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Guo Y, Zhou J, Jia W, Gao H, Zhang H, Zhang C. Characterization of a Novel Milk-Clotting Aspartic Protease from Penicillium sp. and Structural Explanation for its High Milk-Clotting Index. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37017929 DOI: 10.1021/acs.jafc.2c07303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
A novel milk-clotting enzyme isolated from Penicillium sp. ACCC 39790 (PsMCE) was prepared by heterologous expression. The recombinant PsMCE had an apparent molecular mass of 45 kDa and exhibited maximum casein hydrolysis activity at pH 4.0 and 50 °C. The PsMCE activity was enhanced by calcium ions and strongly inhibited by pepstatin A. Through hydrolysis pattern and cleavage site analyses, the milk-clotting activity of PsMCE was related to its specific hydrolysis between Phe105 and Met106 in the κ-casein proteins. The structural basis of PsMCE was characterized using homology modeling, molecular docking, and interactional analysis. The P1' region of PsMCE is critical for its selective binding to the hydrolytic site in κ-casein, and the hydrophobic forces play a decisive role in the specific cleavage of Phe105 and Met106. These interactional analyses between PsMCE and the ligand peptide clarified the fundamentals of its high milk-clotting index (MCI). PsMCE could be applied in cheese making due to its thermolability and high MCI value as a potential milk-clotting enzyme.
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Affiliation(s)
- Yujie Guo
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Xinjiang Taikun Group Co., Ltd., Xinjiang Uygur Autonomous Region, Changji 831100, People's Republic of China
| | - Jiaojiao Zhou
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wei Jia
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Xinjiang Taikun Group Co., Ltd., Xinjiang Uygur Autonomous Region, Changji 831100, People's Republic of China
| | - Hongwei Gao
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Xinjiang Taikun Group Co., Ltd., Xinjiang Uygur Autonomous Region, Changji 831100, People's Republic of China
| | - Hongru Zhang
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chunhui Zhang
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Goedegebuur F, Dankmeyer L, Gualfetti P, Karkehabadi S, Hansson H, Jana S, Huynh V, Kelemen BR, Kruithof P, Larenas EA, Teunissen PJM, Ståhlberg J, Payne CM, Mitchinson C, Sandgren M. Improving the thermal stability of cellobiohydrolase Cel7A from Hypocrea jecorina by directed evolution. J Biol Chem 2017; 292:17418-17430. [PMID: 28860192 DOI: 10.1074/jbc.m117.803270] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/24/2017] [Indexed: 11/06/2022] Open
Abstract
Secreted mixtures of Hypocrea jecorina cellulases are able to efficiently degrade cellulosic biomass to fermentable sugars at large, commercially relevant scales. H. jecorina Cel7A, cellobiohydrolase I, from glycoside hydrolase family 7, is the workhorse enzyme of the process. However, the thermal stability of Cel7A limits its use to processes where temperatures are no higher than 50 °C. Enhanced thermal stability is desirable to enable the use of higher processing temperatures and to improve the economic feasibility of industrial biomass conversion. Here, we enhanced the thermal stability of Cel7A through directed evolution. Sites with increased thermal stability properties were combined, and a Cel7A variant (FCA398) was obtained, which exhibited a 10.4 °C increase in Tm and a 44-fold greater half-life compared with the wild-type enzyme. This Cel7A variant contains 18 mutated sites and is active under application conditions up to at least 75 °C. The X-ray crystal structure of the catalytic domain was determined at 2.1 Å resolution and showed that the effects of the mutations are local and do not introduce major backbone conformational changes. Molecular dynamics simulations revealed that the catalytic domain of wild-type Cel7A and the FCA398 variant exhibit similar behavior at 300 K, whereas at elevated temperature (475 and 525 K), the FCA398 variant fluctuates less and maintains more native contacts over time. Combining the structural and dynamic investigations, rationales were developed for the stabilizing effect at many of the mutated sites.
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Affiliation(s)
- Frits Goedegebuur
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands,
| | - Lydia Dankmeyer
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands
| | | | - Saeid Karkehabadi
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Henrik Hansson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Suvamay Jana
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | - Vicky Huynh
- DuPont Industrial Biosciences, Palo Alto, California 94304
| | | | - Paulien Kruithof
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands
| | | | | | - Jerry Ståhlberg
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Christina M Payne
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | | | - Mats Sandgren
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
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Momeni MH, Goedegebuur F, Hansson H, Karkehabadi S, Askarieh G, Mitchinson C, Larenas EA, Ståhlberg J, Sandgren M. Expression, crystal structure and cellulase activity of the thermostable cellobiohydrolase Cel7A from the fungus Humicola grisea var. thermoidea. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2356-66. [PMID: 25195749 PMCID: PMC4157447 DOI: 10.1107/s1399004714013844] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/13/2014] [Indexed: 11/11/2022]
Abstract
Glycoside hydrolase family 7 (GH7) cellobiohydrolases (CBHs) play a key role in biomass recycling in nature. They are typically the most abundant enzymes expressed by potent cellulolytic fungi, and are also responsible for the majority of hydrolytic potential in enzyme cocktails for industrial processing of plant biomass. The thermostability of the enzyme is an important parameter for industrial utilization. In this study, Cel7 enzymes from different fungi were expressed in a fungal host and assayed for thermostability, including Hypocrea jecorina Cel7A as a reference. The most stable of the homologues, Humicola grisea var. thermoidea Cel7A, exhibits a 10°C higher melting temperature (T(m) of 72.5°C) and showed a 4-5 times higher initial hydrolysis rate than H. jecorina Cel7A on phosphoric acid-swollen cellulose and showed the best performance of the tested enzymes on pretreated corn stover at elevated temperature (65°C, 24 h). The enzyme shares 57% sequence identity with H. jecorina Cel7A and consists of a GH7 catalytic module connected by a linker to a C-terminal CBM1 carbohydrate-binding module. The crystal structure of the H. grisea var. thermoidea Cel7A catalytic module (1.8 Å resolution; R(work) and R(free) of 0.16 and 0.21, respectively) is similar to those of other GH7 CBHs. The deviations of several loops along the cellulose-binding path between the two molecules in the asymmetric unit indicate higher flexibility than in the less thermostable H. jecorina Cel7A.
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Affiliation(s)
- Majid Haddad Momeni
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Frits Goedegebuur
- DuPont, Industrial Biosciences, Archimedesweg 30, 2333 CN Leiden, The Netherlands
| | - Henrik Hansson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Saeid Karkehabadi
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Glareh Askarieh
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Colin Mitchinson
- DuPont, Industrial Biosciences, Page Mill Road, Palo Alto, CA 94304, USA
| | - Edmundo A. Larenas
- DuPont, Industrial Biosciences, Page Mill Road, Palo Alto, CA 94304, USA
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Mats Sandgren
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
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Martínez P, Ljungdahl PO. Divergence of Stp1 and Stp2 transcription factors in Candida albicans places virulence factors required for proper nutrient acquisition under amino acid control. Mol Cell Biol 2005; 25:9435-46. [PMID: 16227594 PMCID: PMC1265835 DOI: 10.1128/mcb.25.21.9435-9446.2005] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida albicans possesses a plasma membrane-localized sensor of extracellular amino acids. Here, we show that in response to amino acids, this sensor induces the proteolytic processing of two latent transcription factors, Stp1 and Stp2. Processing removes negative regulatory motifs present in the N-terminal domains of these factors. Strikingly, Stp1 and Stp2 exhibit a clear dichotomy in the genes they transactivate. The shorter active form of Stp2 activates genes required for amino acid uptake. The processed form of Stp1 activates genes required for degradation of extracellular protein and uptake of peptides, and cells lacking Stp1 do not express the secreted aspartyl protease SAP2 or the oligopeptide transporter OPT1. Consequently, stp1 null mutants are unable to grow on media with protein as the sole nitrogen source. Cells expressing the STP1* allele that encodes a protein lacking the inhibitory N-terminal domain constitutively express SAP2 and OPT1 even in the absence of extracellular proteins or peptides. Also, we show that Stp1 levels, but not Stp2 levels, are downregulated in the presence of millimolar concentrations of extracellular amino acids. These results define the hierarchy of regulatory mechanisms that differentially control two discrete pathways for the assimilation of nitrogen.
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Affiliation(s)
- Paula Martínez
- Ludwig Institute for Cancer Research, Box 240, S-171 77 Stockholm, Sweden.
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Affiliation(s)
- Ben M Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0245, USA.
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Saloheimo M, Paloheimo M, Hakola S, Pere J, Swanson B, Nyyssönen E, Bhatia A, Ward M, Penttilä M. Swollenin, a Trichoderma reesei protein with sequence similarity to the plant expansins, exhibits disruption activity on cellulosic materials. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:4202-11. [PMID: 12199698 DOI: 10.1046/j.1432-1033.2002.03095.x] [Citation(s) in RCA: 264] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Plant cell wall proteins called expansins are thought to disrupt hydrogen bonding between cell wall polysaccharides without hydrolyzing them. We describe here a novel gene with sequence similarity to plant expansins, isolated from the cellulolytic fungus Trichoderma reesei. The protein named swollenin has an N-terminal fungal type cellulose binding domain connected by a linker region to the expansin-like domain. The protein also contains regions similar to mammalian fibronectin type III repeats, found for the first time in a fungal protein. The swollenin gene is regulated in a largely similar manner as the T. reesei cellulase genes. The biological role of SWOI was studied by disrupting the swo1 gene from T. reesei. The disruption had no apparent effect on the growth rate on glucose or on different cellulosic carbon sources. Non-stringent Southern hybridization of Trichoderma genomic DNA with swo1 showed the presence of other swollenin-like genes, which could substitute for the loss of SWOI in the disruptant. The swollenin gene was expressed in yeast and Aspergillus niger var. awamori. Activity assays on cotton fibers and filter paper were performed with concentrated SWOI-containing yeast supernatant that disrupted the structure of the cotton fibers without detectable formation of reducing sugars. It also weakened filter paper as assayed by an extensometer. The SWOI protein was purified from A. niger var. awamori culture supernatant and used in an activity assay with Valonia cell walls. It disrupted the structure of the cell walls without producing detectable amounts of reducing sugars.
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