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Fingerhut MA, Henrich L, Lauber C, Broel N, Ghezellou P, Karrer D, Spengler B, Langfelder K, Stressler T, Zorn H, Gand M. Characterization of a GDS(L)-like hydrolase from Pleurotus sapidus with an unusual SGNH motif. AMB Express 2024; 14:98. [PMID: 39225819 PMCID: PMC11372007 DOI: 10.1186/s13568-024-01752-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
The GDS(L)-like lipase from the Basidiomycota Pleurotus sapidus (PSA_Lip) was heterologously expressed using Trichoderma reesei with an activity of 350 U L-1. The isoelectric point of 5.0 was determined by isoelectric focusing. The novel PSA_Lip showed only 23.8-25.1%, 25.5%, 26.6% and 28.4% identity to the previously characterized GDSL-like enzymes phospholipase, plant lipase, acetylcholinesterase and acetylxylan esterase, from the carbohydrate esterase family 16, respectively. Therefore, the enzyme was purified from the culture supernatant and the catalytic properties and the substrate specificity of the enzyme were investigated using different assays to reveal its potential function. While no phospholipase, acetylcholinesterase and acetylxylan esterase activities were detected, studies on the hydrolysis of ferulic acid methyl ester (~ 8.3%) and feruloylated carbohydrate 5-O-transferuloyl-arabino-furanose (~ 0.8%) showed low conversions of these substrates. By investigating the hydrolytic activity towards p-nitrophenyl-(pNP)-esters with various chain-lengths, the highest activity was determined for medium chain-length pNP-octanoate at 65 °C and a pH value of 8, while almost no activity was detected for pNP-hexanoate. The enzyme is highly stable when stored at pH 10 and 4 °C for at least 7 days. Moreover, using consensus sequence analysis and homology modeling, we could demonstrate that the PSA_Lip does not contain the usual SGNH residues in the actives site, which are usually present in GDS(L)-like enzymes.
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Affiliation(s)
- Miriam A Fingerhut
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Lea Henrich
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Christiane Lauber
- Hochschule Fresenius - University of Applied Sciences, 65510, Idstein, Germany
| | - Niklas Broel
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Parviz Ghezellou
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Dominik Karrer
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Kim Langfelder
- AB Enzymes GmbH, Feldbergstrasse 78, 64293, Darmstadt, Germany
| | - Timo Stressler
- AB Enzymes GmbH, Feldbergstrasse 78, 64293, Darmstadt, Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392, Giessen, Germany
| | - Martin Gand
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany.
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Abstract
Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular ‘digestive enzymes’ whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.
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Bürger F, Koch M, Fraatz MA, Omarini AB, Berger RG, Zorn H. Production of an Anise- and Woodruff-like Aroma by Monokaryotic Strains of Pleurotus sapidus Grown on Citrus Side Streams. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030651. [PMID: 35163915 PMCID: PMC8838675 DOI: 10.3390/molecules27030651] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/16/2022]
Abstract
The production of natural flavors by means of microorganisms is of great interest for the food and flavor industry, and by-products of the agro-industry are particularly suitable as substrates. In the present study, Citrus side streams were fermented using monokaryotic strains of the fungus Pleurotus sapidus. Some of the cultures exhibited a pleasant smell, reminiscent of woodruff and anise, as well as herbaceous notes. To evaluate the composition of the overall aroma, liquid/liquid extracts of submerged cultures of a selected monokaryon were prepared, and the volatiles were isolated via solvent-assisted flavor evaporation. Aroma extract dilution analyses revealed p-anisaldehyde (sweetish, anisic- and woodruff-like) with a flavor dilution factor of 218 as a character impact compound. The coconut-like, herbaceous, and sweetish smelling acyloin identified as (2S)-hydroxy-1-(4-methoxyphenyl)-1-propanone also contributed to the overall aroma and was described as an aroma-active substance with an odor threshold in air of 0.2 ng L−1 to 2.4 ng L−1 for the first time. Supplementation of the culture medium with isotopically substituted l-tyrosine elucidated this phenolic amino acid as precursor of p-anisaldehyde as well as of (2S)-hydroxy-1-(4-methoxyphenyl)-1-propanone. Chiral analysis via HPLC revealed an enantiomeric excess of 97% for the isolated product produced by P. sapidus.
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Affiliation(s)
- Friederike Bürger
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany; (F.B.); (M.K.); (M.A.F.)
| | - Maximilian Koch
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany; (F.B.); (M.K.); (M.A.F.)
| | - Marco A. Fraatz
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany; (F.B.); (M.K.); (M.A.F.)
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Alejandra B. Omarini
- CONICET Asociación para el Desarrollo de Villa Elisa y Zona Héctor de Elia 1247, Villa Elisa E3265, Entre Ríos, Argentina;
- Institute of Food Chemistry, Leibniz University Hannover, Callinstrasse 5, 30167 Hannover, Germany;
| | - Ralf G. Berger
- Institute of Food Chemistry, Leibniz University Hannover, Callinstrasse 5, 30167 Hannover, Germany;
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany; (F.B.); (M.K.); (M.A.F.)
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
- Correspondence: ; Tel.: +49-(0)-641-99-349-00
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Scope and limitations of biocatalytic carbonyl reduction with white-rot fungi. Bioorg Chem 2021; 108:104651. [PMID: 33508677 DOI: 10.1016/j.bioorg.2021.104651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/07/2021] [Indexed: 11/24/2022]
Abstract
The reductive activity of various basidiomycetous fungi towards carbonyl compounds was screened on an analytical level. Some strains displayed high reductive activities toward aromatic carbonyls and aliphatic ketones. Utilizing growing whole-cell cultures of Dichomitus albidofuscus, the reactions were up-scaled to a preparative level in an aqueous system. The reactions showed excellent selectivities and gave the respective alcohols in high yields. Carboxylic acids were also reduced to aldehydes and alcohols under the same conditions. In particular, benzoic, vanillic, ferulic, and p-coumaric acid were reduced to benzyl alcohol, vanillin, dihydroconiferyl alcohol and 1-hydroxy-3-(4-hydroxyphenyl)propan, respectively.
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Trapp T, Kirchner T, Birk F, Fraatz MA, Zorn H. Biosynthesis of Stereoisomers of Dill Ether and Wine Lactone by Pleurotus sapidus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13400-13411. [PMID: 30813719 DOI: 10.1021/acs.jafc.8b07263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The white-rot fungus Pleurotus sapidus (PSA) biosynthesizes the bicyclic monoterpenoids 3,6-dimethyl-2,3,3a,4,5,7a-hexahydrobenzofuran (dill ether) (1) and 3,6-dimethyl-3a,4,5,7a-tetrahydro-1-benzofuran-2(3H)-one (wine lactone) (2). Submerged cultures grown in different media were analyzed by gas chromatography-mass spectrometry. The stereochemistry of the formed isomers was elucidated by comparing their retention indices to those of reference compounds by enantioselective multidimensional gas chromatography. The basidiomycete produced the rare (3R,3aR,7aS) and (3S,3aR,7aS) stereoisomers of dill ether and wine lactone. Kinetic analyses of the volatilome and bioprocess parameters revealed that the biosynthesis of the bicyclic monoterpenoids correlated with the availability of the primary carbon source glucose. Spiking the media with 13C-labeled glucose demonstrated that the compounds were produced de novo. Supplementation studies i.a. with isotopically labeled substrates further identified limonene and p-menth-1-en-9-ol as intermediate compounds in the fungal pathways. PSA was able to biotransform all enantiomeric forms of the latter compounds to the respective isomers of dill ether and wine lactone.
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Affiliation(s)
- Tobias Trapp
- Institute of Food Chemistry and Food Biotechnology , Justus Liebig University Giessen , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Tabea Kirchner
- Institute of Food Chemistry and Food Biotechnology , Justus Liebig University Giessen , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Florian Birk
- Institute of Food Chemistry and Food Biotechnology , Justus Liebig University Giessen , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Marco Alexander Fraatz
- Institute of Food Chemistry and Food Biotechnology , Justus Liebig University Giessen , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology , Justus Liebig University Giessen , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology , Winchester Straße 2 , 35394 Giessen , Germany
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Taupp DE, Nimtz M, Berger RG, Zorn H. Stress response of Nidula niveo-tomentosa to UV-A light. Mycologia 2017; 100:529-38. [DOI: 10.3852/07-179r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Daniela E. Taupp
- Zentrum Angewandte Chemie, Institut für, Lebensmittelchemie der Leibniz Universität Hannover, Wunstorfer Straße 14, D-30453 Hannover, Germany
| | - Manfred Nimtz
- Helmholtz-Zentrum für Infektionsforschung, Abteilung, Biophysikalische Analytik, Inhoffenstr. 7, D-38124, Braunschweig, Germany
| | - Ralf G. Berger
- Zentrum Angewandte Chemie, Institut für, Lebensmittelchemie der Leibniz Universität Hannover, Wunstorfer Straße 14, D-30453 Hannover, Germany
| | - Holger Zorn
- AG Technische Biochemie, Universität Dortmund, Emil-Figge-Straße 68, D-44221 Dortmund, Germany
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Vasina DV, Pavlov AR, Koroleva OV. Extracellular proteins of Trametes hirsuta st. 072 induced by copper ions and a lignocellulose substrate. BMC Microbiol 2016; 16:106. [PMID: 27296712 PMCID: PMC4906887 DOI: 10.1186/s12866-016-0729-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 06/06/2016] [Indexed: 11/10/2022] Open
Abstract
Background Fungi are organisms with the highest natural capacity to degrade lignocellulose substrates, which is enabled by complex systems of extracellular enzymes, whose expression and secretion depend on the characteristics of substrates and the environment. Results This study reports a secretome analysis for white-rot basidiomycete Trametes hirsuta cultivated on a synthetic media and a lignocellulose substrate. We demonstrate that T. hirsuta st. 072 produces multiple extracellular ligninolytic, cellulolytic, hemicellulolytic, peroxide generating, and proteolytic enzymes, as well as cerato-platanins. In contrast to other white rot species described earlier, which mostly secreted glucanases and mannosidases in response to the presence of the lignocellulose substrate, T. hirsuta expressed a spectrum of extracellular cellulolytic enzymes containing predominantly cellobiases and xylanases. As proteomic analysis could not detect lignin peroxidase (LiP) among the secreted lignin degrading enzymes, we attributed the observed extracellular LiP - like activity to the expressed versatile peroxidase (VP). An accessory enzyme, glyoxal oxidase, was found among the proteins secreted in the media during submerged cultivation of T. hirsuta both in the presence and in the absence of copper. However, aryl-alcohol oxidase (AAO) was not identified, despite the presence of AAO enzymatic activity secreted by the fungus. The spectra of the expressed enzymes dramatically changed depending on the growth conditions. Transfer from submerged cultivation to surface cultivation with the lignocellulose substrate switched off expression of exo-β-1,3-glucanase and α-amylase and turned on secretion of endo-β-1,3-glucanase and a range of glycosidases. In addition, an aspartic peptidase started being expressed instead of family S53 protease. For the first time, we report production of cerato-platanin proteins by Trametes species. The secretion of cerato-platanins was observed only in response to contact with lignocellulose, thus indicating a specific role of these proteins in degradation of the lignocellulose substrates. Conclusions Our results suggest a sequential mechanism of natural substrate degradation by T. hirsuta, in which the fungus produces different sets of enzymes to digest all main components of the substrate during cultivation. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0729-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria V Vasina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia.
| | - Andrey R Pavlov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia
| | - Olga V Koroleva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia
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Al-Obaidi JR. Proteomics of edible mushrooms: A mini-review. Electrophoresis 2016; 37:1257-63. [PMID: 26891916 DOI: 10.1002/elps.201600031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/22/2016] [Accepted: 02/14/2016] [Indexed: 12/12/2022]
Abstract
Mushrooms are considered an important food for their traditionally famous nutritional and medicinal values, although much information about their potential at the molecular level is unfortunately unknown. Edible mushrooms include fungi that are either collected wild or cultivated. Many important species are difficult to cultivate but attempts have been made with varying degrees of success, with the results showing unsatisfactory economical cultivation methods. Recently, proteomic analysis has been developed as a powerful tool to study the protein content of fungi, particularly basidiomycetes. This mini-review article highlights the contribution of proteomics platforms to the study of edible mushrooms, focusing on the molecular mechanisms involved in developmental stages. This includes extracellular and cytoplasmic effector proteins that have potential or are involved in the synthesis of anticancer, antidiabetic, antioxidant, and antibiotic, in blood pressure control, in the supply of vitamins and minerals, and in other responses to environmental changes. The contribution of different proteomics techniques including classical and more advanced techniques is also highlighted.
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Affiliation(s)
- Jameel R Al-Obaidi
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, 43400 Serdang, Selangor, Malaysia
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Quecine MC, Leite TF, Bini AP, Regiani T, Franceschini LM, Budzinski IGF, Marques FG, Labate MTV, Guidetti-Gonzalez S, Moon DH, Labate CA. Label-Free Quantitative Proteomic Analysis of Puccinia psidii Uredospores Reveals Differences of Fungal Populations Infecting Eucalyptus and Guava. PLoS One 2016; 11:e0145343. [PMID: 26731728 PMCID: PMC4701387 DOI: 10.1371/journal.pone.0145343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 12/02/2015] [Indexed: 12/21/2022] Open
Abstract
Puccinia psidii sensu lato (s.l.) is the causal agent of eucalyptus and guava rust, but it also attacks a wide range of plant species from the myrtle family, resulting in a significant genetic and physiological variability among populations accessed from different hosts. The uredospores are crucial to P. psidii dissemination in the field. Although they are important for the fungal pathogenesis, their molecular characterization has been poorly studied. In this work, we report the first in-depth proteomic analysis of P. psidii s.l. uredospores from two contrasting populations: guava fruits (PpGuava) and eucalyptus leaves (PpEucalyptus). NanoUPLC-MSE was used to generate peptide spectra that were matched to the UniProt Puccinia genera sequences (UniProt database) resulting in the first proteomic analysis of the phytopathogenic fungus P. psidii. Three hundred and fourty proteins were detected and quantified using Label free proteomics. A significant number of unique proteins were found for each sample, others were significantly more or less abundant, according to the fungal populations. In PpGuava population, many proteins correlated with fungal virulence, such as malate dehydrogenase, proteossomes subunits, enolases and others were increased. On the other hand, PpEucalyptus proteins involved in biogenesis, protein folding and translocation were increased, supporting the physiological variability of the fungal populations according to their protein reservoirs and specific host interaction strategies.
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Affiliation(s)
- Maria Carolina Quecine
- Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba -SP, Brazil
| | - Thiago Falda Leite
- Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba -SP, Brazil
| | - Andressa Peres Bini
- Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba -SP, Brazil
| | - Thais Regiani
- Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba -SP, Brazil
| | - Lívia Maria Franceschini
- Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba -SP, Brazil
| | | | - Felipe Garbelini Marques
- Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba -SP, Brazil
| | - Mônica Teresa Veneziano Labate
- Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba -SP, Brazil
| | - Simone Guidetti-Gonzalez
- Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba -SP, Brazil
| | - David Henry Moon
- Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba -SP, Brazil
| | - Carlos Alberto Labate
- Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba -SP, Brazil
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Fernández-Fueyo E, Ruiz-Dueñas FJ, López-Lucendo MF, Pérez-Boada M, Rencoret J, Gutiérrez A, Pisabarro AG, Ramírez L, Martínez AT. A secretomic view of woody and nonwoody lignocellulose degradation by Pleurotus ostreatus. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:49. [PMID: 26933449 PMCID: PMC4772462 DOI: 10.1186/s13068-016-0462-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/11/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Pleurotus ostreatus is the second edible mushroom worldwide, and a model fungus for delignification applications, with the advantage of growing on woody and nonwoody feedstocks. Its sequenced genome is available, and this gave us the opportunity to perform proteomic studies to identify the enzymes overproduced in lignocellulose cultures. RESULTS Monokaryotic P. ostreatus (PC9) was grown with poplar wood or wheat straw as the sole C/N source and the extracellular proteins were analyzed, together with those from glucose medium. Using nano-liquid chromatography coupled to tandem mass spectrometry of whole-protein hydrolyzate, over five-hundred proteins were identified. Thirty-four percent were unique of the straw cultures, while only 15 and 6 % were unique of the glucose and poplar cultures, respectively (20 % were produced under the three conditions, and additional 19 % were shared by the two lignocellulose cultures). Semi-quantitative analysis showed oxidoreductases as the main protein type both in the poplar (39 % total abundance) and straw (31 %) secretomes, while carbohydrate-active enzymes (CAZys) were only slightly overproduced (14-16 %). Laccase 10 (LACC10) was the main protein in the two lignocellulose secretomes (10-14 %) and, together with LACC2, LACC9, LACC6, versatile peroxidase 1 (VP1), and manganese peroxidase 3 (MnP3), were strongly overproduced in the lignocellulose cultures. Seven CAZys were also among the top-50 proteins, but only CE16 acetylesterase was overproduced on lignocellulose. When the woody and nonwoody secretomes were compared, GH1 and GH3 β-glycosidases were more abundant on poplar and straw, respectively and, among less abundant proteins, VP2 was overproduced on straw, while VP3 was only found on poplar. The treated lignocellulosic substrates were analyzed by two-dimensional nuclear magnetic resonance (2D NMR), and a decrease of lignin relative to carbohydrate signals was observed, together with the disappearance of some minor lignin substructures, and an increase of sugar reducing ends. CONCLUSIONS Oxidoreductases are strongly induced when P. ostreatus grows on woody and nonwoody lignocellulosic substrates. One laccase occupied the first position in both secretomes, and three more were overproduced together with one VP and one MnP, suggesting an important role in lignocellulose degradation. Preferential removal of lignin vs carbohydrates was shown by 2D NMR, in agreement with the above secretomic results.
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Affiliation(s)
- Elena Fernández-Fueyo
- />Department of Biotechnology, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands
| | | | | | - Marta Pérez-Boada
- />Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jorge Rencoret
- />Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, PO Box 1052, 41080 Seville, Spain
| | - Ana Gutiérrez
- />Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, PO Box 1052, 41080 Seville, Spain
| | - Antonio G. Pisabarro
- />Department of Agrarian Production, Universidad Pública de Navarra, 31006, Pamplona, Spain
| | - Lucía Ramírez
- />Department of Agrarian Production, Universidad Pública de Navarra, 31006, Pamplona, Spain
| | - Angel T. Martínez
- />Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Xie C, Luo W, Li Z, Yan L, Zhu Z, Wang J, Hu Z, Peng Y. Secretome analysis of Pleurotus eryngii reveals enzymatic composition for ramie stalk degradation. Electrophoresis 2015; 37:310-20. [PMID: 26525014 DOI: 10.1002/elps.201500312] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 08/27/2015] [Accepted: 10/18/2015] [Indexed: 11/07/2022]
Abstract
Pleurotus eryngii (P. eryngii) can secrete large amount of hydrolytic and oxidative enzymes to degrade lignocellulosic biomass. In spite of several researches on the individual lignolytic enzymes, a direct deconstruction of lignocellulose by enzyme mixture is not yet possible. Identifying more high-performance enzymes or enzyme complexes will lead to efficient in vitro lignocelluloses degradation. In this report, secretomic analysis was used to search for the new or interesting enzymes for lignocellulose degradation. Besides, the utilization ability of P. eryngii to ramie stalk substrate was evaluated from the degradation of cellulose, hemicellulose, and lignin in medium and six extracellular enzymes activities during different growth stages were discussed. The results showed that a high biological efficiency of 71% was obtained; cellulose, hemicelluloses, and lignin decomposition rates of P. eryngii were 29.2, 26.0, and 51.2%, respectively. Enzyme activity showed that carboxymethyl cellulase, xylanase, laccase, and peroxidase activity peaks appeared at the primordial initiation stage. In addition, we profiled a global view of the secretome of P. eryngii cultivated in ramie stalk media to understand the mechanism behind lignocellulosic biomass hydrolysis. Eighty-seven nonredundant proteins were identified and a diverse group of enzymes, including cellulases, hemicellulases, pectinase, ligninase, protease, peptidases, and phosphatase implicated in lignocellulose degradation were found. In conclusion, the information in this report will be helpful to better understand the lignocelluloses degradation mechanisms of P. eryngii.
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Affiliation(s)
- Chunliang Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, P. R. China
| | - Wei Luo
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, P. R. China
| | - Zhimin Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, P. R. China
| | - Li Yan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, P. R. China
| | - Zuohua Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, P. R. China
| | - Jing Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, P. R. China
| | - Zhenxiu Hu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, P. R. China
| | - Yuande Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, P. R. China
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Imami A, Riemer S, Schulze M, Amelung F, Gorshkov V, Rühl M, Ammenn J, Zorn H. Depolymerization of lignosulfonates by submerged cultures of the basidiomycete Irpex consors and cloning of a putative versatile peroxidase. Enzyme Microb Technol 2015; 81:8-15. [PMID: 26453467 DOI: 10.1016/j.enzmictec.2015.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/15/2015] [Accepted: 07/24/2015] [Indexed: 11/28/2022]
Abstract
Lignosulfonates are abundantly available byproducts of the paper and pulping industry, and they therefore represent a promising feedstock for new sustainable processes. For industrial applications of lignosulfonates, their molecular weight distribution is a critical factor. In order to decrease the average molecular weight of lignosulfonates, Seventeen basidiomycetes were screened for their capability to depolymerize lignosulfonates from spent sulfite liquor (SSL) in surface and liquid cultures. Five basidiomycetes polymerized the lignosulfonates under the selected conditions. Only Irpex consors was found to efficiently degrade calcium lignosulfonates when SSL (0.5%, w/w) was used as the sole carbon and nitrogen source. The average molecular weight of the lignosulfonates was reduced from ∼26 to ∼4 kDa as determined by size exclusion chromatography (SEC) within two weeks. Various extracellular enzyme activities of I. consors were determined over the culture period. High peroxidase activities were correlating with a high degradation rate and the culture was harvested at the day of highest peroxidase activity. A putative versatile peroxidase was isolated by fast protein liquid chromatography (FPLC) and its encoding cDNA was cloned.
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Affiliation(s)
- A Imami
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff Ring 58, 35392 Giessen, Germany
| | - S Riemer
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff Ring 58, 35392 Giessen, Germany
| | - M Schulze
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff Ring 58, 35392 Giessen, Germany
| | - F Amelung
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff Ring 58, 35392 Giessen, Germany
| | - V Gorshkov
- Institute of Analytical Chemistry, Justus Liebig University Giessen, Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Schubertstraße 60, 35392 Giessen, Germany
| | - M Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff Ring 58, 35392 Giessen, Germany
| | - J Ammenn
- BASF SE, G-EVX/LAD-G100, 67056 Ludwigshafen, Germany
| | - H Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff Ring 58, 35392 Giessen, Germany.
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Inácio FD, Ferreira RO, de Araujo CAV, Brugnari T, Castoldi R, Peralta RM, de Souza CGM. Proteases of Wood Rot Fungi with Emphasis on the Genus Pleurotus. BIOMED RESEARCH INTERNATIONAL 2015; 2015:290161. [PMID: 26180792 PMCID: PMC4477095 DOI: 10.1155/2015/290161] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/20/2014] [Indexed: 01/28/2023]
Abstract
Proteases are present in all living organisms and they play an important role in physiological conditions. Cell growth and death, blood clotting, and immune defense are all examples of the importance of proteases in maintaining homeostasis. There is growing interest in proteases due to their use for industrial purposes. The search for proteases with specific characteristics is designed to reduce production costs and to find suitable properties for certain industrial sectors, as well as good producing organisms. Ninety percent of commercialized proteases are obtained from microbial sources and proteases from macromycetes have recently gained prominence in the search for new enzymes with specific characteristics. The production of proteases from saprophytic basidiomycetes has led to the identification of various classes of proteases. The genus Pleurotus has been extensively studied because of its ligninolytic enzymes. The characteristics of this genus are easy cultivation techniques, high yield, low nutrient requirements, and excellent adaptation. There are few studies in the literature about proteases of Pleurotus spp. This review gathers together information about proteases, especially those derived from basidiomycetes, and aims at stimulating further research about fungal proteases because of their physiological importance and their application in various industries such as biotechnology and medicine.
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Affiliation(s)
- Fabíola Dorneles Inácio
- Laboratory of Biochemistry of Microorganisms, Department of Biochemistry, State University of Maringá, Avenue Colombo 5790, 87015-900 Maringá, PR, Brazil
- Federal Institute of Paraná, Campus Jacarezinho, Avenue Doutor Tito s/n, Jardim Panorama, 86400-000 Jacarezinho, PR, Brazil
| | - Roselene Oliveira Ferreira
- Laboratory of Biochemistry of Microorganisms, Department of Biochemistry, State University of Maringá, Avenue Colombo 5790, 87015-900 Maringá, PR, Brazil
| | - Caroline Aparecida Vaz de Araujo
- Laboratory of Biochemistry of Microorganisms, Department of Biochemistry, State University of Maringá, Avenue Colombo 5790, 87015-900 Maringá, PR, Brazil
| | - Tatiane Brugnari
- Laboratory of Biochemistry of Microorganisms, Department of Biochemistry, State University of Maringá, Avenue Colombo 5790, 87015-900 Maringá, PR, Brazil
| | - Rafael Castoldi
- Laboratory of Biochemistry of Microorganisms, Department of Biochemistry, State University of Maringá, Avenue Colombo 5790, 87015-900 Maringá, PR, Brazil
| | - Rosane Marina Peralta
- Laboratory of Biochemistry of Microorganisms, Department of Biochemistry, State University of Maringá, Avenue Colombo 5790, 87015-900 Maringá, PR, Brazil
| | - Cristina Giatti Marques de Souza
- Laboratory of Biochemistry of Microorganisms, Department of Biochemistry, State University of Maringá, Avenue Colombo 5790, 87015-900 Maringá, PR, Brazil
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Knop D, Yarden O, Hadar Y. The ligninolytic peroxidases in the genus Pleurotus: divergence in activities, expression, and potential applications. Appl Microbiol Biotechnol 2014; 99:1025-38. [PMID: 25503316 DOI: 10.1007/s00253-014-6256-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 11/29/2022]
Abstract
Mushrooms of the genus Pleurotus are comprised of cultivated edible ligninolytic fungi with medicinal properties and a wide array of biotechnological and environmental applications. Like other white-rot fungi (WRF), they are able to grow on a variety of lignocellulosic biomass substrates and degrade both natural and anthropogenic aromatic compounds. This is due to the presence of the non-specific oxidative enzymatic systems, which are mainly consisted of lacasses, versatile peroxidases (VPs), and short manganese peroxidases (short-MnPs). Additional, less studied, peroxidase are dye-decolorizing peroxidases (DyPs) and heme-thiolate peroxidases (HTPs). During the past two decades, substantial information has accumulated concerning the biochemistry, structure and function of the Pleurotus ligninolytic peroxidases, which are considered to play a key role in many biodegradation processes. The production of these enzymes is dependent on growth media composition, pH, and temperature as well as the growth phase of the fungus. Mn(2+) concentration differentially affects the expression of the different genes. It also severs as a preferred substrate for these preoxidases. Recently, sequencing of the Pleurotus ostreatus genome was completed, and a comprehensive picture of the ligninolytic peroxidase gene family, consisting of three VPs and six short-MnPs, has been established. Similar enzymes were also discovered and studied in other Pleurotus species. In addition, progress has been made in the development of molecular tools for targeted gene replacement, RNAi-based gene silencing and overexpression of genes of interest. These advances increase the fundamental understanding of the ligninolytic system and provide the opportunity for harnessing the unique attributes of these WRF for applied purposes.
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Affiliation(s)
- Doriv Knop
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
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Zelena K, Eisele N, Berger RG. Escherichia coli as a production host for novel enzymes from basidiomycota. Biotechnol Adv 2014; 32:1382-95. [DOI: 10.1016/j.biotechadv.2014.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/14/2014] [Accepted: 08/25/2014] [Indexed: 01/14/2023]
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Schüttmann I, Bouws H, Szweda RT, Suckow M, Czermak P, Zorn H. Induction, characterization, and heterologous expression of a carotenoid degrading versatile peroxidase from Pleurotus sapidus. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Comparative analysis of secretomes in basidiomycete fungi. J Proteomics 2014; 102:28-43. [DOI: 10.1016/j.jprot.2014.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/19/2014] [Accepted: 03/03/2014] [Indexed: 12/29/2022]
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Fernandes I, Alves A, Correia A, Devreese B, Esteves AC. Secretome analysis identifies potential virulence factors of Diplodia corticola, a fungal pathogen involved in cork oak (Quercus suber) decline. Fungal Biol 2014; 118:516-23. [DOI: 10.1016/j.funbio.2014.04.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/16/2014] [Accepted: 04/09/2014] [Indexed: 01/06/2023]
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Baldrian P, López-Mondéjar R. Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods. Appl Microbiol Biotechnol 2014; 98:1531-7. [PMID: 24384749 DOI: 10.1007/s00253-013-5457-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/30/2013] [Accepted: 12/05/2013] [Indexed: 11/28/2022]
Abstract
Molecular methods for the analysis of biomolecules have undergone rapid technological development in the last decade. The advent of next-generation sequencing methods and improvements in instrumental resolution enabled the analysis of complex transcriptome, proteome and metabolome data, as well as a detailed annotation of microbial genomes. The mechanisms of decomposition by model fungi have been described in unprecedented detail by the combination of genome sequencing, transcriptomics and proteomics. The increasing number of available genomes for fungi and bacteria shows that the genetic potential for decomposition of organic matter is widespread among taxonomically diverse microbial taxa, while expression studies document the importance of the regulation of expression in decomposition efficiency. Importantly, high-throughput methods of nucleic acid analysis used for the analysis of metagenomes and metatranscriptomes indicate the high diversity of decomposer communities in natural habitats and their taxonomic composition. Today, the metaproteomics of natural habitats is of interest. In combination with advanced analytical techniques to explore the products of decomposition and the accumulation of information on the genomes of environmentally relevant microorganisms, advanced methods in microbial ecophysiology should increase our understanding of the complex processes of organic matter transformation.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Vídeňská 1083, 14220, Prague 4, Czech Republic,
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20
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Salvachúa D, Martínez AT, Tien M, López-Lucendo MF, García F, de los Ríos V, Martínez MJ, Prieto A. Differential proteomic analysis of the secretome of Irpex lacteus and other white-rot fungi during wheat straw pretreatment. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:115. [PMID: 23937687 PMCID: PMC3750859 DOI: 10.1186/1754-6834-6-115] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/06/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Identifying new high-performance enzymes or enzyme complexes to enhance biomass degradation is the key for the development of cost-effective processes for ethanol production. Irpex lacteus is an efficient microorganism for wheat straw pretreatment, yielding easily hydrolysable products with high sugar content. Thus, this fungus was selected to investigate the enzymatic system involved in lignocellulose decay, and its secretome was compared to those from Phanerochaete chrysosporium and Pleurotus ostreatus which produced different degradation patterns when growing on wheat straw. Extracellular enzymes were analyzed through 2D-PAGE, nanoLC/MS-MS, and homology searches against public databases. RESULTS In wheat straw, I. lacteus secreted proteases, dye-decolorizing and manganese-oxidizing peroxidases, and H2O2 producing-enzymes but also a battery of cellulases and xylanases, excluding those implicated in cellulose and hemicellulose degradation to their monosaccharides, making these sugars poorly available for fungal consumption. In contrast, a significant increase of β-glucosidase production was observed when I. lacteus grew in liquid cultures. P. chrysosporium secreted more enzymes implicated in the total hydrolysis of the polysaccharides and P. ostreatus produced, in proportion, more oxidoreductases. CONCLUSION The protein pattern secreted during I. lacteus growth in wheat straw plus the differences observed among the different secretomes, justify the fitness of I. lacteus for biopretreatment processes in 2G-ethanol production. Furthermore, all these data give insight into the biological degradation of lignocellulose and suggest new enzyme mixtures interesting for its efficient hydrolysis.
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Affiliation(s)
- Davinia Salvachúa
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park PA, 16802 USA
| | - María F López-Lucendo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Francisco García
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Vivian de los Ríos
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Alicia Prieto
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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21
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Manavalan T, Manavalan A, Thangavelu KP, Heese K. Secretome analysis of Ganoderma lucidum cultivated in sugarcane bagasse. J Proteomics 2012; 77:298-309. [DOI: 10.1016/j.jprot.2012.09.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 08/31/2012] [Accepted: 09/08/2012] [Indexed: 10/27/2022]
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22
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Zorn H, Lauber C, Lorenz P, Schüttmann I, Rühl M. Entwicklung eines Zwei-Enzym-Systems aus einer Peroxidase und einer Arylalkoholoxidase zum Aufschluss von Lignocellulosen. CHEM-ING-TECH 2012. [DOI: 10.1002/cite.201250513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Adav SS, Chao LT, Sze SK. Quantitative secretomic analysis of Trichoderma reesei strains reveals enzymatic composition for lignocellulosic biomass degradation. Mol Cell Proteomics 2012; 11:M111.012419. [PMID: 22355001 DOI: 10.1074/mcp.m111.012419] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Trichoderma reesei is a mesophilic, filamentous fungus, and it is a major industrial source of cellulases, but its lignocellulolytic protein expressions on lignocellulosic biomass are poorly explored at present. The extracellular proteins secreted by T. reesei QM6a wild-type and hypercellulolytic mutant Rut C30 grown on natural lignocellulosic biomasses were explored using a quantitative proteomic approach with 8-plex high throughput isobaric tags for relative and absolute quantification (iTRAQ) and analyzed by liquid chromatography tandem mass spectrometry. We quantified 230 extracellular proteins, including cellulases, hemicellulases, lignin-degrading enzymes, proteases, protein-translocating transporter, and hypothetical proteins. Quantitative iTRAQ results suggested that the expressions and regulations of these lignocellulolytic proteins in the secretome of T. reesei wild-type and mutant Rut C30 were dependent on both nature and complexity of different lignocellulosic carbon sources. Therefore, we discuss here the essential lignocellulolytic proteins for designing an enzyme mixture for optimal lignocellulosic biomass hydrolysis.
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Affiliation(s)
- Sunil S Adav
- School of Biological Sciences, Nanyang Technological University, Singapore
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24
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Heterologous expression, refolding and characterization of a salt activated subtilase from Pleurotus ostreatus. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lau BF, Aminudin N, Abdullah N. Comparative SELDI-TOF-MS profiling of low-molecular-mass proteins from Lignosus rhinocerus (Cooke) Ryvarden grown under stirred and static conditions of liquid fermentation. J Microbiol Methods 2011; 87:56-63. [PMID: 21801760 DOI: 10.1016/j.mimet.2011.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 07/06/2011] [Accepted: 07/06/2011] [Indexed: 11/29/2022]
Abstract
Mushrooms are considered as important source of biologically active compounds which include low-molecular-mass protein/peptides (LMMP). In this study, we attempted to profile the LMMP from Lignosus rhinocerus, a wild medicinal mushroom, grown by static cultures (SC) and in stirred tank reactor (STR). Crude water extract (CWE) and protein fractions were profiled using H50 ProteinChip® arrays and SELDI-TOF-MS. Three protein peaks of 5.8, 6.9 and 9.1 kDa were found to be common to spectra of L. rhinocerus CWE from both culture conditions. Partial protein purification has resulted in detection of more peaks in the spectra of protein fractions. For protein fractions of L. rhinocerus cultured in STR, most peaks were observed in the range of 3-8 kDa whereas some peaks with molecular mass up to 14.3 kDa were noted in spectra of protein fractions from SC. Our results have demonstrated the optimization of profiling method using SELDI-TOF-MS for fungal LMMP.
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Affiliation(s)
- Beng Fye Lau
- Mushroom Research Centre, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
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26
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A proteomic analysis of the Pichia pastoris secretome in methanol-induced cultures. Appl Microbiol Biotechnol 2011; 90:235-47. [DOI: 10.1007/s00253-011-3118-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 01/03/2011] [Accepted: 01/05/2011] [Indexed: 12/27/2022]
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Proteomics of plant pathogenic fungi. J Biomed Biotechnol 2010; 2010:932527. [PMID: 20589070 PMCID: PMC2878683 DOI: 10.1155/2010/932527] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 02/03/2010] [Accepted: 03/01/2010] [Indexed: 12/15/2022] Open
Abstract
Plant pathogenic fungi cause important yield losses in crops. In order to develop efficient and environmental friendly crop protection strategies, molecular studies of the fungal biological cycle, virulence factors, and interaction with its host are necessary. For that reason, several approaches have been performed using both classical genetic, cell biology, and biochemistry and the modern, holistic, and high-throughput, omic techniques. This work briefly overviews the tools available for studying Plant Pathogenic Fungi and is amply focused on MS-based Proteomics analysis, based on original papers published up to December 2009. At a methodological level, different steps in a proteomic workflow experiment are discussed. Separate sections are devoted to fungal descriptive (intracellular, subcellular, extracellular) and differential expression proteomics and interactomics. From the work published we can conclude that Proteomics, in combination with other techniques, constitutes a powerful tool for providing important information about pathogenicity and virulence factors, thus opening up new possibilities for crop disease diagnosis and crop protection.
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Vincent D, Balesdent MH, Gibon J, Claverol S, Lapaillerie D, Lomenech AM, Blaise F, Rouxel T, Martin F, Bonneu M, Amselem J, Dominguez V, Howlett BJ, Wincker P, Joets J, Lebrun MH, Plomion C. Hunting down fungal secretomes using liquid-phase IEF prior to high resolution 2-DE. Electrophoresis 2010; 30:4118-36. [PMID: 19960477 DOI: 10.1002/elps.200900415] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The secreted proteins (secretome) of fungi play a key role in interactions of pathogenic and symbiotic fungi with plants. Using the plant pathogenic fungus Leptosphaeria maculans and symbiont Laccaria bicolor grown in culture, we have established a proteomic protocol for extraction, concentration and resolution of the fungal secretome. As no proteomic data were available on mycelium tissues from both L. maculans and L. bicolor, mycelial proteins were studied; they also helped verifying the purity of secretome samples. The quality of protein extracts was initially assessed by both 1-DE and 2-DE using first a broad pH range for IEF, and then narrower acidic and basic pH ranges, prior to 2-DE. Compared with the previously published protocols for which only dozens of 2-D spots were recovered from fungal secretome samples, up to approximately 2000 2-D spots were resolved by our method. MS identification of proteins along several pH gradients confirmed this high resolution, as well as the presence of major secretome markers such as endopolygalacturonases, beta-glucanosyltransferases, pectate lyases and endoglucanases. Shotgun proteomic experiments evidenced the enrichment of secreted protein within the liquid medium. This is the first description of the proteome of L. maculans and L. bicolor, and the first application of liquid-phase IEF to any fungal extracts.
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30
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Fragner D, Zomorrodi M, Kües U, Majcherczyk A. Optimized protocol for the 2-DE of extracellular proteins from higher basidiomycetes inhabiting lignocellulose. Electrophoresis 2009; 30:2431-41. [DOI: 10.1002/elps.200800770] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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Shah P, Atwood JA, Orlando R, El Mubarek H, Podila GK, Davis MR. Comparative Proteomic Analysis of Botrytis cinerea Secretome. J Proteome Res 2009; 8:1123-30. [DOI: 10.1021/pr8003002] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Punit Shah
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
| | - James A. Atwood
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
| | - Ron Orlando
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
| | - Hind El Mubarek
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
| | - Gopi K. Podila
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
| | - Maria R. Davis
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
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32
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Fungal secretomes—nature’s toolbox for white biotechnology. Appl Microbiol Biotechnol 2008; 80:381-8. [DOI: 10.1007/s00253-008-1572-5] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 06/09/2008] [Accepted: 06/09/2008] [Indexed: 10/21/2022]
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Guais O, Borderies G, Pichereaux C, Maestracci M, Neugnot V, Rossignol M, François JM. Proteomics analysis of "Rovabiot Excel", a secreted protein cocktail from the filamentous fungus Penicillium funiculosum grown under industrial process fermentation. J Ind Microbiol Biotechnol 2008; 35:1659-68. [PMID: 18696134 DOI: 10.1007/s10295-008-0430-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 07/30/2008] [Indexed: 11/25/2022]
Abstract
MS/MS techniques are well customized now for proteomic analysis, even for non-sequenced organisms, since peptide sequences obtained by these methods can be matched with those found in databases from closely related sequenced organisms. We used this approach to characterize the protein content of the "Rovabio Excel", an enzymatic cocktail produced by Penicillium funiculosum that is used as feed additive in animal nutrition. Protein separation by bi-dimensional electrophoresis yielded more than 100 spots, from which 37 proteins were unambiguously assigned from peptide sequences. By one-dimensional SDS-gel electrophoresis, 34 proteins were identified among which 8 were not found in the 2-DE analysis. A third method, termed 'peptidic shotgun', which consists in a direct treatment of the cocktail by trypsin followed by separation of the peptides on two-dimensional liquid chromatography, resulted in the identification of two additional proteins not found by the two other methods. Altogether, more than 50 proteins, among which several glycosylhydrolytic, hemicellulolytic and proteolytic enzymes, were identified by combining three separation methods in this enzymatic cocktail. This work confirmed the power of proteome analysis to explore the genome expression of a non-sequenced fungus by taking advantage of sequences from phylogenetically related filamentous fungi and pave the way for further functional analysis of P. funiculosum.
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Michalski C, Mohagheghi H, Nimtz M, Pasteels J, Ober D. Salicyl alcohol oxidase of the chemical defense secretion of two chrysomelid leaf beetles. Molecular and functional characterization of two new members of the glucose-methanol-choline oxidoreductase gene family. J Biol Chem 2008; 283:19219-28. [PMID: 18482980 DOI: 10.1074/jbc.m802236200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Salicyl alcohol oxidase is an extracellular enzyme that occurs in glandular reservoirs of chrysomelid leaf beetle larvae and catalyzes the formation of salicylaldehyde, a volatile deterrent used by the larvae against predators. Salicyl alcohol is the hydrolysis product of salicin, a plant-derived precursor taken up by the beetle larvae from the leaves of willow and poplar trees. The cDNA encoding salicyl alcohol oxidase from two related species Chrysomela tremulae and Chrysomela populi has been identified, cloned, and expressed in an active form in Escherichia coli. The open reading frame of 623 amino acids begins in both enzymes with an N-terminal signal peptide of 21 amino acids. Sequence comparison has revealed that salicyl alcohol oxidase belongs to the family of glucose-methanol-choline oxidoreductase-like sequences with mostly unknown function. Enzymes of this family share similar overall structure with an essentially identical FAD-binding site but possess different catalytic activities. The data suggest that salicyl alcohol oxidase, essential for the activation of the plant-derived precursor salicin, was originally recruited from an oxidase involved in the autogenous biosynthesis of iridoid monoterpenes and found in related chrysomelid leaf beetle species.
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Affiliation(s)
- Carmen Michalski
- Botanisches Institut und Botanischer Garten, Universität Kiel, Olshausenstrasse 40, 24098 Kiel, Germany
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Hatano N, Hamada T. Proteome Analysis of Pitcher Fluid of the Carnivorous Plant Nepenthes alata. J Proteome Res 2008; 7:809-16. [DOI: 10.1021/pr700566d] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naoya Hatano
- Harima Institute at Spring-8, RIKEN, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan, and Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi-machi, Ishikawa-gun, Ishikawa 921-8836, Japan
| | - Tatsuro Hamada
- Harima Institute at Spring-8, RIKEN, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan, and Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi-machi, Ishikawa-gun, Ishikawa 921-8836, Japan
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Abstract
Filamentous fungi have been recognized as extraordinary producers of secreted proteins and are known to produce novel proteins and enzymes through dispensable metabolic pathways. Here, methods are described for the isolation and enrichment of samples of secreted proteins from cultures of filamentous fungi for analysis by gel electrophoresis and mass spectrometry techniques. These methods can be readily applied to the study of differential protein expression and secretion and metabolic pathways in filamentous fungi by proteomic approaches.
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Scheibner M, Hülsdau B, Zelena K, Nimtz M, de Boer L, Berger RG, Zorn H. Novel peroxidases of Marasmius scorodonius degrade beta-carotene. Appl Microbiol Biotechnol 2007; 77:1241-50. [PMID: 18038130 DOI: 10.1007/s00253-007-1261-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Revised: 10/22/2007] [Accepted: 10/23/2007] [Indexed: 10/22/2022]
Abstract
Two extracellular enzymes (MsP1 and MsP2) capable of efficient beta-carotene degradation were purified from culture supernatants of the basidiomycete Marasmius scorodonius (garlic mushroom). Under native conditions, the enzymes exhibited molecular masses of approximately 150 and approximately 120 kDa, respectively. SDS-PAGE and mass spectrometric data suggested a composition of two identical subunits for both enzymes. Biochemical characterisation of the purified proteins showed isoelectric points of 3.7 and 3.5, and the presence of heme groups in the active enzymes. Partial amino acid sequences were derived from N-terminal Edman degradation and from mass spectrometric ab initio sequencing of internal peptides. cDNAs of 1,604 to 1,923 bp, containing open reading frames (ORF) of 508 to 513 amino acids, respectively, were cloned from a cDNA library of M. scorodonius. These data suggest glycosylation degrees of approximately 23% for MsP1 and 8% for MsP2. Databank homology searches revealed sequence homologies of MsP1 and MsP2 to unusual peroxidases of the fungi Thanatephorus cucumeris (DyP) and Termitomyces albuminosus (TAP).
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Affiliation(s)
- Manuela Scheibner
- Zentrum Angewandte Chemie, Institut für Lebensmittelchemie der Universität Hannover, Wunstorfer Strasse 14, 30453, Hannover, Germany
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Kim Y, Nandakumar MP, Marten MR. Proteomics of filamentous fungi. Trends Biotechnol 2007; 25:395-400. [PMID: 17681627 DOI: 10.1016/j.tibtech.2007.07.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 05/24/2007] [Accepted: 07/18/2007] [Indexed: 10/23/2022]
Abstract
Proteomic analysis, defined here as the global assessment of cellular proteins expressed in a particular biological state, is a powerful tool that can provide a systematic understanding of events at the molecular level. Proteomic studies of filamentous fungi have only recently begun to appear in the literature, despite the prevalence of these organisms in the biotechnology industry, and their importance as both human and plant pathogens. Here, we review recent publications that have used a proteomic approach to develop a better understanding of filamentous fungi, highlighting sample preparation methods and whole-cell cytoplasmic proteomics, as well as subproteomics of cell envelope, mitochondrial and secreted proteins.
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Affiliation(s)
- Yonghyun Kim
- Department of Chemical and Biochemical Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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Wu S, Zorn H, Krings U, Berger RG. Volatiles from submerged and surface-cultured beefsteak fungus,Fistulina hepatica. FLAVOUR FRAG J 2006. [DOI: 10.1002/ffj.1758] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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