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Xavier BM, Zein AA, Venes A, Wang J, Lee JY. Transmembrane Polar Relay Drives the Allosteric Regulation for ABCG5/G8 Sterol Transporter. Int J Mol Sci 2020; 21:ijms21228747. [PMID: 33228147 PMCID: PMC7699580 DOI: 10.3390/ijms21228747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/14/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022] Open
Abstract
The heterodimeric ATP-binding cassette (ABC) sterol transporter, ABCG5/G8, is responsible for the biliary and transintestinal secretion of cholesterol and dietary plant sterols. Missense mutations of ABCG5/G8 can cause sitosterolemia, a loss-of-function disorder characterized by plant sterol accumulation and premature atherosclerosis. A new molecular framework was recently established by a crystal structure of human ABCG5/G8 and reveals a network of polar and charged amino acids in the core of the transmembrane domains, namely, a polar relay. In this study, we utilize genetic variants to dissect the mechanistic role of this transmembrane polar relay in controlling ABCG5/G8 function. We demonstrated a sterol-coupled ATPase activity of ABCG5/G8 by cholesteryl hemisuccinate (CHS), a relatively water-soluble cholesterol memetic, and characterized CHS-coupled ATPase activity of three loss-of-function missense variants, R543S, E146Q, and A540F, which are respectively within, in contact with, and distant from the polar relay. The results established an in vitro phenotype of the loss-of-function and missense mutations of ABCG5/G8, showing significantly impaired ATPase activity and loss of energy sufficient to weaken the signal transmission from the transmembrane domains. Our data provide a biochemical evidence underlying the importance of the polar relay and its network in regulating the catalytic activity of ABCG5/G8 sterol transporter.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily G, Member 5/chemistry
- ATP Binding Cassette Transporter, Subfamily G, Member 5/genetics
- ATP Binding Cassette Transporter, Subfamily G, Member 5/metabolism
- ATP Binding Cassette Transporter, Subfamily G, Member 8/chemistry
- ATP Binding Cassette Transporter, Subfamily G, Member 8/genetics
- ATP Binding Cassette Transporter, Subfamily G, Member 8/metabolism
- Adenosine Triphosphatases/chemistry
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Adenosine Triphosphate/chemistry
- Adenosine Triphosphate/metabolism
- Allosteric Regulation
- Binding Sites
- Biological Transport
- Cholesterol/chemistry
- Cholesterol/metabolism
- Cholesterol Esters/chemistry
- Cholesterol Esters/metabolism
- Cholic Acid/chemistry
- Cholic Acid/metabolism
- Gene Expression
- Humans
- Hypercholesterolemia/genetics
- Hypercholesterolemia/metabolism
- Hypercholesterolemia/pathology
- Intestinal Diseases/genetics
- Intestinal Diseases/metabolism
- Intestinal Diseases/pathology
- Kinetics
- Lipid Metabolism, Inborn Errors/genetics
- Lipid Metabolism, Inborn Errors/metabolism
- Lipid Metabolism, Inborn Errors/pathology
- Lipoproteins/chemistry
- Lipoproteins/genetics
- Lipoproteins/metabolism
- Models, Molecular
- Mutation
- Phytosterols/adverse effects
- Phytosterols/genetics
- Phytosterols/metabolism
- Pichia/chemistry
- Pichia/genetics
- Pichia/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Thermodynamics
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Affiliation(s)
- Bala M. Xavier
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (B.M.X.); (A.A.Z.); (A.V.)
| | - Aiman A. Zein
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (B.M.X.); (A.A.Z.); (A.V.)
| | - Angelica Venes
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (B.M.X.); (A.A.Z.); (A.V.)
- Biomedical Sciences Program, Department of Biology, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15206, USA
- Correspondence: (J.W.); (J.-Y.L.); Tel.: +1-412-383-3268 (J.W.); +1-613-562-5800 (ext. 8308) (J.-Y.L.)
| | - Jyh-Yeuan Lee
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (B.M.X.); (A.A.Z.); (A.V.)
- Correspondence: (J.W.); (J.-Y.L.); Tel.: +1-412-383-3268 (J.W.); +1-613-562-5800 (ext. 8308) (J.-Y.L.)
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Schoeny H, Rampler E, Hermann G, Grienke U, Rollinger JM, Koellensperger G. Preparative supercritical fluid chromatography for lipid class fractionation-a novel strategy in high-resolution mass spectrometry based lipidomics. Anal Bioanal Chem 2020; 412:2365-2374. [PMID: 32130438 PMCID: PMC7118041 DOI: 10.1007/s00216-020-02463-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/08/2020] [Accepted: 01/28/2020] [Indexed: 01/01/2023]
Abstract
In this work, a lipidomics workflow based on offline semi-preparative lipid class-specific fractionation by supercritical fluid chromatography (SFC) followed by high-resolution mass spectrometry was introduced. The powerful SFC approach offered separation of a wide polarity range for lipids, enabled enrichment (up to 3 orders of magnitude) of lipids, selective fractionation of 14 lipid classes/subclasses, and increased dynamic range enabling in-depth characterization. A significantly increased coverage of low abundant lipids improving lipid identification by numbers and degree (species and molecular level) was obtained in Pichia pastoris when comparing high-resolution mass spectrometry based lipidomics with and without prior fractionation. Proof-of-principle experiments using a standard reference material (SRM 1950, NIST) for human plasma showed that the proposed strategy enabled quantitative lipidomics. Indeed, for 70 lipids, the consensus values available for this sample could be met. Thus, the novel workflow is ideally suited for lipid class-specific purification/isolation from milligram amounts of sample while not compromising on omics type of analysis (identification and quantification). Finally, compared with established fractionation/pre-concentration approaches, semi-preparative SFC is superior in terms of versatility, as it involved only volatile modifiers and salt additives facilitating any follow-up use such as qualitative or quantitate analysis or further purification down to the single lipid species level. Graphical Abstract.
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Affiliation(s)
- Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Chemistry Meets Microbiology, Althanstrasse 14, 1090, Vienna, Austria
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
- ISOtopic Solutions, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Ulrike Grienke
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Pharmacognosy, Faculty of Life Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Judith M Rollinger
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Pharmacognosy, Faculty of Life Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- Chemistry Meets Microbiology, Althanstrasse 14, 1090, Vienna, Austria.
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Ali R, Clark LD, Zahm JA, Lemoff A, Ramesh K, Rosenbaum DM, Rosen MK. Improved strategy for isoleucine 1H/ 13C methyl labeling in Pichia pastoris. J Biomol NMR 2019; 73:687-697. [PMID: 31541396 PMCID: PMC6875547 DOI: 10.1007/s10858-019-00281-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Site specific methyl labeling combined with methyl TROSY offers a powerful NMR approach to study structure and dynamics of proteins and protein complexes of high molecular weight. Robust and cost-effective methods have been developed for site specific protein 1H/13C methyl labeling in an otherwise deuterated background in bacteria. However, bacterial systems are not suitable for expression and isotope labeling of many eukaryotic and membrane proteins. The yeast Pichia pastoris (P. pastoris) is a commonly used host for expression of eukaryotic proteins, and site-specific methyl labeling of perdeuterated eukaryotic proteins has recently been achieved with this system. However, the practical utility of methyl labeling and deuteration in P. pastoris is limited by high costs. Here, we describe an improved method for 1H/13C-labeling of the δ-methyl group of isoleucine residues in a perdeuterated background, which reduces the cost by ≥ 50% without compromising the efficiency of isotope enrichment. We have successfully implemented this method to label actin and a G-protein coupled receptor. Our approach will facilitate studies of the structure and dynamics of eukaryotic proteins by NMR spectroscopy.
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Affiliation(s)
- Rustam Ali
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Lindsay D Clark
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Jacob A Zahm
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 130 Longwood Avenue, Boston, MA, 02115, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Karthik Ramesh
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Michael K Rosen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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Demiray E, Karatay SE, Dönmez G. Improvement of bioethanol production from pomegranate peels via acidic pretreatment and enzymatic hydrolysis. Environ Sci Pollut Res Int 2019; 26:29366-29378. [PMID: 31396876 DOI: 10.1007/s11356-019-06020-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
The aim of this study was to improve the ethanol production from pomegranate peels (PPs). Therefore, the effect of enzymatic hydrolysis and different pretreatments on ethanol production by yeasts was examined. There were three different enzyme concentrations (3.6, 7.2, 14.4 FPU/g substrate) tested for enzymatic hydrolysis, and four different PP media, such as WSPP (whole slurry of PP), LFPP (liquid fraction of PP), WSFPP (washed solid fraction of PP) and N-WSFPP (non-washed solid fraction of PP), were prepared. Bioethanol production was monitored for 96 h. Maximum ethanol concentrations were obtained at WSPP medium as 12.69 g/L, 14.35 g/L and 4.23 g/L in Saccharomyces cerevisiae, Kluyveromyces marxianus and Pichia stipitis, respectively. On the other hand, the washing step of biomass increased the kinetic parameters dramatically and the highest theoretical ethanol yields and YP/S values were obtained from WSFPP medium in all tested yeasts. Theoretical ethanol yields were 97.8%, 98.7% and 35.5% for S. cerevisiae, K. marxianus and P. stipitis, respectively. Qp values were observed as 0.98 g/L h, 0.99 g/L h and 0.04 g/L h for the same yeasts. The highest YP/S values were detected as 0.50 g/g for S. cerevisiae, 0.50 g/g for K. marxianus and 0.30 g/g for P. stipitis in the washed pomegranate peel biomass.
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Affiliation(s)
- Ekin Demiray
- Department of Biology, Faculty of Science, Ankara University, Beşevler, 06100, Ankara, Turkey
| | - Sevgi Ertuğrul Karatay
- Department of Biology, Faculty of Science, Ankara University, Beşevler, 06100, Ankara, Turkey.
| | - Gönül Dönmez
- Department of Biology, Faculty of Science, Ankara University, Beşevler, 06100, Ankara, Turkey
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5
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Lemma T, Wang J, Arstila K, Hytönen VP, Toppari JJ. Identifying yeasts using surface enhanced Raman spectroscopy. Spectrochim Acta A Mol Biomol Spectrosc 2019; 218:299-307. [PMID: 31005737 DOI: 10.1016/j.saa.2019.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/05/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
The molecular fingerprints of yeasts Saccharomyces cerevisiae, Dekkera bruxellensis, and Wickerhamomyces anomalus (former name Pichia anomala) have been examined using surface-enhanced Raman spectroscopy (SERS) and helium ion microscopy (HIM). The SERS spectra obtained from cell cultures (lysate and non-treated cells) distinguish between these very closely related fungal species. Highly SERS active silver nano-particles suitable for detecting complex biomolecules were fabricated using a simple synthesis route. The yeast samples mixed with aggregated Ag nanoparticles yielded highly enhanced and reproducible Raman signal owing to the high density of the hot spots at the junctions of two or more Ag nanoparticles and enabled to differentiate the three species based on their unique features (spectral fingerprint). We also collected SERS spectra of the three yeast species in beer medium to demonstrate the potential of the method for industrial application. These findings demonstrate the great potential of SERS for detection and identification of fungi species based on the biochemical compositions, even in a chemically complex sample.
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Affiliation(s)
- Tibebe Lemma
- Faculdade de Clências e Tecnologia (FCT)-Universidade Estadual Paulista (UNESP)-Presidente Prudente, SP 19060-900, Brazil.
| | - Jin Wang
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Kai Arstila
- NanoScience Center, Department of Physics, P.O. Box 35 (YN), FI-40014, University of Jyväskylä, Finland
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, BioMediTech, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland; Fimlab Laboratories, Biokatu 4, FI-33520 Tampere, Finland
| | - J Jussi Toppari
- NanoScience Center, Department of Physics, P.O. Box 35 (YN), FI-40014, University of Jyväskylä, Finland
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Miyamoto K, Aoki W, Ohtani Y, Miura N, Aburaya S, Matsuzaki Y, Kajiwara K, Kitagawa Y, Ueda M. Peptide barcoding for establishment of new types of genotype-phenotype linkages. PLoS One 2019; 14:e0215993. [PMID: 31013333 PMCID: PMC6478338 DOI: 10.1371/journal.pone.0215993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/06/2019] [Indexed: 01/15/2023] Open
Abstract
Measuring binding properties of binders (e.g., antibodies) is essential for developing useful experimental reagents, diagnostics, and pharmaceuticals. Display technologies can evaluate a large number of binders in a high-throughput manner, but the immobilization effect and the avidity effect prohibit the precise evaluation of binding properties. In this paper, we propose a novel methodology, peptide barcoding, to quantitatively measure the binding properties of multiple binders without immobilization. In the experimental scheme, unique peptide barcodes are fused with each binder, and they represent genotype information. These peptide barcodes are designed to have high detectability for mass spectrometry, leading to low identification bias and a high identification rate. A mixture of different peptide-barcoded nanobodies is reacted with antigen-coated magnetic beads in one pot. Peptide barcodes of functional nanobodies are cleaved on beads by a specific protease, and identified by selected reaction monitoring using triple quadrupole mass spectrometry. To demonstrate proof-of-principle for peptide barcoding, we generated peptide-barcoded anti-CD4 nanobody and anti-GFP nanobody, and determined whether we could simultaneously quantify their binding activities. We showed that peptide barcoding did not affect the properties of the nanobodies, and succeeded in measuring the binding activities of these nanobodies in one shot. The results demonstrate the advantages of peptide barcoding, new types of genotype–phenotype linkages.
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Affiliation(s)
- Kana Miyamoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 7 Goban-cho, Chiyoda-ku, Tokyo, Japan
- Kyoto Integrated Science & Technology Bio-Analysis Center, 134 Chudoji Minamimachi, Simogyo-ku, Kyoto, Japan
| | - Yuta Ohtani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Natsuko Miura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1–1 Gakuen-cho, Naka-ku, Sakai, Osaka, Japan
| | - Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, Japan
| | - Yusei Matsuzaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Kaho Kajiwara
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Yoshinori Kitagawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 7 Goban-cho, Chiyoda-ku, Tokyo, Japan
- Kyoto Integrated Science & Technology Bio-Analysis Center, 134 Chudoji Minamimachi, Simogyo-ku, Kyoto, Japan
- * E-mail:
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Li X, Xia W, Bai Y, Ma R, Yang H, Luo H, Shi P. A Novel Thermostable GH3 β-Glucosidase from Talaromyce leycettanus with Broad Substrate Specificity and Significant Soybean Isoflavone Glycosides-Hydrolyzing Capability. Biomed Res Int 2018; 2018:4794690. [PMID: 30426008 PMCID: PMC6218797 DOI: 10.1155/2018/4794690] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 09/17/2018] [Indexed: 12/19/2022]
Abstract
A novel β-glucosidase gene (Bgl3B) of glycoside hydrolase (GH) family 3 was cloned from the thermophilic fungus Talaromyce leycettanus JM12802 and successfully expressed in Pichia pastoris. The deduced Bgl3B contains 860 amino acid residues with a calculated molecular mass of 91.2 kDa. The purified recombinant Bgl3B exhibited maximum activities at pH 4.5 and 65°C and remained stable at temperatures up to 60°C and pH 3.0-9.0, respectively. The enzyme exhibited broad substrate specificities, showing β-glucosidase, glucanase, cellobiase, xylanase, and isoflavone glycoside hydrolase activities, and its activities were stimulated by short-chain alcohols. The catalytic efficiencies of Bgl3B were 693 and 104/mM/s towards pNPG and cellobiose, respectively. Moreover, Bgl3B was highly effective in converting isoflavone glycosides to aglycones at 37°C within 10 min, with the hydrolysis rates of 95.1%, 76.0%, and 75.3% for daidzin, genistin, and glycitin, respectively. These superior properties make Bgl3B potential for applications in the food, animal feed, and biofuel industries.
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Affiliation(s)
- Xinxin Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Xia
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hong Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pengjun Shi
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Schmuck B, Gudmundsson M, Blomqvist J, Hansson H, Härd T, Sandgren M. Production of Ready-To-Use Functionalized Sup35 Nanofibrils Secreted by Komagataella pastoris. ACS Nano 2018; 12:9363-9371. [PMID: 30207696 DOI: 10.1021/acsnano.8b04450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Amyloid nanofibrils are excellent scaffolds for designable materials that can be endowed with biotechnologically relevant functions. However, most of all excellent ideas and concepts that have been reported in the literature might never see real-world implementation in biotechnological applications. One bottleneck is the large-scale production of these materials. In this paper, we present an attempt to create a generic and scalable platform for producing ready-to-use functionalized nanofibrils directly from a eukaryotic organism. As a model material, we assembled Sup35(1-61) amyloid nanofibrils from Saccharomyces cerevisiae decorated with the Z-domain dimer, which has a high affinity toward antibody molecules. To this end, Komagataella pastoris was engineered by inserting gene copies of Sup35(1-61) and the protein chimera Sup35(1-61)-ZZ into the genome. This strain has the capability to constantly secrete amyloidogenic proteins into the extracellular medium, where the mature functionalized fibrils form, with a production yield of 35 mg/L culture. Another striking feature of this strategy is that the separation of the fibril material from the cells requires only centrifugation and resuspension in saline water. The fast production rates, minimal hands-on time, and high stability of the assembled material are some highlights that make the direct assembly of functionalized fibrils in the extracellular medium an alternative to production methods that are not suitable for large-scale production of designed amyloids.
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Affiliation(s)
- Benjamin Schmuck
- Department of Molecular Sciences , Swedish University of Agricultural Sciences , 756 51 Uppsala , Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences , Swedish University of Agricultural Sciences , 756 51 Uppsala , Sweden
| | - Johanna Blomqvist
- Department of Molecular Sciences , Swedish University of Agricultural Sciences , 756 51 Uppsala , Sweden
| | - Henrik Hansson
- Department of Molecular Sciences , Swedish University of Agricultural Sciences , 756 51 Uppsala , Sweden
| | - Torleif Härd
- Department of Molecular Sciences , Swedish University of Agricultural Sciences , 756 51 Uppsala , Sweden
| | - Mats Sandgren
- Department of Molecular Sciences , Swedish University of Agricultural Sciences , 756 51 Uppsala , Sweden
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De la Torre González FJ, Avendaño DOG, Mathis ACG, Kirchmayr MR. Evaluation of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for differentiation of Pichia kluyveri strains isolated from traditional fermentation processes. Rapid Commun Mass Spectrom 2018; 32:1514-1520. [PMID: 29873842 DOI: 10.1002/rcm.8192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/18/2018] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Non-Saccharomyces yeasts are widespread microorganisms that nowadays have gained importance for their ability to produce volatile compounds which in alcoholic beverages improve aromatic complexity and therefore the overall quality. Their rapid identification and differentiation in fermentation processes is vital for timely decision making. METHODS A total of 19 strains of Pichia kluyveri isolated from mezcal, tejuino and cacao fermentations were analyzed with rep-PCR fingerprinting using the primer (GTG)5 and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) on a Microflex LT mass spectrometer using Biotyper 3.1 software (Bruker Daltonics). RESULTS The comparative analysis between MS spectra and rep-PCR patterns obtained from these strains showed a high similarity between both methods. However, minimal differences between the obtained rep-PCR and MALDI-TOF MS clusters could be observed, especially by the presence and/or absence of one or more discriminating peaks even when they have similarities in their main spectra projection, observing that isolates from the same fermentative process were grouped into the same sub-cluster based on their MALDI-TOF MS profiles. CONCLUSIONS The data shown suggests that MALDI-TOF MS is a promising alternative technique for rapid, reliable and cost-effective differentiation of native yeast strains isolated from different traditional fermented foods and beverages.
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Affiliation(s)
- Francisco Javier De la Torre González
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, México
| | - Daniel Oswaldo Gutiérrez Avendaño
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, México
| | - Anne Christine Gschaedler Mathis
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, México
| | - Manuel Reinhart Kirchmayr
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, México
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Suzuki R, Sakakura M, Mori M, Fujii M, Akashi S, Takahashi H. Methyl-selective isotope labeling using α-ketoisovalerate for the yeast Pichia pastoris recombinant protein expression system. J Biomol NMR 2018; 71:213-223. [PMID: 29869771 DOI: 10.1007/s10858-018-0192-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Methyl-detected NMR spectroscopy is a useful tool for investigating the structures and interactions of large macromolecules such as membrane proteins. The procedures for preparation of methyl-specific isotopically-labeled proteins were established for the Escherichia coli (E. coli) expression system, but typically it is not feasible to express eukaryotic proteins using E. coli. The Pichia pastoris (P. pastoris) expression system is the most common yeast expression system, and is known to be superior to the E. coli system for the expression of mammalian proteins, including secretory and membrane proteins. However, this system has not yet been optimized for methyl-specific isotope labeling, especially for Val/Leu-methyl specific isotope incorporation. To overcome this difficulty, we explored various culture conditions for the yeast cells to efficiently uptake Val/Leu precursors. Among the searched conditions, we found that the cultivation pH has a critical effect on Val/Leu precursor uptake. At an acidic cultivation pH, the uptake of the Val/Leu precursor was increased, and methyl groups of Val and Leu in the synthesized recombinant protein yielded intense 1H-13C correlation signals. Based on these results, we present optimized protocols for the Val/Leu-methyl-selective 13C incorporation by the P. pastoris expression system.
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Affiliation(s)
- Rika Suzuki
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masayoshi Sakakura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masaki Mori
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Moe Fujii
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hideo Takahashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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11
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Clark L, Dikiy I, Rosenbaum DM, Gardner KH. On the use of Pichia pastoris for isotopic labeling of human GPCRs for NMR studies. J Biomol NMR 2018; 71:203-211. [PMID: 30121871 PMCID: PMC7282444 DOI: 10.1007/s10858-018-0204-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 05/21/2023]
Abstract
NMR studies of human integral membrane proteins provide unique opportunities to probe structure and dynamics at specific locations and on multiple timescales, often with significant implications for disease mechanism and drug development. Since membrane proteins such as G protein-coupled receptors (GPCRs) are highly dynamic and regulated by ligands or other perturbations, NMR methods are potentially well suited to answer basic functional questions (such as addressing the biophysical basis of ligand efficacy) as well as guiding applications (such as novel ligand design). However, such studies on eukaryotic membrane proteins have often been limited by the inability to incorporate optimal isotopic labels for NMR methods developed for large protein/lipid complexes, including methyl TROSY. We review the different expression systems for production of isotopically labeled membrane proteins and highlight the use of the yeast Pichia pastoris to achieve perdeuteration and 13C methyl probe incorporation within isoleucine sidechains. We further illustrate the use of this method for labeling of several biomedically significant GPCRs.
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Affiliation(s)
- Lindsay Clark
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA
- Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Igor Dikiy
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA.
- Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, New York, NY, 10016, USA.
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12
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Eddy MT, Gao ZG, Mannes P, Patel N, Jacobson KA, Katritch V, Stevens RC, Wüthrich K. Extrinsic Tryptophans as NMR Probes of Allosteric Coupling in Membrane Proteins: Application to the A 2A Adenosine Receptor. J Am Chem Soc 2018; 140:8228-8235. [PMID: 29874058 PMCID: PMC6192543 DOI: 10.1021/jacs.8b03805] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tryptophan indole 15N-1H signals are well separated in nuclear magnetic resonance (NMR) spectra of proteins. Assignment of the indole 15N-1H signals therefore enables one to obtain site-specific information on complex proteins in supramacromolecular systems, even when extensive assignment of backbone 15N-1H resonances is challenging. Here we exploit the unique indole 15N-1H chemical shift by introducing extrinsic tryptophan reporter residues at judiciously chosen locations in a membrane protein for increased coverage of structure and function by NMR. We demonstrate this approach with three variants of the human A2A adenosine receptor (A2AAR), a class A G protein-coupled receptor, each containing a single extrinsic tryptophan near the receptor intracellular surface, in helix V, VI, or VII, respectively. We show that the native A2AAR global protein fold and ligand binding activity are preserved in these A2AAR variants. The indole 15N-1H signals from the extrinsic tryptophan reporter residues show different responses to variable efficacy of drugs bound to the receptor orthosteric cavity, and the indole 15N-1H chemical shift of the tryptophan introduced at the intracellular end of helix VI is sensitive to conformational changes resulting from interactions with a polypeptide from the carboxy terminus of the GαS intracellular partner protein. Introducing extrinsic tryptophans into proteins in complex supramolecular systems thus opens new avenues for NMR investigations in solution.
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Affiliation(s)
- Matthew T. Eddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Bridge Institute, Departments of Biological Sciences and Chemistry, Michelson Center, University of Southern California, Los Angeles, California 90089, United States
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Philip Mannes
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Nilkanth Patel
- Bridge Institute, Departments of Biological Sciences and Chemistry, Michelson Center, University of Southern California, Los Angeles, California 90089, United States
| | - Kenneth A. Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Vsevolod Katritch
- Bridge Institute, Departments of Biological Sciences and Chemistry, Michelson Center, University of Southern California, Los Angeles, California 90089, United States
| | - Raymond C. Stevens
- Bridge Institute, Departments of Biological Sciences and Chemistry, Michelson Center, University of Southern California, Los Angeles, California 90089, United States
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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13
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Guijas C, Montenegro-Burke JR, Domingo-Almenara X, Palermo A, Warth B, Hermann G, Koellensperger G, Huan T, Uritboonthai W, Aisporna AE, Wolan DW, Spilker ME, Benton HP, Siuzdak G. METLIN: A Technology Platform for Identifying Knowns and Unknowns. Anal Chem 2018; 90:3156-3164. [PMID: 29381867 PMCID: PMC5933435 DOI: 10.1021/acs.analchem.7b04424] [Citation(s) in RCA: 576] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
METLIN originated as a database to characterize known metabolites and has since expanded into a technology platform for the identification of known and unknown metabolites and other chemical entities. Through this effort it has become a comprehensive resource containing over 1 million molecules including lipids, amino acids, carbohydrates, toxins, small peptides, and natural products, among other classes. METLIN's high-resolution tandem mass spectrometry (MS/MS) database, which plays a key role in the identification process, has data generated from both reference standards and their labeled stable isotope analogues, facilitated by METLIN-guided analysis of isotope-labeled microorganisms. The MS/MS data, coupled with the fragment similarity search function, expand the tool's capabilities into the identification of unknowns. Fragment similarity search is performed independent of the precursor mass, relying solely on the fragment ions to identify similar structures within the database. Stable isotope data also facilitate characterization by coupling the similarity search output with the isotopic m/ z shifts. Examples of both are demonstrated here with the characterization of four previously unknown metabolites. METLIN also now features in silico MS/MS data, which has been made possible through the creation of algorithms trained on METLIN's MS/MS data from both standards and their isotope analogues. With these informatic and experimental data features, METLIN is being designed to address the characterization of known and unknown molecules.
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Affiliation(s)
- Carlos Guijas
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - J. Rafael Montenegro-Burke
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Xavier Domingo-Almenara
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Amelia Palermo
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Benedikt Warth
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Waehringerstrasse 38, Vienna 1090, Austria
| | - Gerrit Hermann
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 38, Vienna 1090, Austria
- ISOtopic Solutions, Waehringerstrasse 38, Vienna 1090, Austria
| | - Gunda Koellensperger
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 38, Vienna 1090, Austria
| | - Tao Huan
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Winnie Uritboonthai
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Aries E. Aisporna
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dennis W. Wolan
- Departments of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Mary E. Spilker
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - H. Paul Benton
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gary Siuzdak
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Departments of Chemistry, Molecular, and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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14
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Rivera-Hoyos CM, Morales-Álvarez ED, Abelló-Esparza J, Buitrago-Pérez DF, Martínez-Aldana N, Salcedo-Reyes JC, Poutou-Piñales RA, Pedroza-Rodríguez AM. Detoxification of pulping black liquor with Pleurotus ostreatus or recombinant Pichia pastoris followed by CuO/TiO 2/visible photocatalysis. Sci Rep 2018; 8:3503. [PMID: 29472555 PMCID: PMC5823849 DOI: 10.1038/s41598-018-21597-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 02/07/2018] [Indexed: 12/28/2022] Open
Abstract
Cellulose-pulping requires chemicals such as Cl2, ClO2, H2O2, and O2. The black liquor (BL) generated exhibits a high chemical oxygen demand (COD), five-day biochemical oxygen demand (BOD5), and chlorophenol content, along with an augmented colour and increased pH. BL is often discharged into water bodies, where it has a negative impact on the environment. Towards that end, laccases are of great interest for bioremediation, since they can degrade aromatic and non-aromatic compounds while reducing O2 to water instead of H2O2. As such, we evaluated Pleurotus ostreatus and Pichia pastoris (which produces rPOXA 1B laccase) in the treatment of synthetic BL (SBL) in an "in vitro" modified Kraft process followed by CuO/TiO2/visible light photocatalysis. Treating SBL with P. ostreatus viable biomass (VB) followed by CuO/TiO2/visible light photocatalysis resulted in 80.3% COD removal and 70.6% decolourisation. Toxic compounds such as 2-methylphenol, 4-methylphenol, and 2-methoxyphenol were eliminated. Post-treated SBL exhibited low phytotoxicity, as evidenced by a Lactuca sativa L seed germination index (GI) > 50%. Likewise, SBL treatment with P. pastoris followed by VB/CuO/TiO2/visible light photocatalysis resulted in 63.7% COD removal and 46% decolourisation. Moreover, this treatment resulted in the elimination of most unwanted compounds, with the exception of 4-chlorophenol. The Lactuca sativa L seed GI of the post-treated SBL was 40%, indicating moderate phytotoxicity.
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Affiliation(s)
- Claudia M Rivera-Hoyos
- Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI) Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia.
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia.
| | - Edwin D Morales-Álvarez
- Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI) Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
- Departamento de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas. Manizales, Caldas, Colombia
| | - Juanita Abelló-Esparza
- Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI) Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Daniel F Buitrago-Pérez
- Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI) Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Nicolás Martínez-Aldana
- Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI) Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Juan C Salcedo-Reyes
- Laboratorio de Películas Delgadas y Nanofotónica, Departamento de Física, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Raúl A Poutou-Piñales
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Aura M Pedroza-Rodríguez
- Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI) Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia.
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15
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Li S, Hong T, Wang K, Lu Y, Zhou M. Dissociation and purification of the endogenous membrane-bound Vo complex from Pichia pastoris. Protein Expr Purif 2017; 138:76-80. [PMID: 28709863 DOI: 10.1016/j.pep.2017.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/29/2017] [Accepted: 07/11/2017] [Indexed: 01/22/2023]
Abstract
Most proteins occur and function in complexes rather than as isolated entities in membranes. In most cases macromolecules with multiple subunits are purified from endogenous sources. In this study, an endogenous membrane-protein complex was obtained from Pichia pastoris, which can be grown at high densities to significantly improve the membrane protein yield. We successfully isolated the membrane-bound Vo complex of V-ATPase from P. pastoris using a fusion FLAG tag attached to the C-terminus of subunit a to generate the vph-tag strain, which was used for dissociation and purification. After FLAG affinity and size exclusion chromatography purification, the production quantity and purity of the membrane-bound Vo complex was 20 μg l-1 and >98%, respectively. The subunits of the endogenous membrane-bound Vo complex observed in P. pastoris were similar to those obtained from S. cerevisiae, as demonstrated by liquid chromatography-tandem mass spectrometry (LC-MS-MS). Therefore, successful dissociation and purification of the membrane-bound Vo complex at a high purity and sufficient quantity was achieved via a rapid and simple procedure that can be used to obtain the endogenous membrane-protein complexes from P. pastoris.
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Affiliation(s)
- Sumei Li
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China.
| | - Tao Hong
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Kun Wang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Yinghong Lu
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Min Zhou
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China.
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16
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Wang P, Zhang L, Fisher R, Chen M, Liang S, Han S, Zheng S, Sui H, Lin Y. Accurate analysis of fusion expression of Pichia pastoris glycosylphosphatidylinositol-modified cell wall proteins. J Ind Microbiol Biotechnol 2017; 44:1355-1365. [PMID: 28660369 DOI: 10.1007/s10295-017-1962-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/15/2017] [Indexed: 11/24/2022]
Abstract
Glycosylphosphatidylinositol (GPI)-anchored glycoproteins have diverse intrinsic functions in yeasts, and they also have different uses in vitro. The GPI-modified cell wall proteins GCW21, GCW51, and GCW61 of Pichia pastoris were chosen as anchoring proteins to construct co-expression strains in P. pastoris GS115. The hydrolytic activity and the amount of Candida antarctica lipase B (CALB) displayed on cell surface increased significantly following optimization of the fusion gene dosage and combination of the homogeneous or heterogeneous cell wall proteins. Maximum CALB hydrolytic activity was achieved at 4920 U/g dry cell weight in strain GS115/CALB-GCW (51 + 51 + 61 + 61) after 120 h of methanol induction. Changes in structural morphology and the properties of the cell surfaces caused by co-expression of fusion proteins were observed by transmission electron microscopy (TEM) and on plates containing cell-wall-destabilizing reagent. Our results suggested that both the outer and inner cell layers were significantly altered by overexpression of GPI-modified cell wall proteins. Interestingly, quantitative analysis of the inner layer components showed an increase in β-1,3-glucan, but no obvious changes in chitin in the strains overexpressing GPI-modified cell wall proteins.
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Affiliation(s)
- Pan Wang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Li Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Rebecca Fisher
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
| | - Meiqi Chen
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Haixin Sui
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China.
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17
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Liu X, Dong Y, Wang J, Li L, Zhong Z, Li YP, Chen SJ, Fu YC, Xu WC, Wei CJ. VSV-G Viral Envelope Glycoprotein Prepared from Pichia pastoris Enhances Transfection of DNA into Animal Cells. J Microbiol Biotechnol 2017; 27:1098-1105. [PMID: 28297751 DOI: 10.4014/jmb.1611.11082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Vesicular stomatitis virus G glycoprotein (VSV-G) has been widely used for pseudotyping retroviral, lentiviral, and artificial viral vectors. The objective of this study was to establish a potential approach for large-scale production of VSV-G. To this end, VSV-G was cloned with an N-terminal His-tag into Pichia pastoris expression vector pPIC3.5K. Three clones (Muts) containing the VSV-G expression cassette were identified by PCR. All clones proliferated normally in expansion medium, whereas the proliferation was reduced significantly under induction conditions. VSV-G protein was detected in cell lysates by western blot analysis, and the highest expression level was observed at 96 h post induction. VSV-G could also be obtained from the condition medium of yeast protoplasts. Furthermore, VSV-G could be incorporated into Ad293 cells and was able to induce cell fusion, leading to the transfer of cytoplasmic protein. Finally, VSV-G-mediated DNA transfection was assayed by flow cytometry and luciferase measurement. Incubation of VSV-G lysate with the pGL3-control DNA complex increased the luciferase activity in Ad293 and HeLa cells by about 3-fold. Likewise, incubation of VSV-G lysate with the pCMV-DsRed DNA complex improved the transfection efficiency into Ad293 by 10% and into HeLa cells by about 1-fold. In conclusion, these results demonstrate that VSV-G could be produced from P. pastoris with biofunctionalities, demonstrating that large-scale production of the viral glycoprotein is feasible.
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Affiliation(s)
- Xin Liu
- Multidisciplinary Research Center, Shantou University, Shantou, Guangdong 515063, P.R. China
| | - Ying Dong
- Multidisciplinary Research Center, Shantou University, Shantou, Guangdong 515063, P.R. China
| | - Jingquan Wang
- Multidisciplinary Research Center, Shantou University, Shantou, Guangdong 515063, P.R. China
| | - Long Li
- Multidisciplinary Research Center, Shantou University, Shantou, Guangdong 515063, P.R. China
| | - Zhenmin Zhong
- Multidisciplinary Research Center, Shantou University, Shantou, Guangdong 515063, P.R. China
| | - Yun-Pan Li
- Multidisciplinary Research Center, Shantou University, Shantou, Guangdong 515063, P.R. China
| | - Shao-Jun Chen
- Multidisciplinary Research Center, Shantou University, Shantou, Guangdong 515063, P.R. China
| | - Yu-Cai Fu
- Laboratory of Cell Senescence, Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Wen-Can Xu
- Department of Endocrinology, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Chi-Ju Wei
- Multidisciplinary Research Center, Shantou University, Shantou, Guangdong 515063, P.R. China
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18
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Aponte-Santamaría C, Fischer G, Båth P, Neutze R, de Groot BL. Temperature dependence of protein-water interactions in a gated yeast aquaporin. Sci Rep 2017; 7:4016. [PMID: 28638135 PMCID: PMC5479825 DOI: 10.1038/s41598-017-04180-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/10/2017] [Indexed: 11/18/2022] Open
Abstract
Regulation of aquaporins is a key process of living organisms to counteract sudden osmotic changes. Aqy1, which is a water transporting aquaporin of the yeast Pichia pastoris, is suggested to be gated by chemo-mechanical stimuli as a protective regulatory-response against rapid freezing. Here, we tested the influence of temperature by determining the X-ray structure of Aqy1 at room temperature (RT) at 1.3 Å resolution, and by exploring the structural dynamics of Aqy1 during freezing through molecular dynamics simulations. At ambient temperature and in a lipid bilayer, Aqy1 adopts a closed conformation that is globally better described by the RT than by the low-temperature (LT) crystal structure. Locally, for the blocking-residue Tyr31 and the water molecules inside the pore, both LT and RT data sets are consistent with the positions observed in the simulations at room-temperature. Moreover, as the temperature was lowered, Tyr31 adopted a conformation that more effectively blocked the channel, and its motion was accompanied by a temperature-driven rearrangement of the water molecules inside the channel. We therefore speculate that temperature drives Aqy1 from a loosely- to a tightly-blocked state. This analysis provides high-resolution structural evidence of the influence of temperature on membrane-transport channels.
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Affiliation(s)
- Camilo Aponte-Santamaría
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia.
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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Wang QH, Liang L, Liu WC, Gong T, Chen JJ, Hou Q, Yang JL, Zhu P. Enhancement of recombinant BmK AngM1 production in Pichia pastoris by regulating gene dosage, co-expressing with chaperones and fermenting in fed-batch mode. J Asian Nat Prod Res 2017; 19:581-594. [PMID: 28376654 DOI: 10.1080/10286020.2017.1311872] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The scorpion peptide BmK AngM1 was reported to exhibit evident analgesic effect, but its yield by extraction from scorpion venom limits the research and application. The heterologous expression of BmK AngM1 was achieved in Pichia pastoris in our previous study. In order to realize high-level expression of recombinant BmK AngM1 (rBmK AngM1), the gene dosage of BmK AngM1 was optimized in engineered strains. The yield of rBmK AngM1 in the four-copy strain reached up to 100 mg/L, which was further enhanced to 190 mg/L by co-expressing with chaperones of PDI, BiP, and HAC1. Moreover, the yield of rBmK AngM1 was up to 1200 mg/L by high-density fermentation in 10 L fermenter. Finally, 360 mg rBmK AngM1 was purified from 1 L cultures by a two-step purification method. The efficient and convenient techniques presented in this study could facilitate further scale-up for industrial production of rBmK AngM1.
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Affiliation(s)
- Qing-Hua Wang
- a State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
- b Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Lan Liang
- a State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
- b Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Wan-Cang Liu
- c Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Ting Gong
- a State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
- b Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Jing-Jing Chen
- a State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
- b Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Qi Hou
- a State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
- b Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Jin-Ling Yang
- a State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
- b Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Ping Zhu
- a State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
- b Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
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20
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Handley PN, Carroll A, Ferro V. New structural insights into the oligosaccharide phosphate fraction of Pichia (Hansenula) holstii NRRL Y2448 phosphomannan. Carbohydr Res 2017; 446-447:68-75. [PMID: 28531457 DOI: 10.1016/j.carres.2017.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 12/26/2022]
Abstract
The oligosaccharide phosphate fraction (OPF) obtained from mild acid hydrolysis of P. holstii NRRL Y-2448 phosphomannan is the starting material for the preparation of the Phase III anticancer drug candidate PI-88. The OPF was for the first time successfully separated by preparative ion exchange chromatography and the major oligosaccharides isolated and characterized by NMR spectroscopy. The components were also acetylated and subjected to LC-MS analysis. These studies revealed that the OPF also contained all-α(1 → 3)-linked oligosaccharides in addition to the known α(1 → 3)/(1 → 2)-linked species, most likely formed by hydrolysis of the latter. Contrary to previous assumptions, the only phosphorylated disaccharide present is α(1 → 3)-linked. In addition, it was determined that a glycosylamine derivative previously isolated is, in fact, a manufacturing byproduct formed from exposure to aqueous ammonium bicarbonate during chromatographic purification. Based on these findings a new generic structure for PI-88 is proposed which more accurately reflects its composition.
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Affiliation(s)
| | - Anthony Carroll
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Qld 4111, Australia.
| | - Vito Ferro
- Progen Pharmaceuticals Ltd, Darra, Qld 4076, Australia.
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21
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Landry MP, Ando H, Chen A, Cao J, Kottadiel VI, Chio L, Yang D, Dong J, Lu T, Strano M. Single-molecule detection of protein efflux from microorganisms using fluorescent single-walled carbon nanotube sensor arrays. Nat Nanotechnol 2017; 12:368-377. [PMID: 28114298 PMCID: PMC6438169 DOI: 10.1038/nnano.2016.284] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 12/01/2016] [Indexed: 05/14/2023]
Abstract
A distinct advantage of nanosensor arrays is their ability to achieve ultralow detection limits in solution by proximity placement to an analyte. Here, we demonstrate label-free detection of individual proteins from Escherichia coli (bacteria) and Pichia pastoris (yeast) immobilized in a microfluidic chamber, measuring protein efflux from single organisms in real time. The array is fabricated using non-covalent conjugation of an aptamer-anchor polynucleotide sequence to near-infrared emissive single-walled carbon nanotubes, using a variable chemical spacer shown to optimize sensor response. Unlabelled RAP1 GTPase and HIV integrase proteins were selectively detected from various cell lines, via large near-infrared fluorescent turn-on responses. We show that the process of E. coli induction, protein synthesis and protein export is highly stochastic, yielding variability in protein secretion, with E. coli cells undergoing division under starved conditions producing 66% fewer secreted protein products than their non-dividing counterparts. We further demonstrate the detection of a unique protein product resulting from T7 bacteriophage infection of E. coli, illustrating that nanosensor arrays can enable real-time, single-cell analysis of a broad range of protein products from various cell types.
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Affiliation(s)
- Markita Patricia Landry
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720
- California Institute for Quantitative Biosciences (qb3), University of California-Berkeley, Berkeley, CA 94720
| | - Hiroki Ando
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Allen Chen
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Biophysics Program, Harvard University, Cambridge, Massachusetts 02138
| | - Jicong Cao
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Vishal Isaac Kottadiel
- The Rowland Institute at Harvard University, Cambridge, Massachusetts 02142
- Department of Biology, The Catholic University of America, Washington, District of Columbia 20064
| | - Linda Chio
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720
| | - Darwin Yang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720
| | - Juyao Dong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138
| | - Timothy Lu
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Michael Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138
- Corresponding Author: (M.S.S.)
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22
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Yang J, Cheng Y, Zhu Y, Zhu J, Chen T, Xu Y, Yong Q, Yu S. [Effect of phenolic ketones on ethanol fermentation and cellular lipid composition of Pichia stipitis]. Sheng Wu Gong Cheng Xue Bao 2016; 32:185-194. [PMID: 27382768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Lignin degradation products are toxic to microorganisms, which is one of the bottlenecks for fuel ethanol production. We studied the effects of phenolic ketones (4-hydroxyacetophenone, 4-hydroxy-3-methoxy-acetophenone and 4-hydroxy-3,5-dimethoxy-acetophenone) derived from lignin degradation on ethanol fermentation of xylose and cellular lipid composition of Pichia stipitis NLP31. Ethanol and the cellular fatty acid of yeast were analyzed by high performance liquid chromatography (HPLC) and gas chromatography/mass spectrometry (GC/MS). Results indicate that phenolic ketones negatively affected ethanol fermentation of yeast and the lower molecular weight phenolic ketone compound was more toxic. When the concentration of 4-hydroxyacetophenone was 1.5 g/L, at fermentation of 24 h, the xylose utilization ratio, ethanol yield and ethanol concentration decreased by 42.47%, 5.30% and 9.76 g/L, respectively, compared to the control. When phenolic ketones were in the medium, the ratio of unsaturated fatty acids to saturated fatty acids (UFA/SFA) of yeast cells was improved. When 1.5 g/L of three aforementioned phenolic ketones was added to the fermentation medium, the UFA/SFA ratio of yeast cells increased to 3.03, 3.06 and 3.61, respectively, compared to 2.58 of the control, which increased cell membrane fluidity and instability. Therefore, phenolic ketones can reduce the yeast growth, increase the UFA/SFA ratio of yeast and lower ethanol productivity. Effectively reduce or remove the content of lignin degradation products is the key to improve lignocellulose biorefinery.
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Areesirisuk A, Chiu CH, Yen TB, Liu CH, Guo JH. A NOVEL OLEAGINOUS YEAST STRAIN WITH HIGH LIPID PRODUCTIVITY AND ITS APPLICATION TO ALTERNATIVE BIODIESEL PRODUCTION. ACTA ACUST UNITED AC 2015; 51:387-94. [PMID: 26353403 DOI: 10.7868/s0555109915030034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Five lipid-producing yeast strains, CHC08, CHC11, CHC28, CHC34, and CHC35, were revealed by Sudan Black B staining to contain lipid droplets within cells. Molecular analysis demonstrated that they were 2 strains of Candida parapsilosis, Pseudozyma parantarctica, Pichia manshurica, and Pichia occidentalis. Following batch fermentation, P. parantarctica CHC28 was found to have the highest biomass concentration, total lipids and lipid content levels. The major fatty acids in the lipids of this yeast strain were C16 and C18. Predictions of the properties of yeast biodiesel using linear equations resulted in values similar to biodiesel made from plant oils. Preliminary production of yeast biodiesel from P. parantarctica CHC28 was accomplished through esterification and transesterification reactions. It was found that yeast lipids with high acid value are easily converted to biodiesel at an approximately 90% yield. Therefore, it is possible to use crude lipids as alternative raw materials for biodiesel production.
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24
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Chang PK, Hua SST, Sarreal SBL, Li RW. Suppression of Aflatoxin Biosynthesis in Aspergillus flavus by 2-Phenylethanol Is Associated with Stimulated Growth and Decreased Degradation of Branched-Chain Amino Acids. Toxins (Basel) 2015; 7:3887-902. [PMID: 26404375 PMCID: PMC4626709 DOI: 10.3390/toxins7103887] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/02/2015] [Accepted: 09/17/2015] [Indexed: 11/30/2022] Open
Abstract
The saprophytic soil fungus Aspergillus flavus infects crops and produces aflatoxin. Pichia anomala, which is a biocontrol yeast and produces the major volatile 2-phenylethanol (2-PE), is able to reduce growth of A. flavus and aflatoxin production when applied onto pistachio trees. High levels of 2-PE are lethal to A. flavus and other fungi. However, at low levels, the underlying mechanism of 2-PE to inhibit aflatoxin production remains unclear. In this study, we characterized the temporal transcriptome response of A. flavus to 2-PE at a subinhibitory level (1 µL/mL) using RNA-Seq technology and bioinformatics tools. The treatment during the entire 72 h experimental period resulted in 131 of the total A. flavus 13,485 genes to be significantly impacted, of which 82 genes exhibited decreased expression. They included those encoding conidiation proteins and involved in cyclopiazonic acid biosynthesis. All genes in the aflatoxin gene cluster were also significantly decreased during the first 48 h treatment. Gene Ontology (GO) analyses showed that biological processes with GO terms related to catabolism of propionate and branched-chain amino acids (valine, leucine and isoleucine) were significantly enriched in the down-regulated gene group, while those associated with ribosome biogenesis, translation, and biosynthesis of α-amino acids were over-represented among the up-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that metabolic pathways negatively impacted among the down-regulated genes parallel to those active at 30 °C, a condition conducive to aflatoxin biosynthesis. In contrast, metabolic pathways positively related to the up-regulated gene group resembled those at 37 °C, which favors rapid fungal growth and is inhibitory to aflatoxin biosynthesis. The results showed that 2-PE at a low level stimulated active growth of A. flavus but concomitantly rendered decreased activities in branched-chain amino acid degradation. Since secondary metabolism occurs after active growth has ceased, this growth stimulation resulted in suppression of expression of aflatoxin biosynthesis genes. On the other hand, increased activities in degradation pathways for branched-chain amino acids probably are required for the activation of the aflatoxin pathway by providing building blocks and energy regeneration. Metabolic flux in primary metabolism apparently has an important role in the expression of genes of secondary metabolism.
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Affiliation(s)
- Perng-Kuang Chang
- Southern Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, New Orleans, LA 70124, USA.
| | - Sui Sheng T Hua
- Western Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, Albany, CA 94710, USA.
| | - Siov Bouy L Sarreal
- Western Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, Albany, CA 94710, USA.
| | - Robert W Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, U. S. Department of Agriculture, Beltsville, MD 20705, USA.
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25
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Luo Y, Wang J, Liu B, Wang Z, Yuan Y, Yue T. Effect of Yeast Cell Morphology, Cell Wall Physical Structure and Chemical Composition on Patulin Adsorption. PLoS One 2015; 10:e0136045. [PMID: 26295574 PMCID: PMC4546513 DOI: 10.1371/journal.pone.0136045] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/29/2015] [Indexed: 11/18/2022] Open
Abstract
The capability of yeast to adsorb patulin in fruit juice can aid in substantially reducing the patulin toxic effect on human health. This study aimed to investigate the capability of yeast cell morphology and cell wall internal structure and composition to adsorb patulin. To compare different yeast cell morphologies, cell wall internal structure and composition, scanning electron microscope, transmission electron microscope and ion chromatography were used. The results indicated that patulin adsorption capability of yeast was influenced by cell surface areas, volume, and cell wall thickness, as well as 1,3-β-glucan content. Among these factors, cell wall thickness and 1,3-β-glucan content serve significant functions. The investigation revealed that patulin adsorption capability was mainly affected by the three-dimensional network structure of the cell wall composed of 1,3-β-glucan. Finally, patulin adsorption in commercial kiwi fruit juice was investigated, and the results indicated that yeast cells could adsorb patulin from commercial kiwi fruit juice efficiently. This study can potentially simulate in vitro cell walls to enhance patulin adsorption capability and successfully apply to fruit juice industry.
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Affiliation(s)
- Ying Luo
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jianguo Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bin Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhouli Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
- * E-mail:
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26
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Kim H, Thak EJ, Lee DJ, Agaphonov MO, Kang HA. Hansenula polymorpha Pmt4p Plays Critical Roles in O-Mannosylation of Surface Membrane Proteins and Participates in Heteromeric Complex Formation. PLoS One 2015; 10:e0129914. [PMID: 26134523 PMCID: PMC4489896 DOI: 10.1371/journal.pone.0129914] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/14/2015] [Indexed: 01/09/2023] Open
Abstract
O-mannosylation, the addition of mannose to serine and threonine residues of secretory proteins, is a highly conserved post-translational modification found in organisms ranging from bacteria to humans. Here, we report the functional and molecular characterization of the HpPMT4 gene encoding a protein O-mannosyltransferase in the thermotolerant methylotrophic yeast Hansenula polymorpha, an emerging host for the production of therapeutic recombinant proteins. Compared to the deletion of HpPMT1, deletion of another major PMT gene, HpPMT4, resulted in more increased sensitivity to the antibiotic hygromycin B, caffeine, and osmotic stresses, but did not affect the thermotolerance of H. polymorpha. Notably, the deletion of HpPMT4 generated severe defects in glycosylation of the surface sensor proteins HpWsc1p and HpMid2p, with marginal effects on secreted glycoproteins such as chitinase and HpYps1p lacking a GPI anchor. However, despite the severely impaired mannosylation of surface sensor proteins in the Hppmt4∆ mutant, the phosphorylation of HpMpk1p and HpHog1p still showed a high increase upon treatment with cell wall disturbing agents or high concentrations of salts. The conditional Hppmt1pmt4∆ double mutant strains displayed severely impaired growth, enlarged cell size, and aberrant cell separation, implying that the loss of HpPMT4 function might be lethal to cells in the absence of HpPmt1p. Moreover, the HpPmt4 protein was found to form not only a homomeric complex but also a heteromeric complex with either HpPmt1p or HpPmt2p. Altogether, our results support the function of HpPmt4p as a key player in O-mannosylation of cell surface proteins and its participation in the formation of heterodimers with other PMT members, besides homodimer formation, in H. polymorpha.
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Affiliation(s)
- Hyunah Kim
- Department of Life Science, Chung-Ang University, Seoul 156–756, Korea
| | - Eun Jung Thak
- Department of Life Science, Chung-Ang University, Seoul 156–756, Korea
| | - Dong-Jik Lee
- Department of Life Science, Chung-Ang University, Seoul 156–756, Korea
| | - Michael O. Agaphonov
- A.N. Bach Institute of Biochemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul 156–756, Korea
- * E-mail:
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27
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Chu DB, Troyer C, Mairinger T, Ortmayr K, Neubauer S, Koellensperger G, Hann S. Isotopologue analysis of sugar phosphates in yeast cell extracts by gas chromatography chemical ionization time-of-flight mass spectrometry. Anal Bioanal Chem 2015; 407:2865-75. [PMID: 25673246 DOI: 10.1007/s00216-015-8521-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 01/17/2015] [Accepted: 01/27/2015] [Indexed: 01/05/2023]
Abstract
Metabolic flux analysis is based on the measurement of isotopologue ratios. In this work, a new GC-MS-based method was introduced enabling accurate determination of isotopologue distributions of sugar phosphates in cell extracts. A GC-TOFMS procedure was developed involving a two-step online derivatization (ethoximation followed by trimethylsilylation) offering high mass resolution, high mass accuracy and the potential of retrospective data analysis typical for TOFMS. The information loss due to fragmentation intrinsic for isotopologue analysis by electron ionization could be overcome by chemical ionization with methane. A thorough optimization regarding pressure of the reaction gas, emission current, electron energy and temperature of the ion source was carried out. For a substantial panel of sugar phosphates both of the glycolysis and the pentose phosphate pathway, sensitive determination of the protonated intact molecular ions together with low abundance fragment ions was successfully achieved. The developed method was evaluated for analysis of Pichia pastoris cell extracts. The measured isotopologue ratios were in the range of 55:1-2:1. The comparison of the experimental isotopologue fractions with the theoretical fractions was excellent, revealing a maximum bias of 4.6% and an average bias of 1.4%.
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Affiliation(s)
- Dinh Binh Chu
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, BOKU Vienna, Muthgasse 18, 1190, Vienna, Austria
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Higo T, Suka N, Ehara H, Wakamori M, Sato S, Maeda H, Sekine SI, Umehara T, Yokoyama S. Development of a hexahistidine-3× FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris. J Struct Funct Genomics 2014; 15:191-9. [PMID: 25398586 PMCID: PMC4237914 DOI: 10.1007/s10969-014-9190-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/08/2014] [Indexed: 12/11/2022]
Abstract
We developed a method for efficient chromosome tagging in Pichia pastoris, using a useful tandem affinity purification (TAP) tag. The TAP tag, designated and used here as the THF tag, contains a thrombin protease cleavage site for removal of the TAP tag and a hexahistidine sequence (6× His) followed by three copies of the FLAG sequence (3× FLAG) for affinity purification. Using this method, THF-tagged RNA polymerases I, II, and III were successfully purified from P. pastoris. The method also enabled us to purify the tagged RNA polymerase II on a large scale, for its crystallization and preliminary X-ray crystallographic analysis. The method described here will be widely useful for the rapid and large-scale preparation of crystallization grade eukaryotic multi-subunit protein complexes.
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Affiliation(s)
- Toshiaki Higo
- Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Noriyuki Suka
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Department of Interdisciplinary Science and Engineering, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506 Japan
| | - Haruhiko Ehara
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Masatoshi Wakamori
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Shin Sato
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Hideaki Maeda
- Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Shun-ichi Sekine
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Takashi Umehara
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033 Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
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Polonelli L, Beninati C, Teti G, Felici F, Ciociola T, Giovati L, Sperindè M, Passo CL, Pernice I, Domina M, Arigò M, Papasergi S, Mancuso G, Conti S, Magliani W. Yeast killer toxin-like candidacidal Ab6 antibodies elicited through the manipulation of the idiotypic cascade. PLoS One 2014; 9:e105727. [PMID: 25162681 PMCID: PMC4146504 DOI: 10.1371/journal.pone.0105727] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/23/2014] [Indexed: 12/11/2022] Open
Abstract
A mouse anti-anti-anti-idiotypic (Id) IgM monoclonal antibody (mAb K20, Ab4), functionally mimicking a Wyckerhamomyces anomalus (Pichia anomala) killer toxin (KT) characterized by fungicidal activity against yeasts presenting specific cell wall receptors (KTR) mainly constituted by β-1,3-glucan, was produced from animals presenting anti-KT Abs (Ab3) following immunization with a rat IgM anti-Id KT-like mAb (mAb K10, Ab2). MAb K10 was produced by immunization with a KT-neutralizing mAb (mAb KT4, Ab1) bearing the internal image of KTR. MAb K20, likewise mAb K10, proved to be fungicidal in vitro against KT-sensitive Candida albicans cells, an activity neutralized by mAb KT4, and was capable of binding to β-1,3-glucan. MAb K20 and mAb K10 competed with each other and with KT for binding to C. albicans KTR. MAb K20 was used to identify peptide mimics of KTR by the selection of phage clones from random peptide phage display libraries. Using this strategy, four peptides (TK 1-4) were selected and used as immunogen in mice in the form of either keyhole limpet hemocyanin (KLH) conjugates or peptide-encoding minigenes. Peptide and DNA immunization could induce serum Abs characterized by candidacidal activity, which was inhibited by laminarin, a soluble β-1,3-glucan, but not by pustulan, a β-1,6-glucan. These findings show that the idiotypic cascade can not only overcome the barrier of animal species but also the nature of immunogens and the type of technology adopted.
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Affiliation(s)
- Luciano Polonelli
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
| | - Concetta Beninati
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Giuseppe Teti
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Franco Felici
- Dipartimento di Bioscienze e Territorio (DiBT), Università degli Studi del Molise, Contrada Fonte Lappone, Pesche (IS), Italy
| | - Tecla Ciociola
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
| | - Laura Giovati
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
| | - Martina Sperindè
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
| | - Carla Lo Passo
- Dipartimento di Scienze Biologiche ed Ambientali, Università degli Studi di Messina, Messina, Italy
| | - Ida Pernice
- Dipartimento di Scienze Biologiche ed Ambientali, Università degli Studi di Messina, Messina, Italy
| | - Maria Domina
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Milena Arigò
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Salvatore Papasergi
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Giuseppe Mancuso
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Stefania Conti
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
| | - Walter Magliani
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
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30
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Klug L, Tarazona P, Gruber C, Grillitsch K, Gasser B, Trötzmüller M, Köfeler H, Leitner E, Feussner I, Mattanovich D, Altmann F, Daum G. The lipidome and proteome of microsomes from the methylotrophic yeast Pichia pastoris. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:215-26. [PMID: 24246743 DOI: 10.1016/j.bbalip.2013.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 11/05/2013] [Accepted: 11/08/2013] [Indexed: 11/28/2022]
Abstract
The methylotrophic yeast Pichia pastoris is a popular yeast expression system for the production of heterologous proteins in biotechnology. Interestingly, cell organelles which play an important role in this process have so far been insufficiently investigated. For this reason, we started a systematic approach to isolate and characterize organelles from P. pastoris. In this study, we present a procedure to isolate microsomal membranes at high purity. These samples represent endoplasmic reticulum (ER) fractions which were subjected to molecular analysis of lipids and proteins. Organelle lipidomics included a detailed analysis of glycerophospholipids, fatty acids, sterols and sphingolipids. The microsomal proteome analyzed by mass spectrometry identified typical proteins of the ER known from other cell types, especially Saccharomyces cerevisiae, but also a number of unassigned gene products. The lipidome and proteome analysis of P. pastoris microsomes are prerequisite for a better understanding of functions of this organelle and for modifying this compartment for biotechnological applications.
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31
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Peng Z, Wang A, Feng Q, Wang Z, Ivanova IV, He X, Zhang B, Song W. High-level expression, purification and characterisation of porcine β-defensin 2 in Pichia pastoris and its potential as a cost-efficient growth promoter in porcine feed. Appl Microbiol Biotechnol 2014; 98:5487-97. [PMID: 24515729 DOI: 10.1007/s00253-014-5560-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 01/20/2014] [Accepted: 01/20/2014] [Indexed: 01/10/2023]
Abstract
Porcine β-defensin 2 (pBD2), a recently discovered porcine defensin that is produced by the intestine, exerts antimicrobial activities and innate immune effects that are linked to intestinal diseases in pigs. Here, we report a codon-optimised protein corresponding to mature pBD2 cDNA that was expressed and purified in Pichia pastoris yeast. The highest amount of secreted protein (3,694.0 mg/L) was reached 144 h into a 150-h induction during high-density cultivation. Precipitation followed by gel exclusion chromatography yielded 383.7 mg/L purified recombinant pBD2 (rpBD2) with a purity of ~93.7 %. Two recombinant proteins of 5,458.5 and 5,258.4 Da were detected in the mass spectrum due to variation in the amino-terminus. The rpBD2 exhibited high antimicrobial activity against a broad range of pig pathogenic bacteria (minimal inhibitory concentration [MIC] 32-128 μg/mL); the highest activity was observed against Salmonella choleraesuis, Staphylococcus aureus and Streptococcus suis (MIC 32-64 μg/mL). However, rpBD2 also inhibited the growth of probiotics such as Lactobacillus plantarum, Bacillus subtilis and Saccharomyces cerevisiae, but at lower efficacies than the pathogens. Purified or unpurified rpBD2 also maintained high activity over a wide range of pH values (2.0-10.0), a high thermal stability at 100 °C for 40 min and significant resistance to papain, pepsin and trypsin. In addition, the activity of rpBD2 towards S. aureus was unaffected by 10 mM dithiothreitol (DTT) and 20 % dimethyl sulphoxide (DMSO). Our results suggest that pBD2 could be produced efficiently in large quantities in P. pastoris and be a substitute for traditional antibiotics for growth promotion in the porcine industry.
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Affiliation(s)
- Zixin Peng
- State Key Laboratory of Direct-Fed Microbial Engineering, No. B-3 Northern Territory of Zhongguancun Dongsheng Science and Technology Park, Haidian District, Beijing, 100192, People's Republic of China
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32
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Abstract
Easy-to-perform and low-cost protein purification methods are in high demand for the mass production of commonly used enzymes that play an important role in bioeconomy. A low-cost and rapid recombinant protein purification system was developed using CBM3 (family 3 cellulose-binding module) as affinity tag. This protocol describes the purification of CBM3-fusion protein and tag-free protein expressed in Pichia pastoris using CBM3 as an affinity tag.
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Affiliation(s)
- Dongmei Wang
- School of Life Science, University of Science and Technology of China, Huangshan Road 443, 230026, Hefei, Anhui, People's Republic of China
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33
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Abstract
Panomycocin, the killer toxin of Pichia anomala NCYC 434 (K5), is a 49 kDa monomeric glycoprotein with exo-beta-1,3-glucanase activity (patent pending). In this study we evaluated the in vitro activity of panomycocin against a panel of 109 human isolates of seven different pathogenic Candida spp. using microdilution and time-kill methods. Panomycocin was most active against C. tropicalis, C. pseudotropicalis and C. glabrata with MIC(90) values of 1 microg/ml. It displayed significant activity against C. albicans and C. parapsilosis with MIC(90) values of 4 and 2 microg/ml, respectively. For C. krusei, the MIC(90) value was 8 microg/ml. Panomycocin was fungicidal against all the tested Candida spp. The MFC values were only one or 2 dilutions higher than the MICs with the exception of C. krusei isolates with MFCs greater than or equal to 4xMIC. Results of this study indicated that panomycocin could be considered as a natural antifungal agent against Candida infections and has significant potential for further investigation.
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Affiliation(s)
- Fatih Izgü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
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34
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Tkachenko AF, Tigunova EA, Shul'ga SM. [Microbial lipids as a source for biofuel]. Tsitol Genet 2013; 47:22-29. [PMID: 24437195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This review presents the main directions and experimental data to search among the different species of yeast--active producers of lipids and the ways to lipidogenesis process optimization in the most promising stains. It was shown that enzymatic processes course can be directed with maintaining the necessary cultivation conditions. The influence on the growth, development and biochemical activity of microbial medium composition, temperature, aeration and oxidation-reduction conditions was considered. These factors changing have affected the microorganisms biosynthetic activity, lipidogenic yeasts activity and synthesized lipids composition. Lipidogenic yeasts ability and relatively rapid ability on changing the amount and composition of lipids by the direct cultivation leads to the conclusion that lipids obtained by microbial synthesis can be a source of commercial raw materials for biofuel.
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35
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Viader-Salvadó JM, Castillo-Galván M, Fuentes-Garibay JA, Iracheta-Cárdenas MM, Guerrero-Olazarán M. Optimization of five environmental factors to increase beta-propeller phytase production in Pichia pastoris and impact on the physiological response of the host. Biotechnol Prog 2013; 29:1377-85. [PMID: 24123973 DOI: 10.1002/btpr.1822] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 09/25/2013] [Indexed: 12/30/2022]
Abstract
Recently, we engineered Pichia pastoris Mut(s) strains to produce several beta-propeller phytases, one from Bacillus subtilis and the others designed by a structure-guided consensus approach. Furthermore, we demonstrated the ability of P. pastoris to produce and secrete these phytases in an active form in shake-flask cultures. In the present work, we used a design of experiments strategy (Simplex optimization method) to optimize five environmental factors that define the culture conditions in the induction step to increase beta-propeller phytase production in P. pastoris bioreactor cultures. With the optimization process, up to 347,682 U (82,814 U/L or 6.4 g/L culture medium) of phytase at 68 h of induction was achieved. In addition, the impact of the optimization process on the physiological response of the host was evaluated. The results indicate that the increase in extracellular phytase production through the optimization process was correlated with an increase in metabolic activity of P. pastoris, shown by an increase in oxygen demand and methanol consumption, that increase the specific growth rate. The increase in extracellular phytase production also occurred with a decrease in extracellular protease activity. Moreover, the optimized culture conditions increased the recombinant protein secretion by up to 88%, along with the extracellular phytase production efficiency per cell.
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Affiliation(s)
- José M Viader-Salvadó
- Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, Nuevo León, México
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36
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Marbach J, Zentis P, Ellinger P, Müller H, Birkmann E. Expression and characterisation of fully posttranslationally modified cellular prion protein in Pichia pastoris. Biol Chem 2013; 394:1475-83. [PMID: 23893688 DOI: 10.1515/hsz-2013-0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 07/25/2013] [Indexed: 11/15/2022]
Abstract
Prion diseases are fatal neurodegenerative diseases which occur as sporadic, genetic, and transmissible disorders. A molecular hallmark of prion diseases is the conformational conversion of the host-encoded cellular form of the prion protein (PrPC) into its misfolded pathogenic isoform (PrPSc). PrPSc is the main component of the pathological and infectious prion agent. The study of the conversion mechanism from PrPC to PrPSc is a major field in prion research. PrPC is glycosylated and attached to the plasma membrane via its glycosyl phosphatidyl inositol (GPI)-anchor. In this study we established and characterised the expression of fully posttranslationally modified mammalian Syrian golden hamster PrPC in the yeast Pichia pastoris using native PrPC-specific N- and C-terminal signal sequences. In vivo as well as in vitro-studies demonstrated that the signal sequences controlled posttranslational processing and trafficking of native PrPC, resulting in PrPC localised in the plasma membrane of P. pastoris. In addition, the glycosylation pattern of native PrPC could be confirmed.
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Chan AW, Cartwright EJ, Reddy SC, Kraft CS, Wang YF. Pichia anomala (Candida pelliculosa) fungemia in a patient with sickle cell disease. Mycopathologia 2013; 176:273-7. [PMID: 23884540 DOI: 10.1007/s11046-013-9677-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 06/28/2013] [Indexed: 11/26/2022]
Abstract
This case report discusses a patient with sickle cell disease who presented with fungemia from Pichia anomala (teleomorph: Candida pelliculosa). The organism was identified as P. anomala by MALDI-TOF VITEK mass spectrometry and VITEK 2 yeast identification card. Pichia anomala should be considered in sickle cell patients with recurrent fungemia.
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Affiliation(s)
- Austin W Chan
- Department of Medicine, Emory University, Atlanta, GA, USA
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38
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Zou S, Huang S, Kaleem I, Li C. N-Glycosylation enhances functional and structural stability of recombinant β-glucuronidase expressed in Pichia pastoris. J Biotechnol 2013; 164:75-81. [PMID: 23313889 DOI: 10.1016/j.jbiotec.2012.12.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 11/19/2022]
Abstract
Recombinant β-glucuronidase (GUS) expressed in Pichia pastoris GS115 is an important glycoprotein, encoded by a gene with four potential N-glycosylation sites. To investigate the impact of N-linked carbohydrate moieties on the stability of recombinant GUS, it was deglycosylated by peptide-N-glycosidase F (PNGase-F) under native conditions. The enzymatic activities of the glycosylated and deglycosylated GUS were compared under various conditions such as temperature, pH, organic solvents, detergents and chaotropic agent. The results demonstrated that the glycosylated GUS retained greater fraction of maximum enzymatic activity against various types of denaturants compared with the deglycosylated. The conformational stabilities of both GUS were analyzed by monitoring the unfolding equilibrium by using the denaturant guanidinium chloride (dn-HCl). The glycosylated GUS displayed a significant increase in its conformational stability than the deglycosylated counterpart. These results affirmed the key role of N-glycosylation on the structural and functional stability of β-glucuronidase and could have potential applications in the functional enhancement of industrial enzymes.
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Affiliation(s)
- Shuping Zou
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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39
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Farkas Z, Márki-Zay J, Kucsera J, Vágvölgyi C, Golubev WI, Pfeiffer I. Characterization of two different toxins of Wickerhamomyces anomalus (Pichia anomala) VKM Y-159. Acta Biol Hung 2012; 63:277-87. [PMID: 22695525 DOI: 10.1556/abiol.63.2012.2.9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Wickerhamomyces anomalus VKM Y-159 strain produces two types of toxin designated as WAKT a and WAKT b, encoded by chromosomal genes. The WAKT a toxin is heat-labile, pronase sensitive acting in pH range 3-4 affecting on several yeasts including pathogenic Candida species while the WAKT b toxin is protease- and thermo-resistant, acting in pH range 3-7 on two species, Candida alai and Candida norvegica. The rapid decrease of the number of viable cells after toxin treatment demonstrates that both toxins have cytocidic effect.
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Affiliation(s)
- Z Farkas
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
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40
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Cereija TB, Figueiredo AC, de Sanctis D, Tanaka AS, Pereira PJB. Crystallization and preliminary crystallographic characterization of the N-terminal Kunitz domain of boophilin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:436-9. [PMID: 22505414 PMCID: PMC3325814 DOI: 10.1107/s1744309112005532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 02/07/2012] [Indexed: 11/10/2022]
Abstract
Boophilin is a tight-binding thrombin inhibitor composed of two canonical Kunitz-type domains in a tandem arrangement. Thrombin-bound boophilin can inhibit a second trypsin-like serine proteinase, most likely through the reactive loop of its N-terminal Kunitz domain. Here, the crystallization and preliminary crystallographic analysis of the isolated N-terminal domain of boophilin is reported. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1) and diffracted to beyond 1.8 Å resolution using a sealed-tube home source and to 0.87 Å resolution at a synchrotron source.
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Affiliation(s)
- Tatiana B. Cereija
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal
| | - Ana C. Figueiredo
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal
| | - Daniele de Sanctis
- Structural Biology Group, ESRF, 6 Rue Jules Horowitz, 38043 Grenoble CEDEX, France
| | - Aparecida S. Tanaka
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04044-020 São Paulo-SP, Brazil
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Tandiono T, Ow DSW, Driessen L, Chin CSH, Klaseboer E, Choo ABH, Ohl SW, Ohl CD. Sonolysis of Escherichia coli and Pichia pastoris in microfluidics. Lab Chip 2012; 12:780-6. [PMID: 22183135 DOI: 10.1039/c2lc20861j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We report on an efficient ultrasound based technique for lysing Escherichia coli and Pichia pastoris with oscillating cavitation bubbles in an integrated microfluidic system. The system consists of a meandering microfluidic channel and four piezoelectric transducers mounted on a glass substrate, with the ultrasound exposure and gas pressure regulated by an automatic control system. Controlled lysis of bacterial and yeast cells expressing green fluorescence protein (GFP) is studied with high-speed photography and fluorescence microscopy, and quantified with real-time polymerase chain reaction (qRT-PCR) and fluorescence intensity. The effectiveness of cell lysis correlates with the duration of ultrasound exposure. Complete lysis can be achieved within one second of ultrasound exposure with a temperature increase of less than 3.3 °C. The rod-shaped E. coli bacteria are disrupted into small fragments in less than 0.4 seconds, while the more robust elliptical P. pastoris yeast cells require around 1.0 second for complete lysis. Fluorescence intensity measurements and qRT-PCR analysis show that functionality of GFP and genomic DNA for downstream analytical assays is maintained.
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Abstract
COPII vesicles bud from an ER domain known as the transitional ER (tER). Assembly of the COPII coat is initiated by the transmembrane guanine nucleotide exchange factor Sec12. In the budding yeast Pichia pastoris, Sec12 is concentrated at tER sites. Previously, we found that the tER localization of P. pastoris Sec12 requires a saturable binding partner. We now show that this binding partner is Sec16, a peripheral membrane protein that functions in ER export and tER organization. One line of evidence is that overexpression of Sec12 delocalizes Sec12 to the general ER, but simultaneous overexpression of Sec16 retains overexpressed Sec12 at tER sites. Additionally, when P. pastoris Sec12 is expressed in S. cerevisiae, the exogenous Sec12 localizes to the general ER, but when P. pastoris Sec16 is expressed in the same cells, the exogenous Sec12 is recruited to tER sites. In both of these experimental systems, the ability of Sec16 to recruit Sec12 to tER sites is abolished by deleting a C-terminal fragment of Sec16. Biochemical experiments confirm that this C-terminal fragment of Sec16 binds to the cytosolic domain of Sec12. Similarly, we demonstrate that human Sec12 is concentrated at tER sites, likely due to association with a C-terminal fragment of Sec16A. These results suggest that a Sec12-Sec16 interaction has a conserved role in ER export.
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Affiliation(s)
- Elisabeth A Montegna
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, United States of America
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Bellido C, Bolado S, Coca M, Lucas S, González-Benito G, García-Cubero MT. Effect of inhibitors formed during wheat straw pretreatment on ethanol fermentation by Pichia stipitis. Bioresour Technol 2011; 102:10868-74. [PMID: 21983414 DOI: 10.1016/j.biortech.2011.08.128] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 08/29/2011] [Accepted: 08/30/2011] [Indexed: 05/04/2023]
Abstract
The inhibitory effect of the main inhibitors (acetic acid, furfural and 5-hydroxymethylfurfural) formed during steam explosion of wheat straw was studied through ethanol fermentations of model substrates and hydrolysates from wheat straw by Pichia stipitis. Experimental results showed that an increase in acetic acid concentration led to a reduction in ethanol productivity and complete inhibition was observed at 3.5 g/L. Furfural produced a delay on sugar consumption rates with increasing concentration and HMF did not exert a significant effect. Fermentations of the whole slurry from steam exploded wheat straw were completely inhibited by a synergistic effect due to the presence of 1.5 g/L acetic acid, 0.15 g/L furfural and 0.05 g/L HMF together with solid fraction. When using only the solid fraction from steam explosion, hydrolysates presented 0.5 g/L of acetic acid, whose fermentations have submitted promising results, providing an ethanol yield of 0.45 g ethanol/g sugars and the final ethanol concentration reached was 12.2 g/L (10.9 g ethanol/100 g DM).
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Affiliation(s)
- Carolina Bellido
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n, 47011 Valladolid, Spain
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Zhang J, Yang Y, Teng D, Tian Z, Wang S, Wang J. Expression of plectasin in Pichia pastoris and its characterization as a new antimicrobial peptide against Staphyloccocus and Streptococcus. Protein Expr Purif 2011; 78:189-96. [PMID: 21558006 DOI: 10.1016/j.pep.2011.04.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Revised: 04/24/2011] [Accepted: 04/25/2011] [Indexed: 01/08/2023]
Abstract
Recombinant plectasin, the first fungus defensin, was expressed in Pichia pastoris and purified, and its physical, chemical and antimicrobial characteristics were studied. Following a 120 h induction of recombinant yeast, the amount of total secreted protein reached 748.63 μg/ml. The percentage of recombinant plectasin was estimated to be 71.79% of the total protein. After purification with a Sephadex G-25 column and RP-HPLC, the identity of plectasin was verified by MALDI-TOF MS. Plectasin exhibited strong antimicrobial activity against the Gram-positive bacteria Staphyloccocusaureus, Staphylococcus epidermidis, Streptococcus pneumoniae, and Streptococcus suis. At a concentration of 2560 μg/ml, this peptide showed approximately equal activity against S. aureus, S. epidermidis, S. suis, and S. pneumoniae, when compared to 320 μg/ml vancomycin, 640 μg/ml penicillin, 320 μg/ml vancomycin and 160 μg/ml vancomycin, respectively. In addition, plectasin showed anti-S. aureus activity over a wide pH range of 2.0 and 10.0, a high thermal stability at 100 °C for 1h and remarkable resistance to papain and pepsin. The expression and characterization of recombinant plectasin in P. pastoris has potential to treat Streptococcus and Staphyloccocus infections when most traditional antibiotics show no effect on them. Our results indicate that plectasin can be produced in large quantities, and that it has pharmaceutical importance for the prevention and clinical treatment of Staphyloccocus and Streptococcus infections.
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Abstract
Lipase (triacylglycerol acylhydrolases, E.C. 3.1.1.3) is one of the most important enzymes applied to a broad range of industrial application fields. Especially, lipases with abnormal functionality such as thermostability and alkaline, acidic, and cold activities gain special attention because of their applicability in the restricted reaction conditions. In this study, 16 yeast strains prescreened for lipase induction were investigated for their actual lipase production, and we found a novel cold-active lipase produced from Pichia lynferdii Y-7723. The activity of lipase Y-7723 was retained by 74 and 70% at 20 and 10 degrees C, respectively, as compared to the maximum value at 35 degrees C. On the basis of an optimization study, the optimal lipase productivity was obtained at 96 h of incubation with 3% oil substrate in a medium composed of sucrose as a carbon source at pH 7.0. Among carbon sources tested, sucrose showed almost twice as high of a lipase production (184%) as the control, while the cell growth was similar (105%). Yeast extract and ammonium salts were effective as individual nitrogen sources for lipase production. This study demonstrated that the cold activity of lipase Y-7723 at 10 degrees C was highest among the cold-active lipases reported so far.
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Affiliation(s)
- Hak-Ryul Kim
- Department of Animal Science and Biotechnology, Kyungpook National University, Daegu 702-701, Korea.
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Abstract
Two new indole derivatives (3, 4) and three known compounds (1, 2, 5) were isolated as radical scavengers from the culture filtrate of a marine sponge-derived yeast. Their structures were determined to be tyrosol (1), tryptophol (2), 2-(1H-indol-3-yl)ethyl 2-hydroxypropanoate (3), 2-(1H-indol-3-yl)ethyl 5-hydroxypentanoate (4), and cyclo(L-Pro-L-Tyr) (5) on the basis of their spectroscopic data. The absolute configurations of compounds 3 and 5 were determined by chiral HPLC analysis combined with synthesis and Marfey's method, respectively. Each obtained compound was evaluated for DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity, and all compounds exhibited weak activities.
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Affiliation(s)
- Yasumasa Sugiyama
- Laboratory of Applied Microbiology, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.
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Zhao J, Shan T, Huang Y, Liu X, Gao X, Wang M, Jiang W, Zhou L. Chemical composition and in vitro antimicrobial activity of the volatile oils from Gliomastix murorum and Pichia guilliermondii, two endophytic fungi in Paris polyphylla var. yunnanensis. Nat Prod Commun 2009; 4:1491-1496. [PMID: 19967981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
Volatile oils were obtained by hydro-distillation from Gliomastix murorum and Pichia guilliermondii, two endophytic fungi isolated from the traditional Chinese medicinal herb Paris polyphylla var. yunnanensis. The oils were analyzed for their chemical composition by gas chromatography-mass spectrometry (GC-MS). Palmitic acid (15.5%), (E)-9-octadecenoic acid (11.6%), 6-pentyl-5,6-dihydropyran-2-one (9.7%), and (7Z,10Z)-7,10- hexadecadienoic acid (8.3%) were the major compounds of the 40 identified components in G. murorum volatile oil. 1,1,3a,7-Tetramethyl-1a,2,3,3a,4,5,6,7b-octahydro-1H-cyclopropa[a]- naphthalene (25.9%), palmitic acid (15.5%), 1-methyl-2,4-di- (prop-1-en-2-yl)-1- vinylcyclohexane (7.9%), (E)-9-octadecenoic acid (7.3%), and (9E,12E)-ethyl-9,12-octadecadienoate (5.2%) were the major compounds of the 27 identified components in P. guilliermondii volatile oil. The in vitro antimicrobial activity of the volatile oils was also investigated to evaluate their efficacy against six bacteria and one phytopathogenic fungus. The minimum inhibitory concentration (MIC) values of the volatile oils against the test bacteria ranged from 0.20 mg/mL to 1.50 mg/mL. One of the most sensitive bacteria was Xanthomonas vesicatoria with an MIC of 0.20 mg/mL and 0.40 mg/mL for G. murorum and P. guilliermondii, respectively. The mean inhibitory concentration (IC50) of the volatile oils against spore germination of Magnaporthe oryzae was 0.84 mg/mL for G. murorum and 1.56 mg/mL for P. guilliermondii. These results indicated that the volatile oils from the endophytic fungi have strong antimicrobial activity and could be a potential source of antimicrobial ingredients.
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Affiliation(s)
- Jianglin Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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Rakpuang W. Growth temperatures and various concentrations of ricinoleic acid affect fatty acid composition in two strains of Hansenula polymorpha. Pak J Biol Sci 2009; 12:986-990. [PMID: 19817127 DOI: 10.3923/pjbs.2009.986.990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The fatty acid composition of two strains (wild-type and M2 mutant cells of Hansenula polymorpha strain CBS 1976) were studied at different growth temperatures and various concentrations of ricinoleic acid. Two strains of yeast cultured on YEPD medium containing 1, 2, 3 and 8 mM of ricinoleic acid at 25, 30, 37 and 45 degrees C. Lipids were extracted from the yeast culture and the fatty acids esterified with BF3-MeOH. Gas chromatography analysis of total lipids showed that C16:1 (delta7), which has been synthesized in low concentration by WT strain, was found to increase in the M2 mutant. The biotransformation of C16:1 (delta7) found in M2 indicated the presence of dehydroxylation and beta-oxidation systems. An increase in the growth temperature from 25 to 45 degrees C resulted in a decrease in the total unsaturated fatty acids of C16:1, C18:1, C18:2 and C18:3 from 44.0 to 22.1% and 65.0 to 49.3% of the total fatty acids in M2 and wild-type strains, respectively. The differential production of unsaturated fatty acids, especially C16:1, indicated that regulation of unsaturated fatty acid levels, is an important control point in membrane composition in the adaptation of H. polymorpha M2 to diet and temperature.
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Affiliation(s)
- Wanida Rakpuang
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham 44150, Thailand
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Fischer G, Kosinska-Eriksson U, Aponte-Santamaría C, Palmgren M, Geijer C, Hedfalk K, Hohmann S, de Groot BL, Neutze R, Lindkvist-Petersson K. Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism. PLoS Biol 2009; 7:e1000130. [PMID: 19529756 PMCID: PMC2688079 DOI: 10.1371/journal.pbio.1000130] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 05/06/2009] [Indexed: 11/24/2022] Open
Abstract
Atomic-resolution X-ray crystallography, functional analyses, and molecular dynamics simulations suggest a novel mechanism for the regulation of water flux through the yeast Aqy1 water channel. Aquaporins are transmembrane proteins that facilitate the flow of water through cellular membranes. An unusual characteristic of yeast aquaporins is that they frequently contain an extended N terminus of unknown function. Here we present the X-ray structure of the yeast aquaporin Aqy1 from Pichia pastoris at 1.15 Å resolution. Our crystal structure reveals that the water channel is closed by the N terminus, which arranges as a tightly wound helical bundle, with Tyr31 forming H-bond interactions to a water molecule within the pore and thereby occluding the channel entrance. Nevertheless, functional assays show that Aqy1 has appreciable water transport activity that aids survival during rapid freezing of P. pastoris. These findings establish that Aqy1 is a gated water channel. Mutational studies in combination with molecular dynamics simulations imply that gating may be regulated by a combination of phosphorylation and mechanosensitivity. All living organisms must regulate precisely the flow of water into and out of cells in order to maintain cell shape and integrity. Proteins of one family, the aquaporins, are found in virtually every living organism and play a major role in maintaining water homeostasis by acting as regulated water channels. Here we describe the first crystal structure of a yeast aquaporin, Aqy1, at 1.15 Å resolution, which represents the highest resolution structural data obtained to date for a membrane protein. Using this structural information, we address an outstanding biological question surrounding yeast aquaporins: what is the functional role of the amino-terminal extension that is characteristic of yeast aquaporins? Our structural data show that the amino terminus of Aqy1 fulfills a novel gate-like function by folding to form a cytoplasmic helical bundle with a tyrosine residue entering the water channel and occluding the cytoplasmic entrance. Molecular dynamics simulations and functional studies in combination with site-directed mutagenesis suggest that water flow is regulated through a combination of mechanosensitive gating and post-translational modifications such as phosphorylation. Our study therefore provides insight into a unique mechanism for the regulation of water flux in yeast.
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Affiliation(s)
- Gerhard Fischer
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, Göteborg, Sweden
| | | | - Camilo Aponte-Santamaría
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Madelene Palmgren
- Department of Cell and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Cecilia Geijer
- Department of Cell and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Kristina Hedfalk
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, Göteborg, Sweden
| | - Stefan Hohmann
- Department of Cell and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Bert L. de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Richard Neutze
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, Göteborg, Sweden
- * E-mail: (RN); (KL-P)
| | - Karin Lindkvist-Petersson
- Department of Cell and Molecular Biology, University of Gothenburg, Göteborg, Sweden
- * E-mail: (RN); (KL-P)
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Kannan V, Narayanaswamy P, Gadamsetty D, Hazra P, Khedkar A, Iyer H. A tandem mass spectrometric approach to the identification of O-glycosylated glargine glycoforms in active pharmaceutical ingredient expressed in Pichia pastoris. Rapid Commun Mass Spectrom 2009; 23:1035-1042. [PMID: 19253914 DOI: 10.1002/rcm.3965] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Glycoforms of glargine expressed in Pichia pastoris were isolated by high-performance liquid chromatography and analyzed by a series of chemical and mass spectrometric methods for the identification of various glycoforms, glycosylation position, nature and structure of glycans. Reduction and alkylation, peptide mapping techniques were used to decipher the amino acid site at which glycosylation had taken place. Chemical methods were coupled with mass spectrometry techniques such as electrospray ionization and matrix-assisted laser desorption/ionization for identification of the glycosylation site.
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Affiliation(s)
- Vivekanandan Kannan
- Research and Development, Biocon Limited, 20th KM Hosur Road, 560100 Bangalore, India.
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