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Microbiota in Waterlogged Archaeological Wood: Use of Next-Generation Sequencing to Evaluate the Risk of Biodegradation. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10134636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Waterlogged archaeological wood (WAW) is considered a precious material, first-hand account of past civilizations. Like any organic material, it is subjected to biodegradative action of microorganisms whose activity could be particularly fast and dangerous during the phases of excavation, storage and restoration. The present work aimed to characterize the microorganisms present in WAW during these tricky periods to evaluate the biological risk it is exposed to. The bacterial and fungal communities inhabiting woods coming from two archaeological sites (Pisa and Naples) were investigated through Next-Generation Sequencing (NGS). High-throughput sequencing of extracted DNA fragments was performed using the reversible terminator-based sequencing chemistry with the Illumina MiSeq platform. The analyses revealed that the two archaeological sites showed distinct richness and biodiversity, as expected. In all the WAWs, the bacterial community harbored mainly Proteobacteria, whereas Bacteroidetes was well represented only in Naples communities and taxa belonging to the phyla Chloroflexi only in the Pisa site. Concerning the fungal community, the two sites were dominated by different phyla: Ascomycota for Naples samples and Basidiomycota for Pisa. Interestingly, most of the identified bacterial and fungal taxa have cellulolytic or ligninolytic ability. These results provide new and useful background information concerning the composition of WAW microbiota and the threat it represents for this precious material.
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Tovar-Herrera OE, Martha-Paz AM, Pérez-LLano Y, Aranda E, Tacoronte-Morales JE, Pedroso-Cabrera MT, Arévalo-Niño K, Folch-Mallol JL, Batista-García RA. Schizophyllum commune: An unexploited source for lignocellulose degrading enzymes. Microbiologyopen 2018; 7:e00637. [PMID: 29785766 PMCID: PMC6011954 DOI: 10.1002/mbo3.637] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 02/01/2023] Open
Abstract
Lignocellulose represents the most abundant source of carbon in the Earth. Thus, fraction technology of the biomass turns up as an emerging technology for the development of biorefineries. Saccharification and fermentation processes require the formulation of enzymatic cocktails or the development of microorganisms (naturally or genetically modified) with the appropriate toolbox to produce a cost‐effective fermentation technology. Therefore, the search for microorganisms capable of developing effective cellulose hydrolysis represents one of the main challenges in this era. Schizophyllum commune is an edible agarical with a great capability to secrete a myriad of hydrolytic enzymes such as xylanases and endoglucanases that are expressed in a high range of substrates. In addition, a large number of protein‐coding genes for glycoside hydrolases, oxidoreductases like laccases (Lacs; EC 1.10.3.2), as well as some sequences encoding for lytic polysaccharide monooxygenases (LPMOs) and expansins‐like proteins demonstrate the potential of this fungus to be applied in different biotechnological process. In this review, we focus on the enzymatic toolbox of S. commune at the genetic, transcriptomic, and proteomic level, as well as the requirements to be employed for fermentable sugars production in biorefineries. At the end the trend of its use in patent registration is also reviewed.
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Affiliation(s)
- Omar Eduardo Tovar-Herrera
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Adriana Mayrel Martha-Paz
- Laboratorio de Micología y Fitopatología, Unidad de manipulación genética, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Yordanis Pérez-LLano
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Elisabet Aranda
- Instituto del Agua, Universidad de Granada, Granada, Granada, Spain
| | | | | | - Katiushka Arévalo-Niño
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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Cadirci BH, Yasa I, Kocyigit A. Streptomyces sp. TEM 33 possesses high lipolytic activity in solid-state fermentation in comparison with submerged fermentation. Prep Biochem Biotechnol 2014; 46:23-9. [PMID: 25285910 DOI: 10.1080/10826068.2014.970693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Solid-state fermentation (SSF) is a bioprocess that doesn't need an excess of free water, and it offers potential benefits for microbial cultivation for bioprocesses and product development. In comparing the antibiotic production, few detailed reports could be found with lipolytic enzyme production by Streptomycetes in SSF. Taking this knowledge into consideration, we prefer to purify Actinomycetes species as a new source for lipase production. The lipase-producing strain Streptomyces sp. TEM 33 was isolated from soil and lipase production was managed by solid-state fermentation (SSF) in comparison with submerged fermentation (SmF). Bioprocess-affecting factors like initial moisture content, incubation time, and various carbon and nitrogen additives and the other enzymes secreted into the media were optimized. Lipase activity was measured as 1.74 ± 0.0005 U/g dry substrate (gds) by the p-nitrophenylpalmitate (pNPP) method on day 6 of fermentation with 71.43% final substrate moisture content. In order to understand the metabolic priority in SSF, cellulase and xylanase activity of Streptomyces sp. TEM33 was also measured. The microorganism degrades the wheat bran to its usable form by excreting cellulases and xylanases; then it secretes the lipase that is necessary for degrading the oil in the medium.
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Affiliation(s)
- Bilge Hilal Cadirci
- a Department of Bioengineering , Gaziosmanpasa University , Tasliciftlik , Tokat , Turkey
| | - Ihsan Yasa
- b Basic and Industrial Microbiology Section, Department of Biology , Ege University , Izmir , Turkey
| | - Ali Kocyigit
- b Basic and Industrial Microbiology Section, Department of Biology , Ege University , Izmir , Turkey
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Tsujiyama SI, Ueno H. Performance of wood-rotting fungi-based enzymes on enzymic saccharification of rice straw. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:2841-2848. [PMID: 23450755 DOI: 10.1002/jsfa.6118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 02/12/2013] [Accepted: 02/28/2013] [Indexed: 06/01/2023]
Abstract
BACKGROUND For effective saccharification of rice straw we focused on enzyme preparations from wood-rotting fungi that have the ability to degrade cell wall polysaccharides and lignin. We tested extracellular enzyme preparations from 14 species of fungi for saccharification activity and examined the factor for saccharification by statistical analysis. RESULTS An enzyme preparation from Schizophyllum commune had the highest saccharification activity of rice straw. This preparation contained highly active endo-β-xylanase, endo-β-glucanase (CMCase), β-d-glucosidase and acetylxylan esterase. Correlation analysis of the 14 enzyme preparations demonstrated that acetylxylan esterase was closely related to saccharification activity in rice straw. Multiple regression analysis also showed that acetylxylan esterase had an important role in saccharification. Ligninolytic enzymes, which are characteristic of white-rot fungi, did not contribute to saccharification activity of rice straw. CONCLUSION Deacetylation is an essential factor for saccharification of rice straw and enzyme preparations for saccharification need to contain highly active acetylxylan esterase as well as highly active cellulolytic and xylanolytic enzymes, but not ligninolytic ones.
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Affiliation(s)
- Sho-Ichi Tsujiyama
- Laboratory of Chemistry for Forest Bioresources, Graduate School of Life and Environmental Science, Kyoto Prefectural University, Kyoto, 606-8522, Japan
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Abdel-Monem OA, El-Baz AF, Shetaia YM, El-Sabbagh SM. Production and Application of Thermostable Cellulase-Free Xylanase by Aspergillus fumigatusfrom Agricultural Wastes. Ind Biotechnol (New Rochelle N Y) 2012. [DOI: 10.1089/ind.2012.0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Omnia A. Abdel-Monem
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute, Minoufiya University, El-Sadat City, Egypt
| | - Ashraf F. El-Baz
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute, Minoufiya University, El-Sadat City, Egypt
| | - Yousria M. Shetaia
- Department of Microbiology, Faculty of Science, Ain-Shams University, Cairo, Egypt
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Tsujiyama SI, Ueno H. Production of cellulolytic enzymes containing cinnamic acid esterase from Schizophyllum commune. J GEN APPL MICROBIOL 2012; 57:309-17. [PMID: 22353736 DOI: 10.2323/jgam.57.309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To develop enzyme preparations capable of digesting plant biomass, we examined the production of cinnamic acid esterase as well as cellulolytic and xylanolytic enzymes in cultures of Schizophyllum commune. The cinnamic acid esterase was produced in the cultures containing solid cellulosic substrates, with production being enhanced by delignifying the wood powder. This indicates that these esterases are produced by cellulose, despite their substrates being phenolic compounds. Cellulolytic and xylanolytic enzymes, with the exception of α-arabinofuranosidase, were also produced in cultures containing cellulosic substances. These results show that enzyme preparation can have high activity of cinnamic acid esterase and cellulolytic and xylanolytic enzymes when S. commune is incubated in the presence of cellulose. These enzyme preparations will be useful for digesting plant biomass and for releasing cinnamic acid derivatives from plant cell walls.
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Affiliation(s)
- Sho-ichi Tsujiyama
- Department of Environmental Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University.
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Soliman HM, A. Sherief AD, Tanash ABEL. Production of Xylanase by Aspergillus niger and Trichoderma viride using Some Agriculture Residues. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/ijar.2012.46.57] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Holocellulase Activity from Schizophyllum commune Grown on Bamboo: A Comparison with Different Substrates. Curr Microbiol 2011; 63:581-7. [DOI: 10.1007/s00284-011-0023-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Accepted: 09/13/2011] [Indexed: 11/26/2022]
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Chong SL, Battaglia E, Coutinho PM, Henrissat B, Tenkanen M, de Vries RP. The α-glucuronidase Agu1 from Schizophyllum commune is a member of a novel glycoside hydrolase family (GH115). Appl Microbiol Biotechnol 2011; 90:1323-32. [DOI: 10.1007/s00253-011-3157-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 01/28/2011] [Accepted: 01/29/2011] [Indexed: 10/18/2022]
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Tamarind kernel powder co-induces xylanase and cellulase production during submerged fermentation of Termitomyces clypeatus. BIOTECHNOL BIOPROC E 2010. [DOI: 10.1007/s12257-009-3042-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nimura Y, Tsujiyama SI, Ueno M. Bioconversion of cinnamic acid derivatives by Schizophyllum commune. J GEN APPL MICROBIOL 2010; 56:381-7. [DOI: 10.2323/jgam.56.381] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Meshram M, Kulkarni A, Jayaraman V, Kulkarni B, Lele S. Optimal xylanase production using Penicilium janthinellum NCIM 1169: A model based approach. Biochem Eng J 2008. [DOI: 10.1016/j.bej.2008.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hidalgo-Lara ME, Farrés GSA, Montes-Horcasitas MDC. β-Methyl-xyloside: positive effect on xylanase induction in Cellulomonas flavigena. J Ind Microbiol Biotechnol 2005; 32:345-8. [PMID: 15986227 DOI: 10.1007/s10295-005-0258-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Accepted: 05/25/2005] [Indexed: 10/25/2022]
Abstract
Synthesis of extracellular xylanase in Cellulomonas flavigena is induced in the presence of xylan and sugarcane bagasse as substrates. The essential factors for efficient production of xylanase are the appropriate medium composition and an inducing substrate. The increase in xylanase production levels in C. flavigena were tested with a number of carbon sources and different culture conditions. Xylose, arabinose, glycerol and glucose did not induce xylanase production in this microorganism. beta-Methyl-xyloside (beta-mx), a structural analog of xylobiose, also did not induce xylanase when used as the sole carbon source, but when xylan or sugar cane bagasse was supplemented with beta-mx, extracellular xylanase production increased by 25 or 46%, respectively. The response of C. flavigena to xylan plus beta-mx was accompanied by a significant accumulation of reducing sugar, an effect not observed with the combination sugarcane bagasse plus beta-mx as substrate. To our knowledge, this is the first report on the effect of beta-mx on the induction of xylanase in C. flavigena.
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Affiliation(s)
- Marìa Eugenia Hidalgo-Lara
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Ave. IPN 2508, México D.F.C.P. 07360, Mexico
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Purification and characterization of two minor endo-β-1,4-xylanases of Schizophyllum commune. Enzyme Microb Technol 2005. [DOI: 10.1016/j.enzmictec.2005.01.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Sachslehner A, Nidetzky B, Kulbe KD, Haltrich D. Induction of Mannanase, Xylanase, and Endoglucanase Activities in Sclerotium rolfsii. Appl Environ Microbiol 1998; 64:594-600. [PMID: 16349502 PMCID: PMC106088 DOI: 10.1128/aem.64.2.594-600.1998] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/1997] [Accepted: 11/22/1997] [Indexed: 11/20/2022] Open
Abstract
Induction of mannanase, xylanase, and cellulase (endoglucanase) synthesis in the plant-pathogenic basidiomycete Sclerotium rolfsii was studied by incubating noninduced, resting mycelia with a number of mono-, oligo-, and polysaccharides. The simultaneous formation of these three endoglycanases could be provoked by several polysaccharides structurally resembling the carbohydrate constituents of lignocellulose (e.g., mannan and cellulose), by various disaccharide catabolites of these lignocellulose constituents (e.g., cellobiose, mannobiose, and xylobiose), or by structurally related disaccharides (e.g., lactose, sophorose, and galactosyl-beta-1,4-mannose), as well as by l-sorbose. Synthesis of mannanase, xylanase, and endoglucanase always occurred concomitantly and could not be separated by selecting an appropriate inducer. Various structurally different inducing carbohydrates promoted the excretion of the same multiple isoforms of endoglycanases, as judged from the similar banding patterns obtained in zymogram analyses of enzyme preparations obtained in response to these different inducers and resolved by analytical isoelectric focusing. Whereas enhanced xylanase and endoglucanase formation is strictly dependent on the presence of suitable inducers, increased levels of mannanase are excreted by S. rolfsii even under noninducing, derepressed conditions, as shown in growth experiments with glucose as the substrate. Significant mannanase formation commenced only when glucose was exhausted from the medium. Under these conditions, only very low, presumably constitutive levels of xylanase and endoglucanase were formed. Although the induction of the three endoglycanases is very closely related in S. rolfsii, it was concluded that there is no common, coordinated regulatory mechanism that controls the synthesis of mannanase, xylanase, and endoglucanase.
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Affiliation(s)
- A Sachslehner
- Division of Biochemical Engineering, Institute of Food Technology, University of Agricultural Sciences Vienna (Universität für Bodenkultur BOKU), A-1190 Vienna, Austria
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Sachslehner A, Haltrich D, Nidetzky B, Kulbe KD. Production of Hemicellulose- and Cellulose-Degrading enzymes by various strains ofSclerotium Rolfsii. Appl Biochem Biotechnol 1997; 63-65:189-201. [DOI: 10.1007/bf02920424] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kadowaki MK, Polizeli ML, Terenzi HF, Jorge JA. Characterization of trehalase activities from the thermophilic fungus Scytalidium thermophilum. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1291:199-205. [PMID: 8980633 DOI: 10.1016/s0304-4165(96)00065-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The thermophilic fungus Scytalidium thermophilum produced large amounts of intracellular and extracellular trehalase activity when grown on starch as the sole carbon source. The specific activity of the purified proteins: 1700 U (mg protein)-1 (extracellular) and 3700 U (mg protein)-1 (intracellular), was many times higher than the values reported for other microbial sources. The apparent molecular mass of the native enzymes was estimated to be 370 kDa (extracellular trehalase) and 398 kDa (intracellular trehalase) by gel-filtration chromatography. Analysis by SDS-PAGE showed unique polypeptide bands of approx. 82 kDa (extracellular trehalase) and 85 kDa (intracellular trehalase), suggesting that the native enzymes were composed of five subunits. The carbohydrate content of extracellular and intracellular trehalases was estimated to be 81% and 51%, respectively. Electrofocusing indicated a pI of 3.7 and 3.4, respectively, for the extracellular and intracellular enzymes. Both trehalases were highly specific for trehalose and were stimulated by calcium and manganese. Calcium and manganese also protected both trehalases from thermoinactivation. Inhibition was observed in the presence of aluminium, mercurium, copper, zinc, EDTA, ADP, and ATP. Apparent Km values, for the extracellular and intracellular trehalases, were 3.58 mM and 2.24 mM, respectively. The optimum of pH for the extracellular and the intracellular trehalase was 6.0, and the optimum of temperature 60 degrees C and 65 degrees C, respectively.
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Affiliation(s)
- M K Kadowaki
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Brazil
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Biely P, Côté GL, Kremnický L, Weisleder D, Greene RV. Substrate specificity of acetylxylan esterase from Schizophyllum commune: mode of action on acetylated carbohydrates. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1298:209-22. [PMID: 8980647 DOI: 10.1016/s0167-4838(96)00132-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Substrate specificity of a purified acetylxylan esterase from Schizophyllum commune was investigated on a variety of methyl per-O-acetyl glycopyranosides, methyl di-O-acetyl-beta-D-xylopyranosides and acetylated polysaccharides. The enzyme preferentially deacetylated the 3-position of methyl 2,3,4-tri-O-acetyl-beta-D-xylopyranoside and 2,3,4,6-tetra-O-acetyl-beta-D-glucopyranoside. Removal of the 3-acetyl group from the xylopyranoside was accompanied by a slower deacetylation at positions 2 and 4. A similarly slower, accompanying deacetylation occurred primarily at position 2 with the glucopyranoside. Such specificity corresponds well to the expected function of the esterase in acetylxylan degradation. Of the three possible diacetates of methyl beta-D-xylopyranoside, the 3,4-diacetate was found to be the most rapidly deacetylated. Unexpectedly, products of its deacetylation were a mixture of 2- and 4-monoacetate. The formation of the methyl 2-O-acetyl-beta-D-xylopyranoside involved an enzyme-mediated acetyl group transfer because the rate of the enzyme-catalyzed reaction exceeded the rate of spontaneous migration of acetyl groups. This is the likely mechanism for acetyl removal from position 2 in the native substrate. The enzyme exhibited the highest regioselectivity with methyl 2,3,4,6-tetra-O-acetyl-beta-D-mannopyranoside. An 80% conversion of this substrate to methyl 4,6-di-O-acetyl-beta-D-mannopyranoside, a new mannose derivative, was achieved. In contrast to the majority of lipases and esterases exploited for regioselective deacetylation, the S. commune acetylxylan esterase did not attack the C-6 acetyl linkages in methyl hexopyranosides when other acetyl groups were available.
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Affiliation(s)
- P Biely
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
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