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Wang TY, Chen HL, Lu MYJ, Chen YC, Sung HM, Mao CT, Cho HY, Ke HM, Hwa TY, Ruan SK, Hung KY, Chen CK, Li JY, Wu YC, Chen YH, Chou SP, Tsai YW, Chu TC, Shih CCA, Li WH, Shih MC. Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:24. [PMID: 21849025 PMCID: PMC3177772 DOI: 10.1186/1754-6834-4-24] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Accepted: 08/17/2011] [Indexed: 05/10/2023]
Abstract
BACKGROUND Neocallimastix patriciarum is one of the common anaerobic fungi in the digestive tracts of ruminants that can actively digest cellulosic materials, and its cellulases have great potential for hydrolyzing cellulosic feedstocks. Due to the difficulty in culture and lack of a genome database, it is not easy to gain a global understanding of the glycosyl hydrolases (GHs) produced by this anaerobic fungus. RESULTS We have developed an efficient platform that uses a combination of transcriptomic and proteomic approaches to N. patriciarum to accelerate gene identification, enzyme classification and application in rice straw degradation. By conducting complementary studies of transcriptome (Roche 454 GS and Illumina GA IIx) and secretome (ESI-Trap LC-MS/MS), we identified 219 putative GH contigs and classified them into 25 GH families. The secretome analysis identified four major enzymes involved in rice straw degradation: β-glucosidase, endo-1,4-β-xylanase, xylanase B and Cel48A exoglucanase. From the sequences of assembled contigs, we cloned 19 putative cellulase genes, including the GH1, GH3, GH5, GH6, GH9, GH18, GH43 and GH48 gene families, which were highly expressed in N. patriciarum cultures grown on different feedstocks. CONCLUSIONS These GH genes were expressed in Pichia pastoris and/or Saccharomyces cerevisiae for functional characterization. At least five novel cellulases displayed cellulytic activity for glucose production. One β-glucosidase (W5-16143) and one exocellulase (W5-CAT26) showed strong activities and could potentially be developed into commercial enzymes.
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Affiliation(s)
- Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsin-Liang Chen
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Mei-Yeh J Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yo-Chia Chen
- Graduate Institute of Biotechnology, National Pingtung University of Science & Technology, Neipu Hsiang, Pingtung 91201, Taiwan
| | - Huang-Mo Sung
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi-Tang Mao
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University - Academia Sinica, Taipei 115, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan
| | - Hsing-Yi Cho
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University - Academia Sinica, Taipei 115, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- PhD Program in Microbial Genomics, National Chung Hsing University, Taichung 402, Taiwan
| | - Teh-Yang Hwa
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Sz-Kai Ruan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuo-Yen Hung
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Kuan Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Department of Life Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Jeng-Yi Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yueh-Chin Wu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Hsiang Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Shao-Pei Chou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ya-Wen Tsai
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Te-Chin Chu
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
- Department of Computer Science and Information Engineering, National Taiwan Normal University, Taipei 116, Taiwan
| | - Chun-Chieh A Shih
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University - Academia Sinica, Taipei 115, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 402, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Ming-Che Shih
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University - Academia Sinica, Taipei 115, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 402, Taiwan
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Ljungdahl LG. The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use. Ann N Y Acad Sci 2008; 1125:308-21. [PMID: 18378601 DOI: 10.1196/annals.1419.030] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Anaerobic fungi, first described in 1975 by Orpin, live in close contact with bacteria and other microorganisms in the rumen and caecum of herbivorous animals, where they digest ingested plant food. Seventeen distinct anaerobic fungi belonging to five different genera have been described. They have been found in at least 50 different herbivorous animals. Anaerobic fungi do not possess mitochondria, but instead have hydrogenosomes, which form hydrogen and carbon dioxide from pyruvate and malate during fermentation of carbohydrates. In addition, they are very oxygen- and temperature-sensitive, and their DNA has an unusually high AT content of from 72 to 87 mol%. My initial reason for studying anaerobic fungi was because they solubilize lignocellulose and produce all enzymes needed to efficiently hydrolyze cellulose and hemicelluloses. Although some of these enzymes are found free in the medium, most of them are associated with cellulosomal and polycellulosomal complexes, in which the enzymes are attached through fungal dockerins to scaffolding proteins; this is similar to what has been found for cellulosomes from anaerobic bacteria. Although cellulosomes from anaerobic fungi share many properties with cellulosomes of anaerobic cellulolytic bacteria and have comparable structures, their structures differ in their amino acid sequences. I discuss some features of the cellulosome of the anaerobic fungus Orpinomyces sp. PC-2 and some possible uses of its enzymes in industrial settings.
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Affiliation(s)
- Lars G Ljungdahl
- Department of Biochemistry and Molecular Biology, Fred C. Davison Life Sciences Complex, University of Georgia, Athens, GA 30602-7229, USA.
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Kawai R, Igarashi K, Kitaoka M, Ishii T, Samejima M. Kinetics of substrate transglycosylation by glycoside hydrolase family 3 glucan (1→3)-β-glucosidase from the white-rot fungus Phanerochaete chrysosporium. Carbohydr Res 2004; 339:2851-7. [PMID: 15582611 DOI: 10.1016/j.carres.2004.09.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Revised: 09/28/2004] [Accepted: 09/28/2004] [Indexed: 11/23/2022]
Abstract
To elucidate the interaction between substrate inhibition and substrate transglycosylation of retaining glycoside hydrolases (GHs), a steady-state kinetic study was performed for the GH family 3 glucan (1-->3)-beta-glucosidase from the white-rot fungus Phanerochaete chrysosporium, using laminarioligosaccharides as substrates. When laminaribiose was incubated with the enzyme, a transglycosylation product was detected by thin-layer chromatography. The product was purified by size-exclusion chromatography, and was identified as a 6-O-glucosyl-laminaribiose (beta-D-Glcp-(1-->6)-beta-D-Glcp-(1-->3)-D-Glc) by 1H NMR spectroscopy and electrospray ionization mass spectrometry analysis. In steady-state kinetic studies, an apparent decrease of laminaribiose hydrolysis was observed at high concentrations of the substrate, and the plots of glucose production versus substrate concentration were thus fitted to a modified Michaelis-Menten equation including hydrolytic and transglycosylation parameters (K(m), K(m2), k(cat), k(cat2)). The rate of 6-O-glucosyl-laminaribiose production estimated by high-performance anion-exchange chromatography coincided with the theoretical rate calculated using these parameters, clearly indicating that substrate inhibition of this enzyme is fully explained by substrate transglycosylation. Moreover, when K(m), k(cat), and affinity for glucosyl-enzyme intermediates (K(m2)) were estimated for laminarioligosaccharides (DP=3-5), the K(m) value of laminaribiose was approximately 5-9 times higher than those of the other oligosaccharides (DP=3-5), whereas the K(m2) values were independent of the DP of the substrates. The kinetics of transglycosylation by the enzyme could be well interpreted in terms of the subsite affinities estimated from the hydrolytic parameters (K(m) and k(cat)), and a possible mechanism of transglycosylation is proposed.
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Affiliation(s)
- Rie Kawai
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Chen H, Li X, Ljungdahl LG. Isolation and properties of an extracellular beta-glucosidase from the polycentric rumen fungus Orpinomyces sp. strain PC-2. Appl Environ Microbiol 1994; 60:64-70. [PMID: 8117094 PMCID: PMC201270 DOI: 10.1128/aem.60.1.64-70.1994] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
An extracellular beta-glucosidase (EC 3.2.1.21) was purified from culture filtrate of the anaerobic rumen fungus Orpinomyces sp. strain PC-2 grown on 0.3% (wt vol-1) Avicel by using Q Sepharose anion-exchange chromatography, ammonium sulfate precipitation, chromatofocusing ion-exchange chromatography, and Superose 12 gel filtration. The enzyme is monomeric with a M(r) of 85,400, as estimated by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, has a pI of 3.95, and contains about 8.5% (wt vol-1) carbohydrate. The N terminus appears to be blocked. The enzyme catalyzes the hydrolysis of cellobiose and p-nitrophenyl-beta-D-glucoside (PNPG). The Km and Vmax values with cellobiose as the substrate at pH 6.0 and 40 degrees C are 0.25 mM and 27.1 mumol.min-1 x mg-1, respectively; with PNPG as the substrate, the corresponding values are of 0.35 mM and 27.7 mumol.min-1 x mg-1. Glucose (Ki = 8.75 mM, with PNPG as the substrate) and gluconolactone (Ki = 1.68 x 10(-2) and 2.57 mM, with PNPG and cellobiose as the substrates, respectively) are competitive inhibitors. Optimal activity with PNPG and cellobiose as the substrates is at pH 6.2 and 50 degrees C. The enzyme has high activity against sophorose (beta-1,2-glucobiose) and laminaribiose (beta-1,3-glucobiose) but has no activity against gentiobiose (beta-1,6-glucobiose). The activity of the beta-glucosidase is stimulated by Mg2+, Mn2+, Co2+, and Ni2+ and inhibited by Ag+, Fe2+, Cu2+, Hg2+, SDS, and p-chloromercuribenzoate.
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Affiliation(s)
- H Chen
- Center for Biological Resource Recovery, University of Georgia, Athens 30602
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