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Jadhav R, Mach RL, Mach-Aigner AR. Protein secretion and associated stress in industrially employed filamentous fungi. Appl Microbiol Biotechnol 2024; 108:92. [PMID: 38204136 PMCID: PMC10781871 DOI: 10.1007/s00253-023-12985-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Application of filamentous fungi for the production of commercial enzymes such as amylase, cellulase, or xylanase is on the rise due to the increasing demand to degrade several complex carbohydrates as raw material for biotechnological processes. Also, protein production by fungi for food and feed gains importance. In any case, the protein production involves both cellular synthesis and secretion outside of the cell. Unfortunately, the secretion of proteins or enzymes can be hampered due to accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) as a result of too high synthesis of enzymes or (heterologous) protein expression. To cope with this ER stress, the cell generates a response known as unfolded protein response (UPR). Even though this mechanism should re-establish the protein homeostasis equivalent to a cell under non-stress conditions, the enzyme expression might still suffer from repression under secretory stress (RESS). Among eukaryotes, Saccharomyces cerevisiae is the only fungus, which is studied quite extensively to unravel the UPR pathway. Several homologs of the proteins involved in this signal transduction cascade are also found in filamentous fungi. Since RESS seems to be absent in S. cerevisiae and was only reported in Trichoderma reesei in the presence of folding and glycosylation inhibitors such as dithiothreitol and tunicamycin, more in-depth study about this mechanism, specifically in filamentous fungi, is the need of the hour. Hence, this review article gives an overview on both, protein secretion and associated stress responses in fungi. KEY POINTS: • Enzymes produced by filamentous fungi are crucial in industrial processes • UPR mechanism is conserved among many fungi, but mediated by different proteins • RESS is not fully understood or studied in industrially relevant filamentous fungi.
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Affiliation(s)
- Reshma Jadhav
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
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Chen M, Xia L, Wu C, Wang Z, Ding L, Xie Y, Feng W, Chen Y. Microbe-material hybrids for therapeutic applications. Chem Soc Rev 2024. [PMID: 39005165 DOI: 10.1039/d3cs00655g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
As natural living substances, microorganisms have emerged as useful resources in medicine for creating microbe-material hybrids ranging from nano to macro dimensions. The engineering of microbe-involved nanomedicine capitalizes on the distinctive physiological attributes of microbes, particularly their intrinsic "living" properties such as hypoxia tendency and oxygen production capabilities. Exploiting these remarkable characteristics in combination with other functional materials or molecules enables synergistic enhancements that hold tremendous promise for improved drug delivery, site-specific therapy, and enhanced monitoring of treatment outcomes, presenting substantial opportunities for amplifying the efficacy of disease treatments. This comprehensive review outlines the microorganisms and microbial derivatives used in biomedicine and their specific advantages for therapeutic application. In addition, we delineate the fundamental strategies and mechanisms employed for constructing microbe-material hybrids. The diverse biomedical applications of the constructed microbe-material hybrids, encompassing bioimaging, anti-tumor, anti-bacteria, anti-inflammation and other diseases therapy are exhaustively illustrated. We also discuss the current challenges and prospects associated with the clinical translation of microbe-material hybrid platforms. Therefore, the unique versatility and potential exhibited by microbe-material hybrids position them as promising candidates for the development of next-generation nanomedicine and biomaterials with unique theranostic properties and functionalities.
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Affiliation(s)
- Meng Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
- School of Medicine, Shanghai University, Shanghai 200444, P. R. China.
| | - Lili Xia
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Chenyao Wu
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Zeyu Wang
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Li Ding
- Department of Medical Ultrasound, National Clinical Research Center of Interventional Medicine, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Tongji University, Shanghai, 200072, P. R. China.
| | - Yujie Xie
- School of Medicine, Shanghai University, Shanghai 200444, P. R. China.
| | - Wei Feng
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Yu Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
- Shanghai Institute of Materdicine, Shanghai 200051, P. R. China
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Khasin M, Bernhardson LF, O'Neill PM, Palmer NA, Scully ED, Sattler SE, Sarath G, Funnell-Harris DL. Phenylpropanoids Following Wounding and Infection of Sweet Sorghum Lines Differing in Responses to Stalk Pathogens. PHYTOPATHOLOGY 2024; 114:177-192. [PMID: 37486162 DOI: 10.1094/phyto-12-22-0459-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Sweet sorghum (Sorghum bicolor) lines M81-E and Colman were previously shown to differ in responses to Fusarium thapsinum and Macrophomina phaseolina, stalk rot pathogens that can reduce the yields and quality of biomass and extracted sugars. Inoculated tissues were compared for transcriptomic, phenolic metabolite, and enzymatic activity during disease development 3 and 13 days after inoculation (DAI). At 13 DAI, M81-E had shorter mean lesion lengths than Colman when inoculated with either pathogen. Transcripts encoding monolignol biosynthetic and modification enzymes were associated with transcriptional wound (control) responses of both lines at 3 DAI. Monolignol biosynthetic genes were differentially coexpressed with transcriptional activator SbMyb76 in all Colman inoculations, but only following M. phaseolina inoculation in M81-E, suggesting that SbMyb76 is associated with lignin biosynthesis during pathogen responses. In control inoculations, defense-related genes were expressed at higher levels in M81-E than Colman. Line, treatment, and timepoint differences observed in phenolic metabolite and enzyme activities did not account for observed differences in lesions. However, generalized additive models were able to relate metabolites, but not enzyme activities, to lesion length for quantitatively modeling disease progression: in M81-E, but not Colman, sinapic acid levels positively predicted lesion length at 3 DAI when cell wall-bound syringic acid was low, soluble caffeic acid was high, and lactic acid was high, suggesting that sinapic acid may contribute to responses at 3 DAI. These results provide potential gene targets for development of sweet sorghum varieties with increased stalk rot resistance to ensure biomass and sugar quality.
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Affiliation(s)
- Maya Khasin
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583
| | - Lois F Bernhardson
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583
| | - Patrick M O'Neill
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583
| | - Nathan A Palmer
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583
| | - Erin D Scully
- Stored Product Insect and Engineering Research Unit, U.S. Department of Agriculture-Agricultural Research Service Center for Grain and Animal Health Research, Manhattan, KS 66502
| | - Scott E Sattler
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583
| | - Deanna L Funnell-Harris
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583
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Mahmoudi Azar L, Karaman E, Beyaz B, Göktan I, Eyüpoğlu AE, Kizilel S, Erman B, Gül A, Uysal S. Expression and characterization of recombinant IL-1Ra in Aspergillus oryzae as a system. BMC Biotechnol 2023; 23:15. [PMID: 37340430 DOI: 10.1186/s12896-023-00785-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND The interleukin-1 receptor antagonist (IL-1Ra) is a crucial molecule that counteracts the effects of interleukin-1 (IL-1) by binding to its receptor. A high concentration of IL-1Ra is required for complete inhibition of IL-1 activity. However, the currently available Escherichia coli-expressed IL-1Ra (E. coli IL-1Ra, Anakinra) has a limited half-life. This study aims to produce a cost-effective, functional IL-1Ra on an industrial scale by expressing it in the pyrG auxotroph Aspergillus oryzae. RESULTS We purified A. oryzae-expressed IL-1Ra (Asp. IL-1Ra) using ion exchange and size exclusion chromatography (53 mg/L). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis revealed that Asp. IL-1Ra is N-glycosylated and approximately 17 kDa in size. We conducted a comparative study of the bioactivity, binding kinetics, and half-life between Asp. IL-1Ra and E. coli IL-1Ra. Asp. IL-1Ra showed good bioactivity even at a low concentration of 0.5 nM. The in vitro half-life of Asp. IL-1Ra was determined for different time points (0, 24, 48, 72, and 96 h) and showed higher stability than E. coli IL-1Ra, despite exhibiting a 100-fold lower binding affinity (2 nM). CONCLUSION This study reports the production of a functional Asp. IL-1Ra with advantageous stability, without extensive downstream processing. To our knowledge, this is the first report of a recombinant functional and stable IL-1Ra expressed in A. oryzae. Our results suggest that Asp. IL-1Ra has potential for industrial-scale production as a cost-effective alternative to E. coli IL-1Ra.
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Affiliation(s)
- Lena Mahmoudi Azar
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul, 34820, Turkey
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, 10010, USA
- NYU Pain Research Center, New York University College of Dentistry, New York, 10010, USA
| | - Elif Karaman
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul, 34820, Turkey
- Department of Biotechnology, Institute of Health Sciences, Bezmialem Vakif University, Fatih, Istanbul, 34093, Turkey
| | - Burcu Beyaz
- Chemical and Biological Engineering, Koç University, Sariyer, Istanbul, 34450, Turkey
| | - Işılay Göktan
- Chemical and Biological Engineering, Koç University, Sariyer, Istanbul, 34450, Turkey
| | - Alp Ertunga Eyüpoğlu
- Department of of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Sarıyer, 34450, Turkey
| | - Seda Kizilel
- Chemical and Biological Engineering, Koç University, Sariyer, Istanbul, 34450, Turkey
| | - Batu Erman
- Department of of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Sarıyer, 34450, Turkey
| | - Ahmet Gül
- Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University, Fatih, Istanbul, 34134, Turkey
| | - Serdar Uysal
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul, 34820, Turkey.
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Karaman E, Eyüpoğlu AE, Mahmoudi Azar L, Uysal S. Large-Scale Production of Anti-RNase A VHH Expressed in pyrG Auxotrophic Aspergillus oryzae. Curr Issues Mol Biol 2023; 45:4778-4795. [PMID: 37367053 DOI: 10.3390/cimb45060304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023] Open
Abstract
Nanobodies, also referred to as VHH antibodies, are the smallest fragments of naturally produced camelid antibodies and are ideal affinity reagents due to their remarkable properties. They are considered an alternative to monoclonal antibodies (mAbs) with potential utility in imaging, diagnostic, and other biotechnological applications given the difficulties associated with mAb expression. Aspergillus oryzae (A. oryzae) is a potential system for the large-scale expression and production of functional VHH antibodies that can be used to meet the demand for affinity reagents. In this study, anti-RNase A VHH was expressed under the control of the glucoamylase promoter in pyrG auxotrophic A. oryzae grown in a fermenter. The feature of pyrG auxotrophy, selected for the construction of a stable and efficient platform, was established using homologous recombination. Pull-down assay, size exclusion chromatography, and surface plasmon resonance were used to confirm the binding specificity of anti-RNase A VHH to RNase A. The affinity of anti-RNase A VHH was nearly 18.3-fold higher (1.9 nM) when expressed in pyrG auxotrophic A. oryzae rather than in Escherichia coli. This demonstrates that pyrG auxotrophic A. oryzae is a practical, industrially scalable, and promising biotechnological platform for the large-scale production of functional VHH antibodies with high binding activity.
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Affiliation(s)
- Elif Karaman
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820 Istanbul, Turkey
- Department of Biotechnology, Institute of Health Sciences, Bezmialem Vakif University, 34093 Istanbul, Turkey
| | - Alp Ertunga Eyüpoğlu
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, 34450 Istanbul, Turkey
| | - Lena Mahmoudi Azar
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820 Istanbul, Turkey
| | - Serdar Uysal
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820 Istanbul, Turkey
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Wang H, Pang AP, Wang W, Li B, Li C, Wu FG, Lin F. Discovery of ER-localized sugar transporters for cellulase production with lac1 being essential. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:132. [PMID: 36443855 PMCID: PMC9706901 DOI: 10.1186/s13068-022-02230-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/12/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND In the process of cellulose hydrolysis, carbohydrate hydrolysates are transported into cells through membrane transporters, and then affect the expression of cellulase-encoding genes. Sugar transporters play a crucial role in cellulase production in lignocellulolytic fungi, of which relatively few have been functionally validated to date and are all reported to be on cell membrane. RESULT Through transcriptome analysis and qRT-PCR, three putative MFS sugar transporters GST, MFS, and LAC1 were found to display significantly higher mRNA levels in T. reesei grown on cellulose than on glucose. The individual deletion of these three genes compromised cellulase production and delayed sugar absorption by 24 h in T. reesei. Nevertheless, they transported pretty low level of sugars, including galactose, lactose, and mannose, and did not transport glucose, when expressed in yeast system. Meanwhile, all three transporters were unexpectedly found to be intracellular, being located in endoplasmic reticulum (ER). Particularly, the knockout of lac1 almost abolished cellulase production, and significantly inhibited biomass generation regardless of sugar types, indicating that lac1 is essential for cellulase production and biomass formation. The absence of lac1 upregulated genes involved in ribosome biogenesis, while downregulated genes in cellulase production, protein processing in ER (particularly protein glycosylation), and lipid biosynthesis. The inhibition of lac1 deletion on the transcriptional levels of genes related to cellulase biosynthesis was restored after 72 h, but the cellulase production was still inhibited, indicating lac1 might pose a post-transcription regulation on cellulase production that are independent on the known cellulase regulation mediated by CRT1 and XYR1. CONCLUSION For the first time, intracellular sugar transporters (mfs, gst, and lac1) facilitating cellulase production were identified, which was distributed in ER. Their sugar transporting ability was very weak, indicating that they might be related to sugar utilization inside cells rather than the cellular sugar uptake. More importantly, sugar transporter lac1 is first found to be essential for cellulase production and biomass formation by affecting protein processing in ER (particularly protein glycosylation) and lipid biosynthesis. The effect of LAC1 on cellulase production seems to be post-transcriptional at late stage of cellulase production, independent on the well-known cellulase regulation mediated by CRT1 and XYR1. These findings improve the understanding of intracellular sugar transporters in fungi and their important role in cellulase synthesis.
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Affiliation(s)
- Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Bingzhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Chengcheng Li
- School of Light Ind. & Food Sci. and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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Yoshimura Y, Kobayashi Y, Kawaguchi T, Tani S. Improvement of cellulosic biomass-degrading enzyme production by reducing extracellular protease production in <i>Aspergillus aculeatus</i>. J GEN APPL MICROBIOL 2022; 68:143-150. [DOI: 10.2323/jgam.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yuko Yoshimura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Yuri Kobayashi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Takashi Kawaguchi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Shuji Tani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
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Evaluation of Enzyme Protease Activity and Inhibition Effect on Pyricularia grisea with the Leaf Extract of Commela communis L. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.3.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Isolation of Cellulose Degrading Fungi from Decaying Banana Pseudostem and Strelitzia alba. Enzyme Res 2019; 2019:1390890. [PMID: 31428468 PMCID: PMC6683783 DOI: 10.1155/2019/1390890] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/07/2019] [Indexed: 11/17/2022] Open
Abstract
Cellulases are a group of hydrolytic enzymes that break down cellulose to glucose units. These enzymes are used in the food, beverage, textile, pulp, and paper and the biofuel industries. The aim of this study was to isolate fungi from natural compost and produce cellulases in submerged fermentation (SmF). Initial selection was based on the ability of the fungi to grow on agar containing Avicel followed by cellulase activity determination in the form of endoglucanase and total cellulase activity. Ten fungal isolates obtained from the screening process showed good endoglucanase activity on carboxymethyl cellulose-Congo Red agar plates. Six of the fungal isolates were selected based on high total cellulase activity and identified as belonging to the genera Trichoderma and Aspergillus. In SmF of synthetic media with an initial pH of 6.5 at 30°C Trichoderma longibrachiatum LMLSAUL 14-1 produced total cellulase activity of 8 FPU/mL and endoglucanase activity of 23 U/mL whilst Trichoderma harzianum LMLBP07 13-5 produced 6 FPU/mL and endoglucanase activity of 16 U/mL. The produced levels of both cellulases and endoglucanase by Trichoderma species were higher than the levels for the Aspergillus fumigatus strains. Aspergillus fumigatus LMLPS 13-4 produced higher β-glucosidase 38 U/mL activity than Trichoderma species.
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Xie C, Gong W, Zhu Z, Zhou Y, Yan L, Hu Z, Ai L, Peng Y. Mapping the Secretome and Its N-Linked Glycosylation of Pleurotus eryngii and Pleurotus ostreatus Grown on Hemp Stalks. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5486-5495. [PMID: 31012315 DOI: 10.1021/acs.jafc.9b00061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Our previous research showed that Pleurotus eryngii and Pleurotus ostreatus were effective fungi for pretreatment of industrial hemp stalks to improve enzymatic saccharification. The secretomes of these two fungi were analyzed to search for the effective enzyme cocktails degrading hemp lignin during the pretreatment process. In total, 169 and 155 proteins were identified in Pleurotus eryngii and Pleurotus ostreatus, respectively, and 50% of the proteins involved in lignocellulose degradation were CAZymes. Because most of the extracellular proteins secreted by fungi are glycosylated proteins, the N-linked glycosylation of enzymes could be mapped. In total, 27 and 24 N-glycosylated peptides were detected in Pleurotus eryngii and Pleurotus ostreatus secretomes, respectively. N-Glycosylated peptides of laccase, GH92, exoglucanase, phenol oxidase, α-galactosidase, carboxylic ester hydrolase, and pectin lyase were identified. Deglycosylation could decrease enzymatic saccharification of hemp stalks. The activities of laccase, α-galactosidase, and phenol oxidase and the thermal stability of laccase were reduced after deglycosylation.
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Affiliation(s)
- Chunliang Xie
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Wenbing Gong
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Zuohua Zhu
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Yingjun Zhou
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Li Yan
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Zhenxiu Hu
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Lianzhong Ai
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering , University of Shanghai for Science and Technology , Shanghai 200093 , China
| | - Yuande Peng
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
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11
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Farasat M, Arjmand S, Ranaei Siadat SO, Sefidbakht Y, Ghomi H. The effect of non-thermal atmospheric plasma on the production and activity of recombinant phytase enzyme. Sci Rep 2018; 8:16647. [PMID: 30413721 PMCID: PMC6226467 DOI: 10.1038/s41598-018-34239-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/15/2018] [Indexed: 12/31/2022] Open
Abstract
Atmospheric pressure cold plasma (ACP) is introduced as a useful tool in a variety of biological applications. Proteins are the most abundant macromolecules in living systems with a central role in all biological processes. These organic molecules are modified by ACP exposure that is responsible for many of ACP's biological effects. This study evaluated the effect of ACP on the production of recombinant phytase in yeast Pichia pastoris (P. pastoris) as well as the structure and function of the phytase enzyme. The results indicated that yeast cells treated with ACP, directly or indirectly, produced higher amounts of recombinant phytase, which was associated with the time of ACP treatment. The exposure of commercial phytase solution with ACP caused a significant increase in the enzyme activity (125%) after 4 hours. Evaluation of the phytase solution by far- and near-UV circular dichroism (CD) and fluorescence analysis indicated that this protein maintained its secondary structure when exposed to ACP while the tertiary structure was slightly unfolded. The effects of heat and H2O2 on the phytase structure and function were compared with the effect of ACP treatment. The modification of Cys, Tyr and Trp amino acids upon reactive oxygen/nitrogen spices was simulated using a molecular dynamics approach. RMSF and RMSD analysis suggested that this structural alteration occurs owing to changes made by reactive species in accessible amino acids.
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Affiliation(s)
- Mahsa Farasat
- Laser and Plasma research Institute, Shahid Beheshti University, G. C., Tehran, Iran
| | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, G. C., Tehran, Iran.
| | | | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, G. C., Tehran, Iran
| | - Hamid Ghomi
- Laser and Plasma research Institute, Shahid Beheshti University, G. C., Tehran, Iran
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Bedade D, Deska J, Bankar S, Bejar S, Singhal R, Shamekh S. Fermentative production of extracellular amylase from novel amylase producer, Tuber maculatum mycelium, and its characterization. Prep Biochem Biotechnol 2018; 48:549-555. [DOI: 10.1080/10826068.2018.1476876] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Dattatray Bedade
- Department of Food Engineering and Technology, Institute of Chemical Technology, Mumbai, India
| | - Jan Deska
- Department of Chemistry, School of Chemical Technology, Aalto University, Aalto, Finland
| | - Sandip Bankar
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, Aalto, Finland
| | - Samir Bejar
- Laboratory of Microbial Biotechnology and Engineering Enzymes, Centre of Biotechnology of Sfax (CBS), University of Sfax, Sfax, Tunisia
| | - Rekha Singhal
- Department of Food Engineering and Technology, Institute of Chemical Technology, Mumbai, India
| | - Salem Shamekh
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, Aalto, Finland
- Juva Truffle Center, Juva, Finland
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Havlik D, Brandt U, Bohle K, Fleißner A. Establishment of Neurospora crassa as a host for heterologous protein production using a human antibody fragment as a model product. Microb Cell Fact 2017; 16:128. [PMID: 28743272 PMCID: PMC5526295 DOI: 10.1186/s12934-017-0734-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/05/2017] [Indexed: 12/16/2022] Open
Abstract
Background Filamentous fungi are commonly used as production hosts for bulk enzymes in biotechnological applications. Their robust and quick growth combined with their ability to secrete large amounts of protein directly into the culture medium makes fungi appealing organisms for the generation of novel production systems. The red bread mold Neurospora crassa has long been established as a model system in basic research. It can be very easily genetically manipulated and a wealth of molecular tools and mutants are available. In addition, N. crassa is very fast growing and non-toxic. All of these features point to a high but so far untapped potential of this fungus for biotechnological applications. In this study, we used genetic engineering and bioprocess development in a design-build-test-cycle process to establish N. crassa as a production host for heterologous proteins. Results The human antibody fragment HT186-D11 was fused to a truncated version of the endogenous enzyme glucoamylase (GLA-1), which served as a carrier protein to achieve secretion into the culture medium. A modular expression cassette was constructed and tested under the control of different promoters. Protease activity was identified as a major limitation of the production strain, and the effects of different mutations causing protease deficiencies were compared. Furthermore, a parallel bioreactor system (1 L) was employed to develop and optimize a production process, including the comparison of different culture media and cultivation parameters. After successful optimization of the production strain and the cultivation conditions an exemplary scale up to a 10 L stirred tank reactor was performed. Conclusions The data of this study indicate that N. crassa is suited for the production and secretion of heterologous proteins. Controlling expression by the optimized promoter Pccg1nr in a fourfold protease deletion strain resulted in the successful secretion of the heterologous product with estimated yields of 3 mg/L of the fusion protein. The fungus could easily be cultivated in bioreactors and a first scale-up was successful. The system holds therefore much potential, warranting further efforts in optimization. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0734-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Havlik
- Division of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Inhoffenstr. 7, Braunschweig, 38124, Germany.,Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.,Navigo Proteins GmbH, Heinrich-Damerow-Str. 1, 06120, Halle (Saale), Germany
| | - Ulrike Brandt
- Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Kathrin Bohle
- Division of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Inhoffenstr. 7, Braunschweig, 38124, Germany
| | - André Fleißner
- Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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Sheet S, Sathishkumar Y, Sivakumar AS, Shim KS, Lee YS. Low-shear-modeled microgravity-grown Penicillium chrysogenum-mediated biosynthesis of silver nanoparticles with enhanced antimicrobial activity and its anticancer effect in human liver cancer and fibroblast cells. Bioprocess Biosyst Eng 2017; 40:1529-1542. [PMID: 28710569 DOI: 10.1007/s00449-017-1809-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/23/2017] [Indexed: 12/16/2022]
Abstract
Gravitational force and shear forces induce various changes in gene expression and metabolite production of microorganisms. Previous reports have shown that there are differences in the expression of different sets of proteins and enzymes under microgravity conditions compared to normal gravity. The aim of this study is to utilize culture filtrates of Penicillium chrysogenum grown under microgravity and normal conditions to synthesize silver nanoparticles and to examine whether there is any difference between their physiochemical and biological function. Synthesized nanoparticles were characterized using UV-Vis spectroscopy, FTIR, XRD, and TEM. Biological functional studies such as antimicrobial activity, cytotoxic studies, and anticancer activity were carried out. Antimicrobial activity was tested using antibiotic susceptibility testing by Kirby-Bauer method and cytotoxicity tests were carried out using 3T3-L1 normal fibroblasts cells and Hep-G2 cancer cell lines. Interestingly, our results indicated that microgravity-synthesized silver nanoparticles possess enhanced antibacterial activity and cytotoxic effect against cancer cells compared to normal gravity-synthesized silver nanoparticle. This work highlighted the importance of gravitational vector on the fungal enzyme profiles and their role in silver nanoparticle synthesis with enhanced biological activity.
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Affiliation(s)
- Sunirmal Sheet
- Department of Forest Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Yesupatham Sathishkumar
- Department of Forest Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea.,Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daehak-ro, Daejeon, Republic of Korea
| | - Allur Subramaniyam Sivakumar
- Department of Animal Biotechnology, College of Agriculture and Life Sciences, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Kwan Seob Shim
- Department of Animal Biotechnology, College of Agriculture and Life Sciences, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Yang Soo Lee
- Department of Forest Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea.
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15
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Analysis of Agaricus meleagris pyranose dehydrogenase N-glycosylation sites and performance of partially non-glycosylated enzymes. Enzyme Microb Technol 2017; 99:57-66. [PMID: 28193332 DOI: 10.1016/j.enzmictec.2017.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/17/2017] [Accepted: 01/20/2017] [Indexed: 11/22/2022]
Abstract
Pyranose Dehydrogenase 1 from the basidiomycete Agaricus meleagris (AmPDH1) is an oxidoreductase capable of oxidizing a broad variety of sugars. Due to this and its ability of dioxidation of substrates and no side production of hydrogen peroxide, it is studied for use in enzymatic bio-fuel cells. In-vitro deglycosylated AmPDH1 as well as knock-out mutants of the N-glycosylation sites N75 and N175, near the active site entrance, were previously shown to improve achievable current densities of graphite electrodes modified with AmPDH1 and an osmium redox polymer acting as a redox mediator, up to 10-fold. For a better understanding of the role of N-glycosylation of AmPDH1, a systematic set of N-glycosylation site mutants was investigated in this work, regarding expression efficiency, enzyme activity and stability. Furthermore, the site specific extend of N-glycosylation was compared between native and recombinant wild type AmPDH1. Knocking out the site N252 prevented the attachment of significantly extended N-glycan structures as detected on polyacrylamide gel electrophoresis, but did not significantly alter enzyme performance on modified electrodes. This suggests that not the molecule size but other factors like accessibility of the active site improved performance of deglycosylated AmPDH1/osmium redox polymer modified electrodes. A fourth N-glycosylation site of AmPDH1 could be confirmed by mass spectrometry at N319, which appeared to be conserved in related fungal pyranose dehydrogenases but not in other members of the glucose-methanol-choline oxidoreductase structural family. This site was shown to be the only one that is essential for functional recombinant expression of the enzyme.
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16
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Purification and Biochemical Characterization of a Neutral Serine Protease from Trichoderma harzianum. Use in Antibacterial Peptide Production from a Fish By-Product Hydrolysate. Appl Biochem Biotechnol 2016; 182:831-845. [PMID: 27987188 DOI: 10.1007/s12010-016-2365-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/08/2016] [Indexed: 10/20/2022]
Abstract
This study reports the purification and biochemical characterization of an extracellular neutral protease from the fungus Trichoderma harzianum. The protease (Th-Protease) was purified from the culture supernatant to homogeneity by a three-step procedure with 14.2% recovery and 9.06-fold increase in specific activity. The purified enzyme appeared as a single protein band after sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) with a molecular mass of about 20 kDa. The optimum pH and temperature for the proteolytic activity were pH 7.0 and 40 °C, respectively. The enzyme was then investigated for its potential application in the production of antibacterial peptides. Interestingly, Scorpaena notata viscera protein hydrolysate prepared using the purified serine protease (Th-Protease) showed remarkable in vitro antibacterial activities. A peptide with a high antibacterial activity was further purified by a three-step procedure, and its sequence was identified as FPIGMGHGSRPA. The result of this study offers a promising alternative to produce natural antibacterial peptides from fish protein hydrolysate.
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Jin FJ, Katayama T, Maruyama JI, Kitamoto K. Comparative genomic analysis identified a mutation related to enhanced heterologous protein production in the filamentous fungus Aspergillus oryzae. Appl Microbiol Biotechnol 2016; 100:9163-9174. [DOI: 10.1007/s00253-016-7714-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/14/2016] [Accepted: 06/27/2016] [Indexed: 11/27/2022]
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18
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Gómez S, López-Estepa M, Fernández FJ, Suárez T, Vega MC. Alternative Eukaryotic Expression Systems for the Production of Proteins and Protein Complexes. ADVANCED TECHNOLOGIES FOR PROTEIN COMPLEX PRODUCTION AND CHARACTERIZATION 2016; 896:167-84. [DOI: 10.1007/978-3-319-27216-0_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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Gene Expression Systems in Industrial Ascomycetes: Advancements and Applications. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Abstract
Filamentous fungi play an important role not only in the bio-manufacturing of value-added products, but also in bioenergy and environmental research. The bioprocess manipulation of filamentous fungi is more difficult than that of other microbial species because of their different pellet morphologies and the presence of tangled mycelia under different cultivation conditions. Fungal pellets, which have the advantages of harvest ease, low fermentation broth viscosity and high yield of some proteins, have been used for a long time. Many attempts have been made to establish the relationship between pellet and product yield using quantitative approaches. Fungal pellet formation is attributed to the combination of electrostatic interactions, hydrophobicity and specific interactions from spore wall components. Electrostatic interactions result from van der Waals forces and negative charge repulsion from carboxyl groups in the spore wall structure. Electrostatic interactions are also affected by counter-ions (cations) and the physiologic conditions of spores that modify the carboxyl groups. Fungal aggregates are promoted by the hydrophobicity generated by hydrophobins, which form a hydrophobic coat that covers the spore. The specific interactions of spore wall components contribute to spore aggregation through salt bridging. A model of spore aggregation was proposed based on these forces. Additionally, some challenges were addressed, including the limitations of research techniques, the quantitative determination of forces and the complex information of biological systems, to clarify the mechanism of fungal pellet formation.
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Affiliation(s)
- Jianguo Zhang
- a School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology and
| | - Jining Zhang
- b Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences , Shanghai , China
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21
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Improvement of glucoamylase production using axial impellers with low power consumption and homogeneous mass transfer. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.03.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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Aswati Nair R, Geethu C. Purification and characterization of secretory serine protease from necrotrophic oomycete, Pythium myriotylum Dreschler. World J Microbiol Biotechnol 2014; 31:85-94. [DOI: 10.1007/s11274-014-1767-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/28/2014] [Indexed: 01/14/2023]
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23
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Martín JF. Calcium-containing phosphopeptides pave the secretory pathway for efficient protein traffic and secretion in fungi. Microb Cell Fact 2014; 13:117. [PMID: 25205075 PMCID: PMC4180148 DOI: 10.1186/s12934-014-0117-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/01/2014] [Indexed: 02/07/2023] Open
Abstract
Casein phosphopeptides (CPPs) containing chelated calcium drastically increase the secretion of extracellular homologous and heterologous proteins in filamentous fungi. Casein phosphopeptides released by digestion of alpha - and beta-casein are rich in phosphoserine residues (SerP). They stimulate enzyme secretion in the gastrointestinal tract and enhance the immune response in mammals, and are used as food supplements. It is well known that casein phosphopeptides transport Ca2+ across the membranes and play an important role in Ca2+ homeostasis in the cells. Addition of CPPs drastically increases the production of heterologous proteins in Aspergillus as host for industrial enzyme production. Recent proteomics studies showed that CPPs alter drastically the vesicle-mediated secretory pathway in filamentous fungi, apparently because they change the calcium concentration in organelles that act as calcium reservoirs. In the organelles calcium homeostasis a major role is played by the pmr1 gene, that encodes a Ca2+/Mn2+ transport ATPase, localized in the Golgi complex; this transporter controls the balance between intra-Golgi and cytoplasmic Ca2+ concentrations. A Golgi-located casein kinase (CkiA) governs the ER to Golgi directionality of the movement of secretory proteins by interacting with the COPII coat of secretory vesicles when they reach the Golgi. Mutants defective in the casein-2 kinase CkiA show abnormal targeting of some secretory proteins, including cytoplasmic membrane amino acid transporters that in ckiA mutants are miss-targeted to vacuolar membranes. Interestingly, addition of CPPs increases a glyceraldehyde-3-phpshate dehydrogenase protein that is known to associate with microtubules and act as a vesicle/membrane fusogenic agent. In summary, CPPs alter the protein secretory pathway in fungi adapting it to a deregulated protein traffic through the organelles and vesicles what results in a drastic increase in secretion of heterologous and also of some homologous proteins.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
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24
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Mäkelä MR, Donofrio N, de Vries RP. Plant biomass degradation by fungi. Fungal Genet Biol 2014; 72:2-9. [PMID: 25192611 DOI: 10.1016/j.fgb.2014.08.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/19/2014] [Accepted: 08/25/2014] [Indexed: 12/27/2022]
Abstract
Plant biomass degradation by fungi has implications for several fields of science. The enzyme systems employed by fungi for this are broadly used in various industrial sectors such as food & feed, pulp & paper, detergents, textile, wine, and more recently biofuels and biochemicals. In addition, the topic is highly relevant in the field of plant pathogenic fungi as they degrade plant biomass to either gain access to the plant or as carbon source, resulting in significant crop losses. Finally, fungi are the main degraders of plant biomass in nature and as such have an essential role in the global carbon cycle and ecology in general. In this review we provide a global view on the development of this research topic in saprobic ascomycetes and basidiomycetes and in plant pathogenic fungi and link this to the other papers of this special issue on plant biomass degradation by fungi.
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Affiliation(s)
- Miia R Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Nicole Donofrio
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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25
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Nevalainen H, Peterson R. Making recombinant proteins in filamentous fungi- are we expecting too much? Front Microbiol 2014; 5:75. [PMID: 24578701 PMCID: PMC3936196 DOI: 10.3389/fmicb.2014.00075] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/11/2014] [Indexed: 11/13/2022] Open
Abstract
Hosts used for the production of recombinant proteins are typically high-protein secreting mutant strains that have been selected for a specific purpose, such as efficient production of cellulose-degrading enzymes. Somewhat surprisingly, sequencing of the genomes of a series of mutant strains of the cellulolytic Trichoderma reesei, widely used as an expression host for recombinant gene products, has shed very little light on the nature of changes that boost high-level protein secretion. While it is generally agreed and shown that protein secretion in filamentous fungi occurs mainly through the hyphal tip, there is growing evidence that secretion of proteins also takes place in sub-apical regions. Attempts to increase correct folding and thereby the yields of heterologous proteins in fungal hosts by co-expression of cellular chaperones and foldases have resulted in variable success; underlying reasons have been explored mainly at the transcriptional level. The observed physiological changes in fungal strains experiencing increasing stress through protein overexpression under strong gene promoters also reflect the challenge the host organisms are experiencing. It is evident, that as with other eukaryotes, fungal endoplasmic reticulum is a highly dynamic structure. Considering the above, there is an emerging body of work exploring the use of weaker expression promoters to avoid undue stress. Filamentous fungi have been hailed as candidates for the production of pharmaceutically relevant proteins for therapeutic use. One of the biggest challenges in terms of fungally produced heterologous gene products is their mode of glycosylation; fungi lack the functionally important terminal sialylation of the glycans that occurs in mammalian cells. Finally, exploration of the metabolic pathways and fluxes together with the development of sophisticated fermentation protocols may result in new strategies to produce recombinant proteins in filamentous fungi.
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Affiliation(s)
- Helena Nevalainen
- Biomolecular Frontiers Research Centre, Department of Chemistry and Biomolecular Sciences, Macquarie University, SydneyNSW, Australia
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26
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Geethu C, Resna AK, Nair RA. Characterization of major hydrolytic enzymes secreted by Pythium myriotylum, causative agent for soft rot disease. Antonie Van Leeuwenhoek 2013; 104:749-57. [PMID: 23897210 DOI: 10.1007/s10482-013-9983-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 07/22/2013] [Indexed: 12/22/2022]
Abstract
Pythium myriotylum, an oomycetous necrotroph is the causal agent of soft rot disease affecting several crops. Successful colonization by necrotrophs depends on their secretion of a diverse array of plant cell wall degrading enzymes (CWDEs). The induction dynamics of CWDEs secreted by P. myriotylum was analysed as little information is available for this pathogen. Activities of CWDEs that included pectinase, cellulase, xylanase and protease were detected using radial diffusion assay and differential staining. In Czapek Dox minimal medium supplemented with respective substrates as carbon source, the increase in CWDE activities was observed till 8 days of incubation after which a gradual decline in enzymatic activities was observed. With sucrose as sole carbon source, all the enzymes studied showed increase in activity with fungal growth while with cell wall material derived from ginger rhizome as sole carbon source, an initial spurt in cellulase, xylanase and pectinase activities was observed 3 days post incubation while protease activity increased from three days of incubation and reached maximum at 13 days of incubation. To further evaluate the role of CWDEs in pathogenicity, UV-induced mutants (pmN14uv1) were generated wherein significant reduction in cellulase, pectinase and protease activities were observed while that of xylanase remained unchanged compared to wild type isolate (RGCBN14). Bioassays indicated changes in infection potential of pmN14uv1 thereby suggesting the crucial role played by P. myriotylum CWDEs in initiating the rotting process. Hence appropriate strategies that target the production/activity of these secretory hydrolytic enzymes will help in reducing disease incidence/pathogen virulence.
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Affiliation(s)
- C Geethu
- School of Biotechnology, National Institute of Technology Calicut (NITC), Calicut, Kerala, India
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27
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Crystal structures of glycoside hydrolase family 3 β-glucosidase 1 from Aspergillus aculeatus. Biochem J 2013; 452:211-21. [DOI: 10.1042/bj20130054] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GH3 (glycoside hydrolase family 3) BGLs (β-glucosidases) from filamentous fungi have been widely and commercially used for the supplementation of cellulases. AaBGL1 (Aspergillus aculeatus BGL1) belongs to the GH3 and shows high activity towards cellooligosaccharides up to high degree of polymerization. In the present study we determined the crystal structure of AaBGL1. In addition to the substrate-free structure, the structures of complexes with glucose and various inhibitors were determined. The structure of AaBGL1 is highly glycosylated with 88 monosaccharides (18 N-glycan chains) in the dimer. The largest N-glycan chain comprises ten monosaccharides and is one of the largest glycans ever observed in protein crystal structures. A prominent insertion region exists in a fibronectin type III domain, and this region extends to cover a wide surface area of the enzyme. The subsite +1 of AaBGL1 is highly hydrophobic. Three aromatic residues are present at subsite +1 and are located in short loop regions that are uniquely present in this enzyme. There is a long cleft extending from subsite +1, which appears to be suitable for binding long cellooligosaccharides. The crystal structures of AaBGL1 from the present study provide an important structural basis for the technical improvement of enzymatic cellulosic biomass conversion.
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Biesebeke RT, Record E. Scientific Advances with Aspergillus Species that Are Used for Food and Biotech Applications. Microbes Environ 2012; 23:177-81. [PMID: 21558706 DOI: 10.1264/jsme2.23.177] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Yeast and filamentous fungi have been used for centuries in diverse biotechnological processes. Fungal fermentation technology is traditionally used in relation to food production, such as for bread, beer, cheese, sake and soy sauce. Last century, the industrial application of yeast and filamentous fungi expanded rapidly, with excellent examples such as purified enzymes and secondary metabolites (e.g. antibiotics), which are used in a wide range of food as well as non-food industries. Research on protein and/or metabolite secretion by fungal species has focused on identifying bottlenecks in (post-) transcriptional regulation of protein production, metabolic rerouting, morphology and the transit of proteins through the secretion pathway. In past years, genome sequencing of some fungi (e.g. Aspergillus oryzae, Aspergillus niger) has been completed. The available genome sequences have enabled identification of genes and functionally important regions of the genome. This has directed research to focus on a post-genomics era in which transcriptomics, proteomics and metabolomics methodologies will help to explore the scientific relevance and industrial application of fungal genome sequences.
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van den Berg BA, Reinders MJT, Hulsman M, Wu L, Pel HJ, Roubos JA, de Ridder D. Exploring sequence characteristics related to high-level production of secreted proteins in Aspergillus niger. PLoS One 2012; 7:e45869. [PMID: 23049690 PMCID: PMC3462195 DOI: 10.1371/journal.pone.0045869] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 08/22/2012] [Indexed: 12/12/2022] Open
Abstract
Protein sequence features are explored in relation to the production of over-expressed extracellular proteins by fungi. Knowledge on features influencing protein production and secretion could be employed to improve enzyme production levels in industrial bioprocesses via protein engineering. A large set, over 600 homologous and nearly 2,000 heterologous fungal genes, were overexpressed in Aspergillus niger using a standardized expression cassette and scored for high versus no production. Subsequently, sequence-based machine learning techniques were applied for identifying relevant DNA and protein sequence features. The amino-acid composition of the protein sequence was found to be most predictive and interpretation revealed that, for both homologous and heterologous gene expression, the same features are important: tyrosine and asparagine composition was found to have a positive correlation with high-level production, whereas for unsuccessful production, contributions were found for methionine and lysine composition. The predictor is available online at http://bioinformatics.tudelft.nl/hipsec. Subsequent work aims at validating these findings by protein engineering as a method for increasing expression levels per gene copy.
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Affiliation(s)
- Bastiaan A. van den Berg
- Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Marcel J. T. Reinders
- Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Marc Hulsman
- Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Liang Wu
- DSM Biotechnology Center, Delft, The Netherlands
| | | | | | - Dick de Ridder
- Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
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Heterologous production of cellobiose dehydrogenases from the basidiomycete Coprinopsis cinerea and the ascomycete Podospora anserina and their effect on saccharification of wheat straw. Appl Microbiol Biotechnol 2012; 97:4873-85. [PMID: 22940800 DOI: 10.1007/s00253-012-4355-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 07/30/2012] [Accepted: 08/08/2012] [Indexed: 01/09/2023]
Abstract
Cellobiose dehydrogenases (CDHs) are extracellular glycosylated haemoflavoenzymes produced by many different wood-degrading and phytopathogenic fungi. Putative cellobiose dehydrogenase genes are recurrently discovered by genome sequencing projects in various phylogenetically distinct fungi. The genomes from the basidiomycete Coprinopsis cinerea and the ascomycete Podospora anserina were screened for candidate cdh genes, and one and three putative gene models were evidenced, respectively. Two putative cdh genes were selected and successfully expressed for the first time in Aspergillus niger. CDH activity was measured for both constructions (CDHcc and CDHpa), and both recombinant CDHs were purified to homogeneity and subsequently characterised. Kinetic constants were determined for several carbohydrates including β-1,4-linked di- and oligosaccharides. Optimal temperature and pH were 60 °C and 5 for CDHcc and 65-70 °C and 6 for CDHpa. Both CDHs showed a broad range of pH stability between 4 and 8. The effect of both CDHs on saccharification of micronized wheat straw by an industrial Trichoderma reesei secretome was determined. The addition of each CDH systematically decreased the release of total reducing sugars, but to different extents and according to the CDH concentration. Analytical methods were carried out to quantify the release of glucose, xylose and gluconic acid. An increase of glucose and xylose was measured at a low CDHcc concentration. At moderated and high CDHcc and CDHpa concentrations, glucose was severely reduced with a concomitant increase of gluconic acid. In conclusion, these results give new insights into the physical and chemical parameters and diversity of basidiomycetous and ascomycetous CDHs. These findings also demonstrated that CDH drastically influenced the saccharification on a natural substrate, and thus, CDH origin, concentration and potential enzymatic partners should be carefully considered in future artificial secretomes for biofuel applications.
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Zhu L, Nemoto T, Yoon J, Maruyama JI, Kitamoto K. Improved heterologous protein production by a tripeptidyl peptidase gene (AosedD) disruptant of the filamentous fungus Aspergillus oryzae. J GEN APPL MICROBIOL 2012; 58:199-209. [PMID: 22878738 DOI: 10.2323/jgam.58.199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Proteolytic degradation is one of the serious bottlenecks limiting the yields of heterologous protein production by Aspergillus oryzae. In this study, we selected a tripeptidyl peptidase gene AosedD (AO090166000084) as a candidate potentially degrading the heterologous protein, and performed localization analysis of the fusion protein AoSedD-EGFP in A. oryzae. As a result, the AoSedD-EGFP was observed in the septa and cell walls as well as in the culture medium, suggesting that AoSedD is a secretory enzyme. An AosedD disruptant was constructed to investigate an effect of AoSedD on the production level of heterologous proteins and protease activity. Both of the total protease and tripeptidyl peptidase activities in the culture medium of the AosedD disruptant were decreased as compared to those of the control strain. The maximum yields of recombinant bovine chymosin (CHY) and human lysozyme (HLY) produced by the AosedD disruptants showed approximately 2.9- and 1.7-fold increases, respectively, as compared to their control strains. These results suggest that AoSedD is one of the major proteases involved in the proteolytic degradation of recombinant proteins in A. oryzae.
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Affiliation(s)
- Lin Zhu
- Department of Biotechnology, The University of Tokyo, Japan
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Hisada H, Tsutsumi H, Ishida H, Hata Y. High production of llama variable heavy-chain antibody fragment (VHH) fused to various reader proteins by Aspergillus oryzae. Appl Microbiol Biotechnol 2012; 97:761-6. [DOI: 10.1007/s00253-012-4211-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/21/2012] [Accepted: 06/03/2012] [Indexed: 10/28/2022]
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Zhang J, Hu B. Solid-state fermentation of Mortierella isabellina for lipid production from soybean hull. Appl Biochem Biotechnol 2012; 166:1034-46. [PMID: 22198865 DOI: 10.1007/s12010-011-9491-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
Abstract
Soybean hull, generated from soybean processing, is a lignocellulosic material with limited industrial applications and little market value. This research is exploring a new application of soybean hull to be converted to fungal lipids for biodiesel production through solid-state fermentation. Mortierella isabellina was selected as the oil producer because of its high lipid content at low C/N ratio. Several cultivation factors were investigated, including moisture content, inoculums size, fungal spore age, and nutrient supplements, in an attempt to enhance the lipid production of the solid-state fermentation process. The results showed that lipid production with the increase of the moisture content and the spore age, while decreased as the size of inoculums increased. Nutrients addition (KH₂PO₄ 1.2 mg and MgSO₄ 0.6 mg/g soybean hull) improved the lipid production. The total final lipid reached 47.9 mg lipid from 1 g soybean hull after the conversion, 3.3-fold higher than initial lipid reserve in the soybean hull. The fatty acid profile analysis indicated that fatty acid content consisted of 30.0% of total lipid, and 80.4% of total fatty acid was C16 and C18. Therefore, lipid production from soybean hull is a possible option to enable soybean hull as a new resource for biodiesel production and to enhance the overall oil production from soybeans.
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Affiliation(s)
- Jianguo Zhang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, USA
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Kosalková K, García-Estrada C, Barreiro C, Flórez MG, Jami MS, Paniagua MA, Martín JF. Casein phosphopeptides drastically increase the secretion of extracellular proteins in Aspergillus awamori. Proteomics studies reveal changes in the secretory pathway. Microb Cell Fact 2012; 11:5. [PMID: 22234238 PMCID: PMC3283509 DOI: 10.1186/1475-2859-11-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 01/10/2012] [Indexed: 11/24/2022] Open
Abstract
Background The secretion of heterologous animal proteins in filamentous fungi is usually limited by bottlenecks in the vesicle-mediated secretory pathway. Results Using the secretion of bovine chymosin in Aspergillus awamori as a model, we found a drastic increase (40 to 80-fold) in cells grown with casein or casein phosphopeptides (CPPs). CPPs are rich in phosphoserine, but phosphoserine itself did not increase the secretion of chymosin. The stimulatory effect is reduced about 50% using partially dephosphorylated casein and is not exerted by casamino acids. The phosphopeptides effect was not exerted at transcriptional level, but instead, it was clearly observed on the secretion of chymosin by immunodetection analysis. Proteomics studies revealed very interesting metabolic changes in response to phosphopeptides supplementation. The oxidative metabolism was reduced, since enzymes involved in fermentative processes were overrepresented. An oxygen-binding hemoglobin-like protein was overrepresented in the proteome following phosphopeptides addition. Most interestingly, the intracellular pre-protein enzymes, including pre-prochymosin, were depleted (most of them are underrepresented in the intracellular proteome after the addition of CPPs), whereas the extracellular mature form of several of these secretable proteins and cell-wall biosynthetic enzymes was greatly overrepresented in the secretome of phosphopeptides-supplemented cells. Another important 'moonlighting' protein (glyceraldehyde-3-phosphate dehydrogenase), which has been described to have vesicle fusogenic and cytoskeleton formation modulating activities, was clearly overrepresented in phosphopeptides-supplemented cells. Conclusions In summary, CPPs cause the reprogramming of cellular metabolism, which leads to massive secretion of extracellular proteins.
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Novel hydrophobins from Trichoderma define a new hydrophobin subclass: protein properties, evolution, regulation and processing. J Mol Evol 2011; 72:339-51. [PMID: 21424760 DOI: 10.1007/s00239-011-9438-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 03/01/2011] [Indexed: 10/18/2022]
Abstract
Hydrophobins are small proteins, characterised by the presence of eight positionally conserved cysteine residues, and are present in all filamentous asco- and basidiomycetes. They are found on the outer surfaces of cell walls of hyphae and conidia, where they mediate interactions between the fungus and the environment. Hydrophobins are conventionally grouped into two classes (class I and II) according to their solubility in solvents, hydropathy profiles and spacing between the conserved cysteines. Here we describe a novel set of hydrophobins from Trichoderma spp. that deviate from this classification in their hydropathy, cysteine spacing and protein surface pattern. Phylogenetic analysis shows that they form separate clades within ascomycete class I hydrophobins. Using T. atroviride as a model, the novel hydrophobins were found to be expressed under conditions of glucose limitation and to be regulated by differential splicing.
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Kimura S, Maruyama JI, Kikuma T, Arioka M, Kitamoto K. Autophagy delivers misfolded secretory proteins accumulated in endoplasmic reticulum to vacuoles in the filamentous fungus Aspergillus oryzae. Biochem Biophys Res Commun 2011; 406:464-70. [DOI: 10.1016/j.bbrc.2011.02.075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 02/15/2011] [Indexed: 01/26/2023]
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Abstract
Filamentous fungi have received attentions as hosts for heterologous protein production because of their high secretion capability and eukaryotic post-translational modifications. One of the safest hosts for heterologous protein production is Koji mold Aspergillus oryzae since it has been used in the production of Japanese fermented foods for over 1,000 years. The production levels of proteins from higher eukaryotes are much lower than those of homologous (fungal) proteins. Bottlenecks in the heterologous protein production are suggested to be proteolytic degradation of the produced protein in the medium and the secretory pathway. For construction of excellent host strains, many genes causing the bottlenecks should be disrupted rapidly and efficiently. We developed a marker recycling system with the highly efficient gene-targeting background in A. oryzae. By employing this technique, we performed multiple gene disruption of the ten protease genes. The decuple protease gene disruptant showed fourfold production level of a heterologous protein compared with the wild-type strain.
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Yoon J, Maruyama JI, Kitamoto K. Disruption of ten protease genes in the filamentous fungus Aspergillus oryzae highly improves production of heterologous proteins. Appl Microbiol Biotechnol 2010; 89:747-59. [DOI: 10.1007/s00253-010-2937-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/02/2010] [Accepted: 10/04/2010] [Indexed: 11/25/2022]
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In vivo imaging of endoplasmic reticulum and distribution of mutant α-amylase in Aspergillus oryzae. Fungal Genet Biol 2010; 47:1044-54. [PMID: 20884367 DOI: 10.1016/j.fgb.2010.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Revised: 09/14/2010] [Accepted: 09/15/2010] [Indexed: 11/20/2022]
Abstract
Properly folded proteins destined for secretion exit through a specific subdomain of the endoplasmic reticulum (ER) known as transitional ER (tER) sites or ER exit sites (ERES). While such proteins in filamentous fungi localize at the hyphal tips overlapping the Spitzenkörper, the distribution of misfolded proteins remains unknown. In the present study, we analyzed the distribution of mutant protein as well as ER and tER sites visualized by expression of AoClxA and AoSec13 fused with fluorescent protein, respectively, in the filamentous fungus Aspergillus oryzae. Discrete tER subdomains were visualized as the punctate dots of AoSec13 overlapping or associated with AoClxA distribution. Both ER and tER sites were concentrated near hyphal tips and formed apical gradients. Interestingly, while the expression of wild-type α-amylase fusion protein (AmyB-mDsRed) showed its localization coinciding with the Spitzenkörper, a disulfide bond-deletion in AmyB causing its misfolding resulted in its accumulation in the subapical and basal ER, creating a reciprocal gradient to the tER sites. Furthermore, the reciprocal gradient enabled a clear distinction between the tER sites and the mutant AmyB accumulation sites near the apex. Based on these findings, we conclude that A. oryzae accumulates aberrant proteins toward basal hyphae while maintaining polarized tER sites for secretion of properly folded proteins at the hyphal tip.
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Bulky high-mannose-type N-glycan blocks the taste-modifying activity of miraculin. Biochim Biophys Acta Gen Subj 2010; 1800:986-92. [DOI: 10.1016/j.bbagen.2010.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 05/17/2010] [Accepted: 06/04/2010] [Indexed: 11/20/2022]
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Adav SS, Li AA, Manavalan A, Punt P, Sze SK. Quantitative iTRAQ Secretome Analysis of Aspergillus niger Reveals Novel Hydrolytic Enzymes. J Proteome Res 2010; 9:3932-40. [DOI: 10.1021/pr100148j] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Sunil S. Adav
- School of Biological Sciences, Nanyang Technological Universiy, 60 Nanyang Drive, Singapore 637551, and Department of Molecular Genetics and Gene Technology, TNO Nutrition and Food Research Institute, Utrechtseweg 48, PO Box 360, 3700 AJ Zeist, The Netherlands
| | - An A. Li
- School of Biological Sciences, Nanyang Technological Universiy, 60 Nanyang Drive, Singapore 637551, and Department of Molecular Genetics and Gene Technology, TNO Nutrition and Food Research Institute, Utrechtseweg 48, PO Box 360, 3700 AJ Zeist, The Netherlands
| | - Arulmani Manavalan
- School of Biological Sciences, Nanyang Technological Universiy, 60 Nanyang Drive, Singapore 637551, and Department of Molecular Genetics and Gene Technology, TNO Nutrition and Food Research Institute, Utrechtseweg 48, PO Box 360, 3700 AJ Zeist, The Netherlands
| | - Peter Punt
- School of Biological Sciences, Nanyang Technological Universiy, 60 Nanyang Drive, Singapore 637551, and Department of Molecular Genetics and Gene Technology, TNO Nutrition and Food Research Institute, Utrechtseweg 48, PO Box 360, 3700 AJ Zeist, The Netherlands
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological Universiy, 60 Nanyang Drive, Singapore 637551, and Department of Molecular Genetics and Gene Technology, TNO Nutrition and Food Research Institute, Utrechtseweg 48, PO Box 360, 3700 AJ Zeist, The Netherlands
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Chen X, Liang Y, Hua J, Tao L, Qin W, Chen S. Overexpression of bacterial ethylene-forming enzyme gene in Trichoderma reesei enhanced the production of ethylene. Int J Biol Sci 2010; 6:96-106. [PMID: 20150979 PMCID: PMC2820237 DOI: 10.7150/ijbs.6.96] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Accepted: 02/03/2010] [Indexed: 11/18/2022] Open
Abstract
In order to efficiently utilize natural cellulose materials to produce ethylene, three expression vectors containing the ethylene-forming enzyme (efe) gene from Pseudomonas syringae pv. glycinea were constructed. The target gene was respectively controlled by different promoters: cbh I promoter from Trichoderma reesei cellobiohydrolases I gene, gpd promoter from Aspergillus nidulans glyceraldehyde-3-phosphate dehydrogenase gene and pgk I promoter from T. reesei 3-phosphoglycerate kinase I gene. After transforming into T. reesei QM9414, 43 stable transformants were obtained by PCR amplification and ethylene determination. Southern blot analysis of 14 transformants demonstrated that the efe gene was integrated into chromosomal DNA with copy numbers from 1 to 4. Reverse transcription polymerase chain reaction (RT-PCR) analysis of 6 transformants showed that the heterologous gene was transcribed. By using wheat straw as a carbon source, the ethylene production rates of aforementioned 14 transformants were measured. Transformant C30-3 with pgk I promoter had the highest ethylene production (4,012 nl h-1 l-1). This indicates that agricultural wastes could be used to produce ethylene in recombinant filamentous fungus T. reesei.
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Affiliation(s)
- Xi Chen
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
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Systems biology of industrial microorganisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 120:51-99. [PMID: 20503029 DOI: 10.1007/10_2009_59] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.
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Abstract
Environments that are hostile to life are characterized by reduced microbial activity which results in poor soil- and plant-health, low biomass and biodiversity, and feeble ecosystem development. Whereas the functional biosphere may primarily be constrained by water activity (aw) the mechanism(s) by which this occurs have not been fully elucidated. Remarkably we found that, for diverse species of xerophilic fungi at aw values of ≤ 0.72, water activity per se did not limit cellular function. We provide evidence that chaotropic activity determined their biotic window, and obtained mycelial growth at water activities as low as 0.647 (below that recorded for any microbial species) by addition of compounds that reduced the net chaotropicity. Unexpectedly we found that some fungi grew optimally under chaotropic conditions, providing evidence for a previously uncharacterized class of extremophilic microbes. Further studies to elucidate the way in which solute activities interact to determine the limits of life may lead to enhanced biotechnological processes, and increased productivity of agricultural and natural ecosystems in arid and semiarid regions.
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Affiliation(s)
- Jim P Williams
- School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, UK
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Chill L, Trinh L, Azadi P, Ishihara M, Sonon R, Karnaukhova E, Ophir Y, Golding B, Shiloach J. Production, purification, and characterization of human alpha1 proteinase inhibitor from Aspergillus niger. Biotechnol Bioeng 2009; 102:828-44. [PMID: 18828177 DOI: 10.1002/bit.22099] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human alpha one proteinase inhibitor (alpha1-PI) was cloned and expressed in Aspergillus niger, filamentious fungus that can grow in defined media and can perform glycosylation. Submerged culture conditions were established using starch as carbon source, 30% dissolved oxygen concentration, pH 7.0 and 28 degrees C. Eight milligrams per liter of active alpha1-PI were secreted to the growth media in about 40 h. Controlling the protein proteolysis was found to be an important factor in the production. The effects of various carbon sources, pH and temperature on the production and stability of the protein were tested and the product was purified and characterized. Two molecular weights variants of the recombinant alpha1-PI were produced by the fungus; the difference is attributed to the glycosylated part of the molecule. The two glycoproteins were treated with PNGAse F and the released glycans were analyzed by HPAEC, MALDI/TOF-MS, NSI-MS(n), and GC-MS. The MALDI and NSI- full MS spectra of permethylated N-glycans revealed that the N-glycans of both variants contain a series of high-mannose type glycans with 5-20 hexose units. Monosaccharide analysis showed that these were composed of N-acetylglucos-amine, mannose, and galactose. Linkage analysis revealed that the galactosyl component was in the furanoic conformation, which was attaching in a terminal non-reducing position. The Galactofuranose-containing high-mannnose type N-glycans are typical structures, which recently have been found as part of several glycoproteins produced by Aspergillus niger.
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Affiliation(s)
- Liat Chill
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 14A Room 170, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
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Approaches for refining heterologous protein production in filamentous fungi. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0128-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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47
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Mikus M, Hatvani L, Neuhof T, Komoń-Zelazowska M, Dieckmann R, Schwecke T, Druzhinina IS, von Döhren H, Kubicek CP. Differential regulation and posttranslational processing of the class II hydrophobin genes from the biocontrol fungus Hypocrea atroviridis. Appl Environ Microbiol 2009; 75:3222-9. [PMID: 19329667 PMCID: PMC2681635 DOI: 10.1128/aem.01764-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 03/16/2009] [Indexed: 11/20/2022] Open
Abstract
Hydrophobins are small extracellular proteins, unique to and ubiquitous in filamentous fungi, which mediate interactions between the fungus and environment. The mycoparasitic fungus Hypocrea atroviridis has recently been shown to possess 10 different class II hydrophobin genes, which is a much higher number than that of any other ascomycete investigated so far. In order to learn the potential advantage of this hydrophobin multiplicity for the fungus, we have investigated their expression patterns under different physiological conditions (e.g., vegetative growth), various conditions inducing sporulation (light, carbon starvation, and mechanical injury-induced stress), and confrontation with potential hosts for mycoparasitism. The results show that the 10 hydrophobins display different patterns of response to these conditions: one hydrophobin (encoded by hfb-2b) is constitutively induced under all conditions, whereas other hydrophobins were formed only under conditions of carbon starvation (encoded by hfb-1c and hfb-6c) or light plus carbon starvation (encoded by hfb-2c, hfb-6a, and hfb-6b). The hydrophobins encoded by hfb-1b and hfb-5a were primarily formed during vegetative growth and under mechanical injury-provoked stress. hfb-22a was not expressed under any conditions and is likely a pseudogene. None of the 10 genes showed a specific expression pattern during mycoparasitic interaction. Most, but not all, of the expression patterns under the three different conditions of sporulation were dependent on one or both of the two blue-light regulator proteins BLR1 and BLR2, as shown by the use of respective loss-of-function mutants. Matrix-assisted laser desorption ionization-time of flight mass spectrometry of mycelial solvent extracts provided sets of molecular ions corresponding to HFB-1b, HFB-2a, HFB-2b, and HFB-5a in their oxidized and processed forms. These in silico-deduced sequences of the hydrophobins indicate cleavages at known signal peptide sites as well as additional N- and C-terminal processing. Mass peaks observed during confrontation with plant-pathogenic fungi indicate further proteolytic attack on the hydrophobins. Our study illustrates both divergent and redundant functions of the 10 hydrophobins of H. atroviridis.
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Affiliation(s)
- Marianna Mikus
- FB Gentechnik und Angewandte Biochemie, Institut für Verfahrenstechnik, Umwelttechnik und Technische Biowissenschaften, TU Wien, Getreidemarkt 9-166, 1060 Vienna, Austria
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Todaka N, Lopez CM, Inoue T, Saita K, Maruyama JI, Arioka M, Kitamoto K, Kudo T, Moriya S. Heterologous expression and characterization of an endoglucanase from a symbiotic protist of the lower termite, Reticulitermes speratus. Appl Biochem Biotechnol 2009; 160:1168-78. [PMID: 19404781 DOI: 10.1007/s12010-009-8626-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 03/25/2009] [Indexed: 11/24/2022]
Abstract
RsSymEG, an endoglucanase of glycosyl hydrolase family (GHF) 7 encoded by a transcript isolated from the symbiotic protist of the termite Reticulitermes speratus, is expressed in Aspergillus oryzae. Interestingly, purified RsSymEG1 has a relatively higher specific activity (603 micromol min(-1) mg(-1) protein) and V(max) value (769.6 unit/mg protein) than previously reported data for GHF7 endoglucanase of Trichoderma ressei. It also has the same K(m) value (1.97 mg/ml) with Clostridium cellulolyticum enzymes that contain cellulose binding module, a property indicative of high affinity to substrate, though no cellulose binding module is found within it. Thin-layer chromatography analysis revealed that RsSymEG1 preferentially hydrolyzes the beta-1,4-cellulosic linkage of cellodextrins into cellobiose and glucose.
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Affiliation(s)
- Nemuri Todaka
- Laboratory of Environmental Molecular Biology, RIKEN, 1-7-29 Suehiro-cho, Tsurumi-ward, Kanagawa 230-0045, Japan
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Construction of quintuple protease gene disruptant for heterologous protein production in Aspergillus oryzae. Appl Microbiol Biotechnol 2009; 82:691-701. [DOI: 10.1007/s00253-008-1815-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 11/27/2008] [Accepted: 12/07/2008] [Indexed: 10/21/2022]
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50
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Sasaguri S, Maruyama JI, Moriya S, Kudo T, Kitamoto K, Arioka M. Codon optimization prevents premature polyadenylation of heterologously-expressed cellulases from termite-gut symbionts in Aspergillus oryzae. J GEN APPL MICROBIOL 2009; 54:343-51. [PMID: 19164877 DOI: 10.2323/jgam.54.343] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To achieve high expression of glycoside hydrolase family 45 endoglucanase (RsSym45EG1) from a symbiotic protist of the termite Reticulitermes speratus, synthetic sequence RsSym45eg1-co, in which the codon usage was adjusted to that of the highly-expressed tef1 gene encoding translation elongation factor 1alpha, was prepared and introduced into A. oryzae. The transcript level of RsSym45eg1-co was 1.8-fold higher than that of RsSym45eg1. In cells harboring RsSym45eg1, but not RsSym45eg1-co, truncated transcripts in which the coding region was prematurely terminated and followed by a poly A chain were found. The production of endoglucanase in the culture supernatant was improved by codon optimization. Truncated transcripts were also found when cellobiohydrolase and beta-glucosidase from R. speratus symbionts were expressed, and the transcript level of the former was increased by codon-optimization. Our findings suggest that premature polyadenylation frequently occurs in heterologous protein expression in A. oryzae, which might result in the poor yield of expressed proteins.
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Affiliation(s)
- Shiho Sasaguri
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
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