaminants from water bodies under anthropogenic stress. Biotechnological processes involving microorganisms and enzymes have been used for this purpose; specifically, laccases, which are broad spectrum biocatalysts, have been used to degrade several compounds, such as those that can be found in the effluents from industries and hospitals. Laccases have shown high potential in the biotransformation of diverse pollutants using crude enzyme extracts or free enzymes. However, their application in bioremediation and water treatment at a large scale is limited by the complex composition and high salt concentration and pH values of contaminated media that affect protein stability, recovery and recycling. These issues are also associated with operational problems and the necessity of large-scale production of laccase. Hence, more knowledge on the molecular characteristics of water bodies is required to identify and develop new laccases that can be used under complex conditions and to develop novel strategies and processes to achieve their efficient application in treating contaminated water. Recently, stability, efficiency, separation and reuse issues have been overcome by the immobilization of enzymes and development of novel biocatalytic materials. This review provides recent information on laccases from different sources, their structures and biochemical properties, mechanisms of action, and application in the bioremediation and biotransformation of contaminant molecules in water. Moreover, we discuss a series of improvements that have been attempted for better organic solvent tolerance, thermo-tolerance, and operational stability of laccases, as per process requirements.
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Affiliation(s)
- Leticia Arregui
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, C.P. 05348 Mexico City, Mexico
| | - Marcela Ayala
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Chamilpa, 62210 Cuernavaca, Morelos Mexico
| | - Ximena Gómez-Gil
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, Mexico City, CP. 04510 Mexico
| | - Guadalupe Gutiérrez-Soto
- Facultad de Agronomía, Universidad Autónoma de Nuevo León, Francisco Villa, 66059 Colonia Ex hacienda El Canadá, General Escobedo, Nuevo León Mexico
| | - Carlos Eduardo Hernández-Luna
- Laboratorio de Enzimología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Pedro de Alba y Manuel L. Barragán, Cd. Universitaria, 66451 San Nicolás de los Garza, Nuevo León Mexico
| | - Mayra Herrera de los Santos
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, Mexico City, CP. 04510 Mexico
| | - Laura Levin
- Laboratorio de Micología Experimental, DBBE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INMIBO-CONICET, Ciudad Universitaria, Pabellón 2, Piso 4, C1428BGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Arturo Rojo-Domínguez
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, C.P. 05348 Mexico City, Mexico
| | - Daniel Romero-Martínez
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, Mexico City, CP. 04510 Mexico
| | - Mario C. N. Saparrat
- Instituto de Fisiología Vegetal (INFIVE), Universidad Nacional de La Plata (UNLP)-CCT-La Plata-Consejo Nacional de Investigaciones Científicas y técnicas (CONICET), Diag. 113 y 61, 327CC, 1900, La Plata, Argentina
- Instituto de Botánica Spegazzini, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, 53 # 477, 1900, La Plata, Argentina
| | - Mauricio A. Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, Mexico City, CP. 04510 Mexico
| | - Norma A. Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, Mexico City, CP. 04510 Mexico
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Xie M, An F, Wu J, Liu Y, Shi H, Wu R. Meta-omics reveal microbial assortments and key enzymes in bean sauce mash, a traditional fermented soybean product. J Sci Food Agric 2019; 99:6522-6534. [PMID: 31321764 DOI: 10.1002/jsfa.9932] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/20/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Dajiang is fermented based on the metabolism of microbial communities in bean sauce mash, a traditional fermented soybean product in China. The current study first investigated the metaproteome of bean sauce mash. This was followed by an analysis of its biological functions and its microbial community to reveal information about strains and about the expressed proteins to better understand the roles of the microbiota in bean sauce mash. RESULTS The metaproteomic results demonstrated that a total of 1415 microbial protein clusters were expressed mainly by members of the Penicillium and Rhizopus genera and were classified into 100 cellular components, 238 biological processes, and 220 molecular function categories by gene ontology (GO) annotation. Enzymes associated with glycolysis metabolic pathways were also identified. These can provide the energy required for microbial fermentation. Illumina MiSeq sequencing technology results showed that the microorganism communities of bean sauce mash exhibited a high level of diversity. Microbiological analysis demonstrated that the Penicillium, Mucor, Fusarium, Aspergillus, and Rhizopus fungi, and Lactobacillus, Enterococcus, Fructobacillus, Staphylococcus, Carnobacterium genera were predominant 22 samples. CONCLUSION The profiles and insights in the current study are important for research on bean sauce mash and related products in terms of their food microbial ecology. The information obtained from this study will help the development of stable sufu starter cultures with unique sensory qualities. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Mengxi Xie
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Feiyu An
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yiming Liu
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Haishu Shi
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
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Raulo R, Heuson E, Siah A, Phalip V, Froidevaux R. Innovative microscale workflow from fungi cultures to Cell Wall-Degrading Enzyme screening. Microb Biotechnol 2019; 12:1286-1292. [PMID: 31006173 PMCID: PMC6801129 DOI: 10.1111/1751-7915.13405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/17/2019] [Indexed: 11/30/2022] Open
Abstract
This study aimed at developing a complete miniaturized high-throughput screening workflow for the evaluation of the Cell Wall-Degrading Enzyme (CWDE) activities produced by any fungal strain directly cultivated on raw feedstock in a submerged manner. In this study, wheat straw was selected as model substrate as it represents an important carbon source but yet poorly valorised to yield high added value products. Fungi were grown in a microbioreactor in a high-throughput (HT) way to replace the fastidious shaking flask cultivations. Both approaches were compared in order to validate our new methodology. The range of CWDE activities produced from the cultures was assayed using AZO-died and pNP-linked substrates in an SBS plate format using a Biomek FXp pipetting platform. As highlighted in this study, it was shown that the CWDE activities gathered from the microbioreactor cultivations were similar or higher to those obtained from shake flasks cultures, with a lower standard deviation on the measured values, making this new method much faster than the traditional one and suitable for HT CWDE production thanks to its pipetting platform compatibility. Also, the results showed that the enzymatic activities measured were the same when doing the assay manually or using the automated method.
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Affiliation(s)
- Roxane Raulo
- EA 7394 – ICV – Institut Charles ViolletteUniv. Lille 1ISAINRAUniv. ArtoisUniv. Littoral Côte d'OpaleF‐59000LilleFrance
| | - Egon Heuson
- EA 7394 – ICV – Institut Charles ViolletteUniv. Lille 1ISAINRAUniv. ArtoisUniv. Littoral Côte d'OpaleF‐59000LilleFrance
| | - Ali Siah
- EA 7394 – ICV – Institut Charles ViolletteUniv. Lille 1ISAINRAUniv. ArtoisUniv. Littoral Côte d'OpaleF‐59000LilleFrance
| | - Vincent Phalip
- EA 7394 – ICV – Institut Charles ViolletteUniv. Lille 1ISAINRAUniv. ArtoisUniv. Littoral Côte d'OpaleF‐59000LilleFrance
| | - Renato Froidevaux
- EA 7394 – ICV – Institut Charles ViolletteUniv. Lille 1ISAINRAUniv. ArtoisUniv. Littoral Côte d'OpaleF‐59000LilleFrance
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Wang X, Qin X, Hao Z, Luo H, Yao B, Su X. Degradation of Four Major Mycotoxins by Eight Manganese Peroxidases in Presence of a Dicarboxylic Acid. Toxins (Basel) 2019; 11:E566. [PMID: 31569657 PMCID: PMC6833064 DOI: 10.3390/toxins11100566] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/18/2019] [Accepted: 09/26/2019] [Indexed: 01/05/2023] Open
Abstract
Enzymatic treatment is an attractive method for mycotoxin detoxification, which ideally prefers the use of one or a few enzymes. However, this is challenged by the diverse structures and co-contamination of multiple mycotoxins in food and feed. Lignin-degrading fungi have been discovered to detoxify organics including mycotoxins. Manganese peroxidase (MnP) is a major enzyme responsible for lignin oxidative depolymerization in such fungi. Here, we demonstrate that eight MnPs from different lignocellulose-degrading fungi (five from Irpex lacteus, one from Phanerochaete chrysosporium, one from Ceriporiopsis subvermispora, and another from Nematoloma frowardii) could all degrade four major mycotoxins (aflatoxin B1, AFB1; zearalenone, ZEN; deoxynivalenol, DON; fumonisin B1, FB1) only in the presence of a dicarboxylic acid malonate, in which free radicals play an important role. The I. lacteus and C. subvermispora MnPs behaved similarly in mycotoxins transformation, outperforming the P. chrysosporium and N. frowardii MnPs. The large evolutionary diversity of these MnPs suggests that mycotoxin degradation tends to be a common feature shared by MnPs. MnP can, therefore, serve as a candidate enzyme for the degradation of multiple mycotoxins in food and feed if careful surveillance of the residual toxicity of degradation products is properly carried out.
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Affiliation(s)
- Xiaolu Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xing Qin
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Zhenzhen Hao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Abstract
NAD kinase (NADK) is the sole enzyme that phosphorylates nicotinamide adenine dinucleotide (NAD+/NADH) into NADP+/NADPH, which provides the chemical reducing power in anabolic (biosynthetic) pathways. While prokaryotes typically encode a single NADK, eukaryotes encode multiple NADKs. How these different NADK genes are all related to each other and those of prokaryotes is not known. Here we conduct phylogenetic analysis of NADK genes and identify major clade-defining patterns of NADK evolution. First, almost all eukaryotic NADK genes belong to one of two ancient eukaryotic sister clades corresponding to cytosolic (“cyto”) and mitochondrial (“mito”) clades. Secondly, we find that the cyto-clade NADK gene is duplicated in connection with loss of the mito-clade NADK gene in several eukaryotic clades or with acquisition of plastids in Archaeplastida. Thirdly, we find that horizontal gene transfers from proteobacteria have replaced mitochondrial NADK genes in only a few rare cases. Last, we find that the eukaryotic cyto and mito paralogs are unrelated to independent duplications that occurred in sporulating bacteria, once in mycelial Actinobacteria and once in aerobic endospore-forming Firmicutes. Altogether these findings show that the eukaryotic NADK gene repertoire is ancient and evolves episodically with major evolutionary transitions.
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Affiliation(s)
- Oliver Vickman
- Department of Biology, University of Iowa, Iowa City, IA, United States of America
| | - Albert Erives
- Department of Biology, University of Iowa, Iowa City, IA, United States of America
- * E-mail:
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Lange L, Barrett K, Pilgaard B, Gleason F, Tsang A. Enzymes of early-diverging, zoosporic fungi. Appl Microbiol Biotechnol 2019; 103:6885-6902. [PMID: 31309267 PMCID: PMC6690862 DOI: 10.1007/s00253-019-09983-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/26/2022]
Abstract
The secretome, the complement of extracellular proteins, is a reflection of the interaction of an organism with its host or substrate, thus a determining factor for the organism’s fitness and competitiveness. Hence, the secretome impacts speciation and organismal evolution. The zoosporic Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, and Cryptomycota represent the earliest diverging lineages of the Fungal Kingdom. The review describes the enzyme compositions of these zoosporic fungi, underscoring the enzymes involved in biomass degradation. The review connects the lifestyle and substrate affinities of the zoosporic fungi to the secretome composition by examining both classical phenotypic investigations and molecular/genomic-based studies. The carbohydrate-active enzyme profiles of 19 genome-sequenced species are summarized. Emphasis is given to recent advances in understanding the functional role of rumen fungi, the basis for the devastating chytridiomycosis, and the structure of fungal cellulosome. The approach taken by the review enables comparison of the secretome enzyme composition of anaerobic versus aerobic early-diverging fungi and comparison of enzyme portfolio of specialized parasites, pathogens, and saprotrophs. Early-diverging fungi digest most major types of biopolymers: cellulose, hemicellulose, pectin, chitin, and keratin. It is thus to be expected that early-diverging fungi in its entirety represents a rich and diverse pool of secreted, metabolic enzymes. The review presents the methods used for enzyme discovery, the diversity of enzymes found, the status and outlook for recombinant production, and the potential for applications. Comparative studies on the composition of secretome enzymes of early-diverging fungi would contribute to unraveling the basal lineages of fungi.
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Affiliation(s)
- Lene Lange
- Bioeconomy, Research & Advisory, Karensgade 5, Valby, DK-2500, Copenhagen, Denmark.
| | - Kristian Barrett
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800, Kgs. Lyngby, Denmark
| | - Bo Pilgaard
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800, Kgs. Lyngby, Denmark
| | - Frank Gleason
- School of Life and Environmental Sciences, University of Sydney, Sydney, 2006, Australia
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, H4B1R6, Canada
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45
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Rohman A, Dijkstra BW. The role and mechanism of microbial 3-ketosteroid Δ 1-dehydrogenases in steroid breakdown. J Steroid Biochem Mol Biol 2019; 191:105366. [PMID: 30991094 DOI: 10.1016/j.jsbmb.2019.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/26/2019] [Accepted: 04/12/2019] [Indexed: 02/08/2023]
Abstract
3-Ketosteroid Δ1-dehydrogenases are FAD-dependent enzymes that catalyze the introduction of a double bond between the C1 and C2 atoms of the A-ring of 3-ketosteroid substrates. These enzymes are found in a large variety of microorganisms, especially in bacteria belonging to the phylum Actinobacteria. They play a critical role in the early steps of the degradation of the steroid core. 3-Ketosteroid Δ1-dehydrogenases are of particular interest for the etiology of some infectious diseases, for the production of starting materials for the pharmaceutical industry, and for environmental bioremediation applications. Here we summarize and discuss the biochemical and enzymological properties of these enzymes, their microbial sources, and their natural diversity. The three-dimensional structure of a 3-ketosteroid Δ1-dehydrogenase in connection with the enzyme mechanism is highlighted.
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Affiliation(s)
- Ali Rohman
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia; The Laboratory of Proteomics, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; The Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Bauke W Dijkstra
- The Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands.
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Malafatti-Picca L, de Barros Chaves MR, de Castro AM, Valoni É, de Oliveira VM, Marsaioli AJ, de Franceschi de Angelis D, Attili-Angelis D. Hydrocarbon-associated substrates reveal promising fungi for poly (ethylene terephthalate) (PET) depolymerization. Braz J Microbiol 2019; 50:633-648. [PMID: 31175657 PMCID: PMC6863199 DOI: 10.1007/s42770-019-00093-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 04/03/2019] [Indexed: 12/11/2022] Open
Abstract
Recalcitrant characteristics and insolubility in water make the disposal of synthetic polymers a great environmental problem to be faced by modern society. Strategies towards the recycling of post-consumer polymers, like poly (ethylene terephthalate, PET) degradation/depolymerization have been studied but still need improvement. To contribute with this purpose, 100 fungal strains from hydrocarbon-associated environments were screened for lipase and esterase activities by plate assays and high-throughput screening (HTS), using short- and long-chain fluorogenic probes. Nine isolates were selected for their outstanding hydrolytic activity, comprising the genera Microsphaeropsis, Mucor, Trichoderma, Westerdykella, and Pycnidiophora. Two strains of Microsphaeropsis arundinis were able to convert 2-3% of PET nanoparticle into terephthalic acid, and when cultured with two kinds of commercial PET bottle fragments, they also promoted weight loss, surface and chemical changes, increased lipase and esterase activities, and led to PET depolymerization with release of terephthalic acid at concentrations above 20.0 ppm and other oligomers over 0.6 ppm. The results corroborate that hydrocarbon-associated areas are important source of microorganisms for application in environmental technologies, and the sources investigated revealed important strains with potential for PET depolymerization.
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Affiliation(s)
- Lusiane Malafatti-Picca
- Environmental Studies Center, UNESP, São Paulo State University, 24-A Av., 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil.
| | | | - Aline Machado de Castro
- Biotechnology Department, R&D Center, PETROBRAS, Av. Horácio Macedo, 950, Ilha do Fundão, Rio de Janeiro, RJ, 21941-915, Brazil
| | - Érika Valoni
- Biotechnology Department, R&D Center, PETROBRAS, Av. Horácio Macedo, 950, Ilha do Fundão, Rio de Janeiro, RJ, 21941-915, Brazil
| | - Valéria Maia de Oliveira
- Division of Microbial Resources, CPQBA - State University of Campinas, Alexandre Cazellato Str., 999, Paulínia, SP, 13148-218, Brazil
| | - Anita Jocelyne Marsaioli
- Institute of Chemistry, State University of Campinas, PO Box 6154, Campinas, SP, 13084-971, Brazil
| | - Dejanira de Franceschi de Angelis
- Department of Biochemistry and Microbiology, UNESP, São Paulo State University, 24-A Av., 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Derlene Attili-Angelis
- Environmental Studies Center, UNESP, São Paulo State University, 24-A Av., 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
- Division of Microbial Resources, CPQBA - State University of Campinas, Alexandre Cazellato Str., 999, Paulínia, SP, 13148-218, Brazil
- Department of Biochemistry and Microbiology, UNESP, São Paulo State University, 24-A Av., 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
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47
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Shrestha P, Zhou XR, Vibhakaran Pillai S, Petrie J, de Feyter R, Singh S. Comparison of the Substrate Preferences of ω3 Fatty Acid Desaturases for Long Chain Polyunsaturated Fatty Acids. Int J Mol Sci 2019; 20:E3058. [PMID: 31234541 PMCID: PMC6627408 DOI: 10.3390/ijms20123058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 11/16/2022] Open
Abstract
Omega-3 long chain polyunsaturated fatty acids (ω3 LC-PUFAs) such as eicosapentaenoic acid (EPA; 20:5ω3) and docosahexaenoic acid (DHA; 22:6ω3) are important fatty acids for human health. These ω3 LC-PUFAs are produced from their ω3 precursors by a set of desaturases and elongases involved in the biosynthesis pathway and are also converted from ω6 LC-PUFA by omega-3 desaturases (ω3Ds). Here, we have investigated eight ω3-desaturases obtained from a cyanobacterium, plants, fungi and a lower animal species for their activities and compared their specificities for various C18, C20 and C22 ω6 PUFA substrates by transiently expressing them in Nicotiana benthamiana leaves. Our results showed hitherto unreported activity of many of the ω3Ds on ω6 LC-PUFA substrates leading to their conversion to ω3 LC-PUFAs. This discovery could be important in the engineering of EPA and DHA in heterologous hosts.
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Affiliation(s)
| | - Xue-Rong Zhou
- CSIRO Agriculture & Food, Canberra, ACT 2601, Australia.
| | | | - James Petrie
- CSIRO Agriculture & Food, Canberra, ACT 2601, Australia.
| | | | - Surinder Singh
- CSIRO Agriculture & Food, Canberra, ACT 2601, Australia.
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Zhao SF, Chi Z, Liu GL, Hu Z, Wu LF, Chi ZM. Biosynthesis of some organic acids and lipids in industrially important microorganisms is promoted by pyruvate carboxylases. J Biosci 2019; 44:47. [PMID: 31180060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pyruvate carboxylase (Pyc) catalyzes formation of oxaloacetic acid from pyruvic acid by fixing one mole of CO2. Many evidences have confirmed that biosynthesis of some different kinds of organic acids and intracellular and extracellular lipids is driven by Pyc and over-expression of the PYC gene in the industrial microorganisms can promote production of the different kinds of organic acids and intracellular and extracellular lipids. Therefore, the Pyc from different sources is regarded as a key enzyme in microbial biotechnology and is an important target for metabolic engineering of the industrial microbial strains. However, very little is known about the native Pycs and their functions and regulation in the industrial microorganisms.
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Affiliation(s)
- Shou-Feng Zhao
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao 266003, People's Republic of China
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Snyman C, Theron LW, Divol B. Understanding the regulation of extracellular protease gene expression in fungi: a key step towards their biotechnological applications. Appl Microbiol Biotechnol 2019; 103:5517-5532. [PMID: 31129742 DOI: 10.1007/s00253-019-09902-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 12/20/2022]
Abstract
The secretion of proteases by certain species of yeast and filamentous fungi is of importance not only for their biological function and survival, but also for their biotechnological application to various processes in the food, beverage, and bioprocessing industries. A key step towards understanding the role that these organisms play in their environment, and how their protease-secreting ability may be optimally utilised through industrial applications, involves an evaluation of those factors which influence protease production. The objective of this review is to provide an overview of the findings from investigations directed at elucidating the regulatory mechanisms underlying extracellular protease secretion in yeast and filamentous fungi, and the environmental stimuli that elicit these responses. The influence of nitrogen-, carbon-, and sulphur-containing compounds, as well as proteins, temperature, and pH, on extracellular protease regulation, which is frequently exerted at the transcriptional level, is discussed in particular depth. Protease-secreting organisms of biotechnological interest are also presented in this context, in an effort to explore the areas of industrial significance that could possibly benefit from such knowledge. In this way, the establishment of a platform of existing knowledge regarding fungal protease regulation is attempted, with the particular goal of aiding in the practical application of these organisms to processes that require secretion of this enzyme.
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Affiliation(s)
- C Snyman
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Private Bag X1, Matieland, 7602, South Africa
| | - L W Theron
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Private Bag X1, Matieland, 7602, South Africa
| | - B Divol
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Private Bag X1, Matieland, 7602, South Africa.
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50
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Graham EB, Yang F, Bell S, Hofmockel KS. High Genetic Potential for Proteolytic Decomposition in Northern Peatland Ecosystems. Appl Environ Microbiol 2019; 85:e02851-18. [PMID: 30850433 PMCID: PMC6498154 DOI: 10.1128/aem.02851-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/13/2019] [Indexed: 11/28/2022] Open
Abstract
Nitrogen (N) is a scarce nutrient commonly limiting primary productivity. Microbial decomposition of complex carbon (C) into small organic molecules (e.g., free amino acids) has been suggested to supplement biologically fixed N in northern peatlands. We evaluated the microbial (fungal, bacterial, and archaeal) genetic potential for organic N depolymerization in peatlands at Marcell Experimental Forest (MEF) in northern Minnesota. We used guided gene assembly to examine the abundance and diversity of protease genes and further compared them to those of N fixation (nifH) genes in shotgun metagenomic data collected across depths and in two distinct peatland environments (bogs and fens). Microbial protease genes greatly outnumbered nifH genes, with the most abundant genes (archaeal M1 and bacterial trypsin [S01]) each containing more sequences than all sequences attributed to nifH Bacterial protease gene assemblies were diverse and abundant across depth profiles, indicating a role for bacteria in releasing free amino acids from peptides through depolymerization of older organic material and contrasting with the paradigm of fungal dominance in depolymerization in forest soils. Although protease gene assemblies for fungi were much less abundant overall than those for bacteria, fungi were prevalent in surface samples and therefore may be vital in degrading large soil polymers from fresh plant inputs during the early stage of depolymerization. In total, we demonstrate that depolymerization enzymes from a diverse suite of microorganisms, including understudied bacterial and archaeal lineages, are prevalent within northern peatlands and likely to influence C and N cycling.IMPORTANCE Nitrogen (N) is a common limitation on primary productivity, and its source remains unresolved in northern peatlands that are vulnerable to environmental change. Decomposition of complex organic matter into free amino acids has been proposed as an important N source, but the genetic potential of microorganisms mediating this process has not been examined. Such information can inform possible responses of northern peatlands to environmental change. We show high genetic potential for microbial production of free amino acids across a range of microbial guilds in northern peatlands. In particular, the abundance and diversity of bacterial genes encoding proteolytic activity suggest a predominant role for bacteria in regulating productivity and contrasts with a paradigm of fungal dominance of organic N decomposition. Our results expand our current understanding of coupled carbon and nitrogen cycles in northern peatlands and indicate that understudied bacterial and archaeal lineages may be central in this ecosystem's response to environmental change.
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Affiliation(s)
- Emily B Graham
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Fan Yang
- Department of Agricultural & Biosystems Engineering, Iowa State University, Ames, Iowa, USA
| | - Sheryl Bell
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kirsten S Hofmockel
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA
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