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Yang H, Wang H, Wang F, Zhang K, Qu J, Guan J, Shen W, Cao Y, Xia Y, Chen X. Efficient extracellular production of recombinant proteins in E. coli via enhancing expression of dacA on the genome. J Ind Microbiol Biotechnol 2022; 49:6596876. [PMID: 35648451 PMCID: PMC9338883 DOI: 10.1093/jimb/kuac016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/21/2022] [Indexed: 11/14/2022]
Abstract
D, D-carboxypeptidase DacA plays an important role in the synthesis and stabilization of Escherichia coli cell wall peptidoglycan. The production level of extracellular recombinant proteins in E. coli can be enhanced by high D, D-carboxypeptidase activity. Construction of expression systems under optimal promoters is one of the main strategies to realize high protein production in E. coli. In this study, the promoter PdacA-3 from DacA on the genome of E. coli BL21 (DE3) was verified to be efficient for recombinant green fluorescent protein using the plasmid mutant pET28a-PdacA with PdacA-3. Meanwhile, the promoter PdacA-3 was engineered to increase the production level of proteins via inserting one or two Shine–Dalgarno (SD) sequences between the promoter PdacA-3 and the target genes. The expression level of dacA on the genome was increased by the improved transcription of the engineered promoters (especially after inserting one additional SD sequence). The engineered promoters increased cell membrane permeabilities to significantly enhance the secretion production of extracellular recombinant proteins in E. coli. Among them, the extracellular recombinant amylase activities in E. coli BL21::1SD-pET28a-amyK and E. coli BL21::2SD-pET28a-amyK were increased by 2.0- and 1.6-fold that of the control (E. coli BL21-pET28a-amyK), respectively. Promoter engineering also affected the morphology and growth of the E. coli mutants. It was indicated that the engineered promoters enhanced the expression of dacA on the genome to disturb the synthesis and structural stability of cell wall peptidoglycans.
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Affiliation(s)
- Haiquan Yang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Haokun Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fuxiang Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Kunjie Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jinfeng Qu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jianmin Guan
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wei Shen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yu Cao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yuanyuan Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xianzhong Chen
- Correspondence should be addressed to: Xianzhong Chen at
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Son J, Joo JC, Baritugo KA, Jeong S, Lee JY, Lim HJ, Lim SH, Yoo JI, Park SJ. Consolidated microbial production of four-, five-, and six-carbon organic acids from crop residues: Current status and perspectives. BIORESOURCE TECHNOLOGY 2022; 351:127001. [PMID: 35292386 DOI: 10.1016/j.biortech.2022.127001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
The production of platform organic acids has been heavily dependent on petroleum-based industries. However, petrochemical-based industries that cannot guarantee a virtuous cycle of carbons released during various processes are now facing obsolescence because of the depletion of finite fossil fuel reserves and associated environmental pollutions. Thus, the transition into a circular economy in terms of the carbon footprint has been evaluated with the development of efficient microbial cell factories using renewable feedstocks. Herein, the recent progress on bio-based production of organic acids with four-, five-, and six-carbon backbones, including butyric acid and 3-hydroxybutyric acid (C4), 5-aminolevulinic acid and citramalic acid (C5), and hexanoic acid (C6), is discussed. Then, the current research on the production of C4-C6 organic acids is illustrated to suggest future directions for developing crop-residue based consolidated bioprocessing of C4-C6 organic acids using host strains with tailor-made capabilities.
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Affiliation(s)
- Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Kei-Anne Baritugo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seona Jeong
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ji Yeon Lee
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hye Jin Lim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seo Hyun Lim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jee In Yoo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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Mayer J, Knuuti T, Baumgarten L, Menke E, Bischoff L, Bunk B, Biedendieck R. Construction and Application of a Plasmid-Based Signal Peptide Library for Improved Secretion of Recombinant Proteins with Priestia megaterium. Microorganisms 2022; 10:microorganisms10040777. [PMID: 35456829 PMCID: PMC9032162 DOI: 10.3390/microorganisms10040777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 02/04/2023] Open
Abstract
The secretion of recombinant proteins plays an important role in their economic production and purification. The secretion efficiency depends on the responsible signal peptide (SP) in combination with the target protein and the given host and cannot be predicted so far. Due to its high plasmid stability, the lack of alkaline extracellular proteases and only few contaminating extracellular host proteins, Priestia megaterium provides a promising alternative to common Bacillus species. For the development of an easy and fast cloning and screening system to identify the SP best suited to a distinct protein, a plasmid-based SP library containing all predicted 182 Sec-dependent SPs from P. megaterium was established. The splitting of the SPs into 10 groups of individual multi-SP plasmids (pMSPs) allows their grouped amplification and application in screening approaches. The functionality of the whole library was demonstrated by enhancing the amount of the already well-secreted α-amylase AmyE by 1.6-fold. The secretion of a novel penicillin G acylase, which remained as insoluble protein inside the cells, as its native SP is unsuitable for secretion in P. megaterium, could be enhanced even up to 29-fold. Overall, only around 170 recombinant P. megaterium clones based on 50 inserted SPs had to be screened to achieve sufficient amounts for further enzyme characterizations. Thus, this newly developed plasmid-based genetic tool applicable for P. megaterium and also other Bacillus species facilitates the identification of suitable SPs for secretion of recombinant proteins.
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Affiliation(s)
- Janine Mayer
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
| | - Tobias Knuuti
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
| | - Lisa Baumgarten
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
| | - Elise Menke
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
| | - Lena Bischoff
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7, 38124 Braunschweig, Germany;
| | - Rebekka Biedendieck
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
- Correspondence: ; Tel.: +49-531-391-55291
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Pang C, Liu S, Zhang G, Zhou J, Du G, Li J. Enhancing extracellular production of lipoxygenase in Escherichia coli by signal peptides and autolysis system. Microb Cell Fact 2022; 21:42. [PMID: 35305645 PMCID: PMC8933919 DOI: 10.1186/s12934-022-01772-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
Background Lipoxygenase (LOX) is a non-heme iron containing dioxygenase that is widely used to improve food quality and produce active drug intermediates and biodiesel. Escherichia coli is one of the most widely used host microorganisms for recombinant protein expression; however, its weak extracellular secretion ability precludes its effective production of recombinant proteins into the extracellular environment. To facilitate subsequent characterization and application of LOX, improving its secretion efficiency from E. coli is a major challenge that needs to be solved. Results Several strategies were adopted to improve the extracellular secretion of LOX based on the signal peptides and cell wall permeability of E. coli. Here, we studied the effect of signal peptides on LOX secretion, which increased the secretory capacity for LOX marginally. Although surfactants could increase the permeability of the cell membrane to promote LOX secretion, the extracellular LOX yield could not meet the requirements of industrialization production. Subsequently, an autolysis system was constructed in E. coli based on the bacteriophage lysis gene ΦX174-E to enhance the production of extracellular proteins. Thus, the extracellular production of LOX was achieved and the content of inclusion bodies in the cell was reduced by optimizing cell lysis conditions. The extracellular LOX yield reached 368 ± 1.4 U mL−1 in a 5-L bioreactor under optimized lysis conditions that is, an induction time and temperature, and arabinose concentration of 5 h, 25 °C, and 0.6 mM, respectively. Conclusions In this study, the different signal peptides and cell autolysis system were developed and characterized for extracellular LOX production in E. coli. Finally, the cell autolysis system presented a slight advantage on extracellular LOX yield, which also provides reference for other protein extracellular production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01772-x.
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Chao S, Liu Y, Ding N, Lin Y, Wang Q, Tan J, Li W, Zheng Y, Hu X, Li J. Highly Expressed Soluble Recombinant Anti-GFP VHHs in Escherichia coli via Optimized Signal Peptides, Strains, and Inducers. Front Mol Biosci 2022; 9:848829. [PMID: 35359590 PMCID: PMC8960375 DOI: 10.3389/fmolb.2022.848829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Antigen-binding variable domains of the H chain of heavy-chain antibodies (VHHs), also known as nanobodies (Nbs), are of great interest in imaging technique, disease prevention, diagnosis, and therapy. High-level expression of soluble Nbs is very important for its industrial production. In this study, we optimized the expression system of anti-green fluorescent protein (GFP) VHHs with three different signal peptides (SPs), outer-membrane protein A (OmpA), pectate lyase B (PelB), and L-asparaginase II SP (L-AsPsII), in different Escherichia coli strains via isopropyl β-D-thiogalactoside (IPTG) induction and auto-induction, respectively. The solubility of recombinant anti-GFP VHHs with PelB or OmpA was significantly enhanced to the same extent by IPTG induction and auto-induction in BL21 (DE3) E. coli strain and the maximum yield of target protein reached approximately 0.4 mg/l in a shake flask. The binding activity of recombinant anti-GFP VHHs was also confirmed to be retained by native-polyacrylamide gel electrophoresis (PAGE). These results suggest that SPs like OmpA and PelB could efficiently improve the recombinant anti-GFP VHH solubility without changing its bioactivity, providing a novel strategy to optimize the E. coli expression system of soluble VHHs, and lay the foundation for the industrial production of soluble recombinant anti-GFP VHHs and the research of other VHHs in the future.
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Affiliation(s)
- Shuangying Chao
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Yuhang Liu
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Ning Ding
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Yue Lin
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Qian Wang
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Junwen Tan
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Wei Li
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Yang Zheng
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
- *Correspondence: Yang Zheng, ; Xuejun Hu, ; Junming Li,
| | - Xuejun Hu
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
- *Correspondence: Yang Zheng, ; Xuejun Hu, ; Junming Li,
| | - Junming Li
- Department of Clinical Laboratory, Yantai Yuhuangding Hospital, Yantai, China
- *Correspondence: Yang Zheng, ; Xuejun Hu, ; Junming Li,
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Sharma A, Balda S, Capalash N, Sharma P. Engineering multifunctional enzymes for agro-biomass utilization. BIORESOURCE TECHNOLOGY 2022; 347:126706. [PMID: 35033642 DOI: 10.1016/j.biortech.2022.126706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Lignocellulosic biomass is a plentiful renewable resource that can be converted into a wide range of high-value-added industrial products. However, the complexity of its structural integrity is one of the major constraints and requires combinations of different fibrolytic enzymes for the cost-effective, industrially and environmentally feasible transformation. An interesting approach is constructing multifunctional enzymes, either in a single polypeptide or by joining multiple domains with linkers and performing diverse reactions simultaneously, in a single host. The production of such chimera proteins multiplies the advantages of different enzymatic reactions in a single setup, in lesser time, at lower production cost and with desirable and improved catalytic activities. This review embodies the various domain-tailoring and extracellular secretion strategies, possible solutions to their challenges, and efforts to experimentally connect different catalytic activities in a single host, as well as their applications.
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Affiliation(s)
- Aarjoo Sharma
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjeev Balda
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Prince Sharma
- Department of Microbiology, Panjab University, Chandigarh, India.
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Tan Y, Henehan GT, Kinsella GK, Ryan BJ. Extracellular secretion of a cutinase with polyester-degrading potential by E. coli using a novel signal peptide from Amycolatopsis mediterranei. World J Microbiol Biotechnol 2022; 38:60. [PMID: 35195792 PMCID: PMC8866283 DOI: 10.1007/s11274-022-03246-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/24/2022] [Indexed: 10/26/2022]
Abstract
Recent studies in this laboratory showed that an extracellular cutinase from A. mediterranei (AmCut) was able to degrade the plastics polycaprolactone and polybutylene succinate. Such plastics can be slow to degrade in soils due to a lack of efficient polyester degrading organisms. AmCut also showed potential for the biocatalytic synthesis of esters by reverse hydrolysis. The gene for AmCut has an upstream leader sequence whose transcript is not present in the purified enzyme. In this study, we show using predictive modelling, that this sequence codes for an N-terminal signal peptide that directs transmembrane expression via the Sec secretion pathway. E. coli is a useful host for recombinant enzymes used in biocatalysis due to the ease of genetic manipulation in this organism, which allows tuning of enzymes for specific applications, by mutagenesis. When a truncated GST-tagged AmCut gene (lacking its signal peptide) was expressed in E. coli, all cutinase activity was observed in the cytosolic fraction. However, when GST-tagged AmCut was expressed in E. coli along with its native signal peptide, cutinase activity was observed in both the periplasmic space and the culture medium. This finding revealed that the native signal peptide of a Gram-positive organism (AmCut) was being recognised by the Gram-negative (E. coli) Sec transmembrane transport system. AmCut was transported into E. coli's periplasmic space from where it was released into the culture medium. Surprisingly, the presence of a bulky GST tag at the N-terminus of the signal peptide did not hinder transmembrane targeting. Although the periplasmic targeting was unexpected, it is not unprecedented due to the conservation of the Sec pathway across species. It was more surprising that AmCut was secreted from the periplasmic space into the culture medium. This suggests that extracellular AmCut translocation across the E. coli outer membrane may involve non-classical secretion pathways. This tuneable recombinant E. coli expressing extracellular AmCut may be useful for degradation of polyester substrates in the environment; this and other applications are discussed.
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Affiliation(s)
- Yeqi Tan
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, Dublin 7, D07 ADY7, Ireland
| | - Gary T Henehan
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, Dublin 7, D07 ADY7, Ireland
| | - Gemma K Kinsella
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, Dublin 7, D07 ADY7, Ireland
| | - Barry J Ryan
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, Dublin 7, D07 ADY7, Ireland.
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Ezema BO, Omeje KO, Bill RM, Goddard AD, O Eze SO, Fernandez-Castane A. Bioinformatic characterization of a triacylglycerol lipase produced by Aspergillus flavus isolated from the decaying seed of Cucumeropsis mannii. J Biomol Struct Dyn 2022; 41:2587-2601. [PMID: 35147487 DOI: 10.1080/07391102.2022.2035821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lipases are enzymes of industrial importance responsible for the hydrolysis of ester bonds of triglycerides. A lipolytic fungus was isolated and subsequently identified based on the ITS sequence analysis as putative Aspergillus flavus with accession number LC424503. The gene coding for extracellular triacylglycerol lipase was isolated from Aspergillus flavus species, sequenced, and characterised using bioinformatics tools. An open reading frame of 420 amino acid sequence was obtained and designated as Aspergillus flavus lipase (AFL) sequence. Alignment of the amino acid sequence with other lipases revealed the presence GHSLG sequence which is the lipase consensus sequence Gly-X1-Ser-X2-Gly indicating that it a classical lipase. A catalytic active site lid domain composed of TYITDTIIDLS amino acids sequence was also revealed. This lid protects the active site, control the catalytic activity and substrate selectivity in lipases. The 3-Dimensional structural model shared 34.08% sequence identity with a lipase from Yarrowia lipolytica covering 272 amino acid residues of the template model. A search of the lipase engineering database using AFL sequence revealed that it belongs to the class GX-lipase, superfamily abH23 and homologous family abH23.02, molecular weight and isoelectric point values of 46.95 KDa and 5.7, respectively. N-glycosylation sites were predicted at residues 164, 236 and 333, with potentials of 0.7250, 0.7037 and 0.7048, respectively. O-glycosylation sites were predicted at residues 355, 358, 360 and 366. A signal sequence of 37 amino acids was revealed at the N-terminal of the polypeptide. This is a short peptide sequence that marks a protein for transport across the cell membrane and indicates that AFL is an extracellular lipase. The findings on the structural and molecular properties of Aspergillus flavus lipase in this work will be crucial in future studies aiming at engineering the enzyme for biotechnology applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Benjamin O Ezema
- The Biochemistry Unit, Department of Science Laboratory Technology, University of Nigeria, Nsukka, Nigeria.,Department of Biochemistry, University of Nigeria, Nsukka, Nigeria.,Aston Institute of Materials Research, Aston University, Birmingham, UK.,Energy and Bioproducts Research Institute, Aston University, Birmingham, UK
| | - Kingsley O Omeje
- Department of Biochemistry, University of Nigeria, Nsukka, Nigeria
| | | | | | | | - Alfred Fernandez-Castane
- Aston Institute of Materials Research, Aston University, Birmingham, UK.,Energy and Bioproducts Research Institute, Aston University, Birmingham, UK
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Radzlin N, Yaakop AS, Goh KM, Liew KJ, Zakaria II, Kahar UM. Genome Analysis of Celeribacter sp. PS-C1 Isolated from Sekinchan Beach in Selangor, Malaysia, Reveals Its β-Glucosidase and Licheninase Activities. Microorganisms 2022; 10:microorganisms10020410. [PMID: 35208867 PMCID: PMC8874975 DOI: 10.3390/microorganisms10020410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 11/16/2022] Open
Abstract
A halophilic marine bacterial strain, PS-C1, was isolated from Sekinchan beach in Selangor, Malaysia. The 16S rRNA gene sequence analysis indicated that strain PS-C1 was associated with the genus Celeribacter. To date, there have been no reports on enzymes from the genus Celeribacter. The present study reports on the cellular features of Celeribacter sp. PS-C1, its annotated genome sequence, and comparative genome analyses of Celeribacter glycoside hydrolase (GH) enzymes. The genome of strain PS-C1 has a size of 3.87 Mbp and a G+C content of 59.10%, and contains 3739 protein-coding genes. Detailed analysis using the Carbohydrate-Active enZYmes (CAZy) database revealed that Celeribacter genomes harboured at least 12 putative genes encoding industrially important GHs that are grouped as cellulases, β-glucanases, hemicellulases, and starch-degrading enzymes. Herein, the potential applications of these enzymes are discussed. Furthermore, the activities of two types of GHs (β-glucosidase and licheninase) in strain PS-C1 were demonstrated. These findings suggest that strain PS-C1 could be a reservoir of novel GH enzymes for lignocellulosic biomass degradation.
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Affiliation(s)
- Nurfatini Radzlin
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia; (N.R.); (I.I.Z.)
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Amira Suriaty Yaakop
- School of Biological Sciences, Universiti Sains Malaysia, Minden 11800, Pulau Pinang, Malaysia
- Correspondence: (A.S.Y.); (U.M.K.)
| | - Kian Mau Goh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia; (K.M.G.); (K.J.L.)
| | - Kok Jun Liew
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia; (K.M.G.); (K.J.L.)
| | - Iffah Izzati Zakaria
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia; (N.R.); (I.I.Z.)
| | - Ummirul Mukminin Kahar
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia; (N.R.); (I.I.Z.)
- Correspondence: (A.S.Y.); (U.M.K.)
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60
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Loh FK, Nathan S, Chow SC, Fang CM. Cytolysin A-mediated protein exportation efficiency and its role in enhancing the fitness of live recombinant Salmonella Typhi vaccine strain. Lett Appl Microbiol 2022; 74:820-830. [PMID: 35138654 DOI: 10.1111/lam.13669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/13/2022] [Accepted: 02/04/2022] [Indexed: 11/30/2022]
Abstract
The genetic fusion of cytolysin A (ClyA) to heterologous antigen expressed in live Salmonella vector demonstrated efficient translocation into periplasmic space and extracellular medium. Accumulating evidence has shown that clyA-mediated antigen delivery improved growth fitness and enhanced immunogenicity of live vector vaccine, but the factors influencing this protein exportation has not been investigated. In this study, Toxoplasma gondii antigen fused at C-terminal of clyA protein was expressed in live S. Typhi vector via both plasmid and chromosomal-based expressions. The bivalent strains showed comparable growth rates as monovalent strains, but in varies antigen exportation efficiency. ClyA-fusion antigen with positive charges were translocated to the extracellular spaces, whereas those with negative charges were retained in the cytoplasm. Furthermore, excessive cellular resources expenditure on antigen expression, especially antigen with larger size, could limit the clyA-fusion antigen exportation, resulting in undesirable metabolic burden that eventually affects the growth fitness. Altogether, the present work indicates potential linkage of factors mainly on antigen properties and expression platforms that may affect clyA-mediated antigen delivery to enhance the growth fitness of live vector strain.
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Affiliation(s)
- Fei-Kean Loh
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, 43500, Semenyih Selangor, Malaysia
| | - Sheila Nathan
- Faculty of Science & Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Sek-Chuen Chow
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway Selangor, Malaysia
| | - Chee-Mun Fang
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, 43500, Semenyih Selangor, Malaysia
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Schwarz S, Gerlach D, Fan R, Czermak P. GbpA as a secretion and affinity purification tag for an antimicrobial peptide produced in Vibrio natriegens. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Pourhassan N. Z, Cui H, Khosa S, Davari MD, Jaeger KE, Smits SHJ, Schwaneberg U, Schmitt L. Optimized Hemolysin type 1 secretion system in Escherichia coli by directed evolution of the Hly enhancer fragment and including a terminator region. Chembiochem 2022; 23:e202100702. [PMID: 35062047 PMCID: PMC9306574 DOI: 10.1002/cbic.202100702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/21/2022] [Indexed: 11/26/2022]
Abstract
Type 1 secretion systems (T1SS) have a relatively simple architecture compared to other classes of secretion systems and therefore, are attractive to be optimized by protein engineering. Here, we report a KnowVolution campaign for the hemolysin (Hly) enhancer fragment, an untranslated region upstream of the hlyA gene, of the hemolysin T1SS of Escherichia coli to enhance its secretion efficiency. The best performing variant of the Hly enhancer fragment contained five nucleotide mutations at five positions (A30U, A36U, A54G, A81U, and A116U) resulted in a 2‐fold increase in the secretion level of a model lipase fused to the secretion carrier HlyA1. Computational analysis suggested that altered affinity to the generated enhancer fragment towards the S1 ribosomal protein contributes to the enhanced secretion levels. Furthermore, we demonstrate that involving a native terminator region along with the generated Hly enhancer fragment increased the secretion levels of the Hly system up to 5‐fold.
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Affiliation(s)
- Zohreh Pourhassan N.
- Heinrich-Heine-Universität Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Institute of Biochemistry GERMANY
| | - Haiyang Cui
- RWTH Aachen: Rheinisch-Westfalische Technische Hochschule Aachen Institute of Biotechnology GERMANY
| | - Sakshi Khosa
- Heinrich Heine University Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Institute of Biochemistry GERMANY
| | - Mehdi D. Davari
- Leibniz Institute of Plant Biochemistry: Leibniz-Institut fur Pflanzenbiochemie Department of Bioorganic Chemistry GERMANY
| | - Karl-Erich Jaeger
- Forschungszentrum Julich ICG: Forschungszentrum Julich GmbH Institute of Molecular Enzyme Technology GERMANY
| | - Sander H. J. Smits
- Heinrich-Heine-Universität Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Institute of Biochemistry GERMANY
| | - Ulrich Schwaneberg
- RWTH Aachen: Rheinisch-Westfalische Technische Hochschule Aachen Institute of Biotechnology GERMANY
| | - Lutz Schmitt
- Heinrich-Heine-Universität Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Institute of Biochemistry Universitätsstr. 1 40225 Düsseldorf GERMANY
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Rivera-de-Torre E, Rimbault C, Jenkins TP, Sørensen CV, Damsbo A, Saez NJ, Duhoo Y, Hackney CM, Ellgaard L, Laustsen AH. Strategies for Heterologous Expression, Synthesis, and Purification of Animal Venom Toxins. Front Bioeng Biotechnol 2022; 9:811905. [PMID: 35127675 PMCID: PMC8811309 DOI: 10.3389/fbioe.2021.811905] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Animal venoms are complex mixtures containing peptides and proteins known as toxins, which are responsible for the deleterious effect of envenomations. Across the animal Kingdom, toxin diversity is enormous, and the ability to understand the biochemical mechanisms governing toxicity is not only relevant for the development of better envenomation therapies, but also for exploiting toxin bioactivities for therapeutic or biotechnological purposes. Most of toxinology research has relied on obtaining the toxins from crude venoms; however, some toxins are difficult to obtain because the venomous animal is endangered, does not thrive in captivity, produces only a small amount of venom, is difficult to milk, or only produces low amounts of the toxin of interest. Heterologous expression of toxins enables the production of sufficient amounts to unlock the biotechnological potential of these bioactive proteins. Moreover, heterologous expression ensures homogeneity, avoids cross-contamination with other venom components, and circumvents the use of crude venom. Heterologous expression is also not only restricted to natural toxins, but allows for the design of toxins with special properties or can take advantage of the increasing amount of transcriptomics and genomics data, enabling the expression of dormant toxin genes. The main challenge when producing toxins is obtaining properly folded proteins with a correct disulfide pattern that ensures the activity of the toxin of interest. This review presents the strategies that can be used to express toxins in bacteria, yeast, insect cells, or mammalian cells, as well as synthetic approaches that do not involve cells, such as cell-free biosynthesis and peptide synthesis. This is accompanied by an overview of the main advantages and drawbacks of these different systems for producing toxins, as well as a discussion of the biosafety considerations that need to be made when working with highly bioactive proteins.
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Affiliation(s)
- Esperanza Rivera-de-Torre
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Esperanza Rivera-de-Torre, ; Andreas H. Laustsen,
| | - Charlotte Rimbault
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christoffer V. Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Damsbo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Natalie J. Saez
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Yoan Duhoo
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Celeste Menuet Hackney
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Lars Ellgaard
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Esperanza Rivera-de-Torre, ; Andreas H. Laustsen,
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Peng C, Guo Y, Ren S, Li C, Liu F, Lu F. SPSED: A Signal Peptide Secretion Efficiency Database. Front Bioeng Biotechnol 2022; 9:819789. [PMID: 35118058 PMCID: PMC8804277 DOI: 10.3389/fbioe.2021.819789] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Chong Peng
- Key Laboratory of Industrial Fermentation Microbiology, Education Ministry of China, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes (NELIE), Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yixue Guo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shaodong Ren
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Cen Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Education Ministry of China, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes (NELIE), Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Fufeng Liu, ; Fuping Lu,
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Education Ministry of China, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes (NELIE), Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Fufeng Liu, ; Fuping Lu,
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Chen B, Loo BZL, Cheng YY, Song P, Fan H, Latypov O, Kittelmann S. Genome-wide high-throughput signal peptide screening via plasmid pUC256E improves protease secretion in Lactiplantibacillus plantarum and Pediococcus acidilactici. BMC Genomics 2022; 23:48. [PMID: 35021997 PMCID: PMC8756648 DOI: 10.1186/s12864-022-08292-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/03/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Proteases catalyze the hydrolysis of peptide bonds of proteins, thereby improving dietary protein digestibility, nutrient availability, as well as flavor and texture of fermented food and feed products. The lactobacilli Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) and Pediococcus acidilactici are widely used in food and feed fermentations due to their broad metabolic capabilities and safe use. However, extracellular protease activity in these two species is low. Here, we optimized protease expression and secretion in L. plantarum and P. acidilactici via a genetic engineering strategy. RESULTS To this end, we first developed a versatile and stable plasmid, pUC256E, which can propagate in both L. plantarum and P. acidilactici. We then confirmed expression and secretion of protease PepG1 as a functional enzyme in both strains with the aid of the previously described L. plantarum-derived signal peptide LP_0373. To further increase secretion of PepG1, we carried out a genome-wide experimental screening of signal peptide functionality. A total of 155 predicted signal peptides originating from L. plantarum and 110 predicted signal peptides from P. acidilactici were expressed and screened for extracellular proteolytic activity in the two different strains, respectively. We identified 12 L. plantarum signal peptides and eight P. acidilactici signal peptides that resulted in improved yield of secreted PepG1. No significant correlation was found between signal peptide sequence properties and its performance with PepG1. CONCLUSION The vector developed here provides a powerful tool for rapid experimental screening of signal peptides in both L. plantarum and P. acidilactici. Moreover, the set of novel signal peptides identified was widely distributed across strains of the same species and even across some closely related species. This indicates their potential applicability also for the secretion of other proteins of interest in other L. plantarum or P. acidilactici host strains. Our findings demonstrate that screening a library of homologous signal peptides is an attractive strategy to identify the optimal signal peptide for the target protein, resulting in improved protein export.
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Affiliation(s)
- Binbin Chen
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan Zong Lin Loo
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Ying Ying Cheng
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Peng Song
- Wilmar International Limited, Wilmar (Shanghai) Biotechnology Research and Development Center Co. Ltd., Shanghai, China
| | - Huan Fan
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
- Present Address: Huan Fan, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People's Republic of China
| | - Oleg Latypov
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.
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66
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Jin Q, Pan F, Hu CF, Lee SY, Xia XX, Qian ZG. Secretory production of spider silk proteins in metabolically engineered Corynebacterium glutamicum for spinning into tough fibers. Metab Eng 2022; 70:102-114. [DOI: 10.1016/j.ymben.2022.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/06/2022] [Accepted: 01/17/2022] [Indexed: 12/19/2022]
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Balandin T, Volkov D, Alekseev A, Kovalev K, Bratanov D, Gordeliy V. E. coli Expression and Purification of Microbial and Viral Rhodopsins. Methods Mol Biol 2022; 2501:109-124. [PMID: 35857225 DOI: 10.1007/978-1-0716-2329-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microbial rhodopsins have become an indispensable tool for neurobiology. Of thousands of identified microbial rhodopsins, a minute fraction has been studied so far and they have shown remarkable functional diversity suggesting more great promises that this large family holds. Effective production of recombinant microbial and viral rhodopsins is a prerequisite for the success of functional and structural studies of these proteins. Escherichia coli (E. coli) are suitable for high yield expression of many of microbial and viral rhodopsins and they facilitate rapid exploration of this large protein family.
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Affiliation(s)
- Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Dmytro Volkov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Kirill Kovalev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Dmitry Bratanov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
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Abstract
Biochemical analysis is crucial for determining protein functionality changes during various conditions, including oxidative stress conditions. In this chapter, after giving brief guidelines for experimental design, we provide step-by-step instructions to purify recombinant plant proteins from E. coli, to prepare reduced and oxidized proteins for activity assay, and to characterize the protein under reducing and oxidizing conditions, with a focus on thiol-based oxidative modifications, like S-sulfenylation and disulfide formations.
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Affiliation(s)
- Zeya Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
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69
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Kupriyanova EV, Sinetova MA, Leusenko AV, Voronkov AS, Los DA. A leader peptide of the extracellular cyanobacterial carbonic anhydrase ensures the efficient secretion of recombinant proteins in Escherichia coli. J Biotechnol 2021; 344:11-23. [PMID: 34921977 DOI: 10.1016/j.jbiotec.2021.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022]
Abstract
Several forms of EcaA protein, correspondent to the extracellular α-class carbonic anhydrase (CA) of cyanobacterium Crocosphaera subtropica ATCC 51142 were expressed in Escherichia coli. The recombinant proteins with no leader peptide (EcaA and its fusion with thioredoxin or glutathione S-transferase) were allocated inside cells in a full-length form; these cells did not display any extracellular CA activity. Soluble proteins (including that of periplasmic space) of E. coli cells that expressed both ЕсаА equipped with its native leader peptide (L-EcaA) as well as L-EcaA fused with thioredoxin or glutathione S-transferase at N-terminus, mainly contained the processed EcaA. The appearance of mature ЕсаА in outer layers of E. coli cells expressed leader peptide-containing forms of recombinant proteins, has been directly confirmed by immunofluorescent microscopy. Those cells also displayed high extracellular CA activity. In addition, the mature EcaA protein was detected in the culture medium. This suggests that cyanobacterial signal peptide is recognized by the secretory machinery and by the leader peptidase of E. coli even as a part of a fusion protein. The efficiency of EcaA leader peptide was comparable to that of PelB and TorA signal peptides, commonly used for biotechnological production of extracellular recombinant proteins in E. coli.
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Affiliation(s)
- Elena V Kupriyanova
- К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia.
| | - Maria A Sinetova
- К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | - Anna V Leusenko
- К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | - Alexander S Voronkov
- К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | - Dmitry A Los
- К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
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Kang SY, Pokhrel A, Bratsch S, Benson JJ, Seo SO, Quin MB, Aksan A, Schmidt-Dannert C. Engineering Bacillus subtilis for the formation of a durable living biocomposite material. Nat Commun 2021; 12:7133. [PMID: 34880257 PMCID: PMC8654922 DOI: 10.1038/s41467-021-27467-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/17/2021] [Indexed: 01/23/2023] Open
Abstract
Engineered living materials (ELMs) are a fast-growing area of research that combine approaches in synthetic biology and material science. Here, we engineer B. subtilis to become a living component of a silica material composed of self-assembling protein scaffolds for functionalization and cross-linking of cells. B. subtilis is engineered to display SpyTags on polar flagella for cell attachment to SpyCatcher modified secreted scaffolds. We engineer endospore limited B. subtilis cells to become a structural component of the material with spores for long-term storage of genetic programming. Silica biomineralization peptides are screened and scaffolds designed for silica polymerization to fabricate biocomposite materials with enhanced mechanical properties. We show that the resulting ELM can be regenerated from a piece of cell containing silica material and that new functions can be incorporated by co-cultivation of engineered B. subtilis strains. We believe that this work will serve as a framework for the future design of resilient ELMs.
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Affiliation(s)
- Sun-Young Kang
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Anaya Pokhrel
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Sara Bratsch
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Joey J. Benson
- grid.17635.360000000419368657Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Seung-Oh Seo
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Maureen B. Quin
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Alptekin Aksan
- grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA ,grid.17635.360000000419368657Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN, 55455, USA. .,BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.
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Zhu W, Hu L, Wang Y, Lv L, Wang H, Shi W, Zhu J, Lu H. A hemolysin secretion pathway-based novel secretory expression platform for efficient manufacturing of tag peptides and anti-microbial peptides in Escherichia coli. BIORESOUR BIOPROCESS 2021; 8:115. [PMID: 38650268 PMCID: PMC10992379 DOI: 10.1186/s40643-021-00471-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/19/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Although Escherichia coli has been widely used for the expression of exogenous proteins, the secretory expression in this system is still a big obstacle. As one of the most important secretion pathways, hemolysin A (HlyA) system of E. coli can transport substrates directly from the cytoplasm to extracellular medium without the formation of any periplasmic intermediate, making it an ideal candidate for the development of the secretory production platform for exogenous proteins. RESULTS In this work, we developed a novel production platform, THHly, based on the HlyA secretion system, and explored its applications in the efficient preparation and quick detection of tag peptides and anti-microbial peptides. In this novel platform the signal sequence of HlyA is fused to the C-terminal of target peptide, with Tobacco Etch Virus (TEV) protease cleavage site and 6*His tag between them. Five tag peptides displayed good secretory properties in E. coli BL21 (DE3), among which T7 tag and S tag were obtained by two rounds of purification steps and TEV cleavage, and maintained their intrinsic immunogenicity. Furthermore, Cecropin A and Melittin, two different types of widely explored anti-microbial peptides, were produced likewise and verified to possess anti-microbial/anti-tumor bioactivities. No significant bacterial growth inhibition was observed during the fusion protein expression, indicating that the fusion form not only mediated the secretion but also decreased the toxicity of anti-microbial peptides (AMPs) to the host bacteria. To the best of our knowledge, this is the first report to achieve the secretory expression of these two AMPs in E. coli with considerable potential for manufacturing and industrialization purposes. CONCLUSIONS The results demonstrate that the HlyA based novel production platform of E. coli allowed the efficient secretory production and purification of peptides, thus suggesting a promising strategy for the industrialized production of peptide pharmaceuticals or reagents.
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Affiliation(s)
- Wen Zhu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Lifu Hu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yang Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Liangyin Lv
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hui Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Wenqiang Shi
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jianwei Zhu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Huili Lu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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Wang ZK, Gong JS, Qin J, Li H, Lu ZM, Shi JS, Xu ZH. Improving the Intensity of Integrated Expression for Microbial Production. ACS Synth Biol 2021; 10:2796-2807. [PMID: 34738786 DOI: 10.1021/acssynbio.1c00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chromosomal integration of exogenous genes is preferred for industrially related fermentation, as plasmid-mediated fermentation leads to extra metabolic burden and genetic instability. Moreover, with the development and advancement of genome engineering and gene editing technologies, inserting genes into chromosomes has become more convenient; integration expression is extensively utilized in microorganisms for industrial bioproduction and expected to become the trend of recombinant protein expression. However, in actual research and application, it is important to enhance the expression of heterologous genes at the host genome level. Herein, we summarized the basic principles and characteristics of genomic integration; furthermore, we highlighted strategies to improve the expression of chromosomal integration of genes and pathways in host strains from three aspects, including chassis cell optimization, regulation of expression elements in gene expression cassettes, optimization of gene dose level and integration sites on chromosomes. Moreover, we reviewed and summarized the relevant studies on the application of integrated expression in the exploration of gene function and the various types of industrial microorganism production. Consequently, this review would serve as a reference for the better application of integrated expression.
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Affiliation(s)
- Zi-Kai Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Jiufu Qin
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Hui Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Zhen-Ming Lu
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, PR China
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Pourhassan N Z, Smits SHJ, Ahn JH, Schmitt L. Biotechnological applications of type 1 secretion systems. Biotechnol Adv 2021; 53:107864. [PMID: 34767962 DOI: 10.1016/j.biotechadv.2021.107864] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 02/06/2023]
Abstract
Bacteria have evolved a diverse range of secretion systems to export different substrates across their cell envelope. Although secretion of proteins into the extracellular space could offer advantages for recombinant protein production, the low secretion titers of the secretion systems for some heterologous proteins remain a clear drawback of their utility at commercial scales. Therefore, a potential use of most of secretion systems as production platforms at large scales are still limited. To overcome this limitation, remarkable efforts have been made toward improving the secretion efficiency of different bacterial secretion systems in recent years. Here, we review the progress with respect to biotechnological applications of type I secretion system (T1SS) of Gram-negative bacteria. We will also focus on the applicability of T1SS for the secretion of heterologous proteins as well as vaccine development. Last but not least, we explore the employed engineering strategies that have enhanced the secretion efficiencies of T1SS. Attention is also paid to directed evolution approaches that may offer a more versatile approach to optimize secretion efficiency of T1SS.
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Affiliation(s)
- Zohreh Pourhassan N
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Jung Hoon Ahn
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, South Korea
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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Bakkes PJ, Lenz P, Müller C, Bida A, Dohmen-Olma D, Knapp A, Oldiges M, Jaeger KE, Freudl R. Biosensor-Based Optimization of Cutinase Secretion by Corynebacterium glutamicum. Front Microbiol 2021; 12:750150. [PMID: 34777299 PMCID: PMC8581548 DOI: 10.3389/fmicb.2021.750150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
The industrial microbe Corynebacterium glutamicum is gaining substantial importance as a platform host for recombinant protein secretion. We recently developed a fluorescence-based (eYFP) C. glutamicum reporter strain for the quantification of Sec-dependent protein secretion by monitoring the secretion-related stress response and now demonstrate its applicability in optimizing the secretion of the heterologous enzyme cutinase from Fusarium solani pisi. To drive secretion, either the poor-performing PelSP or the potent NprESP Sec signal peptide from Bacillus subtilis was used. To enable easy detection and quantification of the secreted cutinase we implemented the split green fluorescent protein (GFP) assay, which relies on the GFP11-tag fused to the C-terminus of the cutinase, which can complement a truncated GFP thereby reconstituting its fluorescence. The reporter strain was transformed with different mutant libraries created by error-prone PCR, which covered the region of the signal peptide and the N-terminus of the cutinase. Fluorescence-activated cell sorting (FACS) was performed to isolate cells that show increased fluorescence in response to increased protein secretion stress. Five PelSP variants were identified that showed a 4- to 6-fold increase in the amount and activity of the secreted cutinase (up to 4,100 U/L), whereas two improved NprESP variants were identified that showed a ∼35% increase in secretion, achieving ∼5,500 U/L. Most of the isolated variants carried mutations in the h-region of the signal peptide that increased its overall hydrophobicity. Using site-directed mutagenesis it was shown that the combined mutations F11I and P16S within the hydrophobic core of the PelSP are sufficient to boost cutinase secretion in batch cultivations to the same level as achieved by the NprESP. Screening of a PelSP mutant library in addition resulted in the identification of a cutinase variant with an increased specific activity, which was attributed to the mutation A85V located within the substrate-binding region. Taken together the biosensor-based optimization approach resulted in a substantial improvement of cutinase secretion by C. glutamicum, and therefore represents a valuable tool that can be applied to any secretory protein of interest.
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Affiliation(s)
- Patrick J. Bakkes
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Patrick Lenz
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Carolin Müller
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Astrid Bida
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Doris Dohmen-Olma
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Roland Freudl
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
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Budowa i znaczenie II systemu sekrecji białek w ekologii i patogenezie Legionella pneumophila. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Pałeczki Legionella pneumophila pasożytują w komórkach odległych filogenetycznie gospodarzy, w środowisku wodnym w pierwotniakach, a w organizmie człowieka w makrofagach alweolarnych. Zdolność tych bakterii do wewnątrzkomórkowego namnażania się w komórkach fagocytujących, wyspecjalizowanych do niszczenia mikroorganizmów, ma podstawowe znaczenie dla rozwoju nietypowego zapalenia płuc zwanego chorobą legionistów. Umiejscowione na kilku różnych loci chromosomu bakteryjnego geny II systemu sekrecji L. pneumophila kodują co najmniej 25 białek, w tym enzymy o aktywności lipolitycznej, proteolitycznej, rybonukleazy oraz białka unikalne bakterii Legionella. W środowisku naturalnym T2SS L. pneumophila odgrywa decydującą rolę w ekologii tych drobnoustrojów determinując ich zdolność do przeżycia zarówno w postaci planktonicznej, jak i w strukturach biofilmu w słodkowodnych zbiornikach o niskiej temperaturze. Białka T2SS umożliwiają L. pneumophila zakażenie różnych gatunków pierwotniaków, a substraty tego systemu określają zakres pierwotniaczego gospodarza. Namnażanie się bakterii w różnorodnych pierwotniakach przyczynia się do ich rozsiewania oraz transmisji do antropogenicznych źródeł. Białka wydzielane za pomocą II systemu sekrecji determinują również zdolność L. pneumophila do zakażania mysich makrofagów alweolarnych i szpiku kostnego, ludzkich makrofagów linii U937 i THP-1 oraz komórek nabłonkowych pęcherzyków płucnych. Enzymy wydzielane za pomocą tego systemu, takie jak: proteazy, aminopeptydazy czy fosfolipazy umożliwiają pozyskanie substancji pokarmowych oraz powodują destrukcję tkanki płucnej myszy. W organizmie człowieka białka T2SS przyczyniają się do osłabienia wrodzonej odpowiedzi immunologicznej na zakażenie L. pneumophila przez hamowanie indukcji prozapalnych cytokin (IL-6, TNF-α, IL-1 oraz IL-8).
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Vakili O, Khatami SH, Maleksabet A, Movahedpour A, Fana SE, Sadegh R, Salmanzadeh AH, Razeghifam H, Nourdideh S, Tehrani SS, Taheri-Anganeh M. Finding Appropriate Signal Peptides for Secretory Production of Recombinant Glucarpidase: An In SilicoMethod. Recent Pat Biotechnol 2021; 15:302-315. [PMID: 34547999 DOI: 10.2174/1872208315666210921095420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/16/2021] [Accepted: 08/02/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Methotrexate (MTX) is a general chemotherapeutic agent utilized to treat a variety of malignancies, woefully, its high doses can cause nephrotoxicity and subsequent defect in the process of MTX excretion. The recombinant form of glucarpidase is produced by engineered E. coli and is a confirmed choice to overcoming this problem. OBJECTIVE In the present study, in silico analyses were performed to select suitable SPs for the secretion of recombinant glucarpidase in E. coli. METHODS The signal peptide website and UniProt database were employed to collect the SPs and protein sequences. In the next step, SignalP-5.0 helped us to predict the SPs and the position of cleavage sites. Moreover, physicochemical properties and solubility were evaluated using Prot- Param and Protein-sol online software, and finally, ProtCompB was used to predict the final subcellular localization. RESULTS Luckily, all SPs could form soluble fusion proteins. At last, it was found that PPB and TIBA could translocate the glucarpidase into the extracellular compartment. CONCLUSION This study showed that there are only 2 applicable SPs for the extracellular translocation of glucarpidase. Although the findings were remarkable with high degrees of accuracy and precision based on the utilization of bioinformatics analyses, additional experimental assessments are required to confirm and validate it. Recent patents revealed several inventions related to the clinical aspects of vaccine peptides against human disorders.
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Affiliation(s)
- Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Amir Maleksabet
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Ebrahimi Fana
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | | | - Sadra Samavarchi Tehrani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mortaza Taheri-Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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Chen H, Chen Z, Bai N, Yan R, Xu M, Wu W, Liang W, Li H, Mao Y. Construction of a eukaryotic expression system with stable and secretory expression of mycobacterium tuberculosis 38 kDa protein. World J Microbiol Biotechnol 2021; 37:175. [PMID: 34519879 DOI: 10.1007/s11274-021-03143-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/24/2021] [Indexed: 11/26/2022]
Abstract
The 38 kDa protein is a major antigen of mycobacterium tuberculosis and has been widely used in TB serodiagnosis, due to its highly sensitivity and specificity. Here we attempt to establish a production platform of recombinant 38 kDa protein in mammalian cells and to evaluate the potential value of 38 kDa protein in TB serodiagnosis. The 38 kDa gene is synthesized and cloned into a lentiviral expressing vector. Recombinant lentiviral vector LV-CMV-38 kDa-eGFP was packaged, titered, and then transduced into HEK 293 T cells. Recombinant cell lines were selected by limiting dilution. Supernatants were collected and purified by HisTrapTM HP column. Western blot showed a molecular weight of approximate 38 kDa in cell supernatants as expected. ELISA assay confirmed the immunological specificity of the obtained protein in the presence of MTB-infected human serum samples. In all, we have obtained a stable cell line with long-term and robust expression of secretory MTB 38 kDa protein, which may provide a promising candidate antigen for the development of TB serological diagnosis.
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Affiliation(s)
- Huiying Chen
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, China
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen Univsity, Guangzhou, 510000, China
| | - Zedian Chen
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, China
| | - Na Bai
- Department of Nuclear Medicine, Yuxi People's Hospital of Yunnan Province, Yuxi, 653100, China
| | - Renhe Yan
- Guangzhou Bioneeds Biotechnology CO., LTD, Guangzhou, 510000, China
| | - Mingyu Xu
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, China
| | - Wangsheng Wu
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, China
- Animal Science and Technology College, Jilin Agricultural University, Changchun, 130118, China
| | - Wenhan Liang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, China
| | - Hongwei Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, China.
| | - Yingying Mao
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, China.
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Lenz P, Hilgers F, Burmeister A, Zimmermann L, Volkenborn K, Grünberger A, Kohlheyer D, Drepper T, Jaeger KE, Knapp A. The iSplit GFP assay detects intracellular recombinant proteins in Bacillus subtilis. Microb Cell Fact 2021; 20:174. [PMID: 34488765 PMCID: PMC8419962 DOI: 10.1186/s12934-021-01663-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/19/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Bacillus subtilis is one of the most important microorganisms for recombinant protein production. It possesses the GRAS (generally recognized as safe) status and a potent protein secretion capacity. Secretory protein production greatly facilitates downstream processing and thus significantly reduces costs. However, not all heterologous proteins are secreted and intracellular production poses difficulties for quantification. To tackle this problem, we have established a so-called intracellular split GFP (iSplit GFP) assay in B. subtilis as a tool for the in vivo protein detection during expression in batch cultures and at a single-cell level. For the iSplit GFP assay, the eleventh β-sheet of sfGFP is fused to a target protein and can complement a detector protein consisting of the respective truncated sfGFP (GFP1-10) to form fluorescent holo-GFP. RESULTS As proof of concept, the GFP11-tag was fused C-terminally to the E. coli β-glucuronidase GUS, resulting in fusion protein GUS11. Variable GUS and GUS11 production levels in B. subtilis were achieved by varying the ribosome binding site via spacers of increasing lengths (4-12 nucleotides) for the GUS-encoding gene. Differences in intracellular enzyme accumulation were determined by measuring the GUS11 enzymatic activity and subsequently by adding the detector protein to respective cell extracts. Moreover, the detector protein was co-produced with the GUS11 using a two-plasmid system, which enabled the in vivo detection and online monitoring of glucuronidase production. Using this system in combination with flow cytometry and microfluidics, we were able to monitor protein production at a single-cell level thus yielding information about intracellular protein distribution and culture heterogeneity. CONCLUSION Our results demonstrate that the iSplit GFP assay is suitable for the detection, quantification and online monitoring of recombinant protein production in B. subtilis during cultivation as well as for analyzing production heterogeneity and intracellular localization at a single-cell level.
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Affiliation(s)
- Patrick Lenz
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Alina Burmeister
- Institute of Bio- and Geoscience, IBG-1: Biotechnology: Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Multiscale Bioengineering, Bielefeld University, 33615, Bielefeld, Germany
| | - Leonie Zimmermann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Kristina Volkenborn
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geoscience, IBG-1: Biotechnology: Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Multiscale Bioengineering, Bielefeld University, 33615, Bielefeld, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geoscience, IBG-1: Biotechnology: Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- RWTH Aachen University, Microscale Bioengineering (AVT.MSB), 52074, Aachen, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
- Institute of Bio- and Geoscience, IBG-1: Biotechnology: Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany.
- Castrol Germany GmbH, 41179, Mönchengladbach, Germany.
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Elemosho R, Suwanto A, Thenawidjaja M. Extracellular expression in Bacillus subtilis of a thermostable Geobacillus stearothermophilus lipase. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Kavousipour S, Mohammadi S, Eftekhar E, Barazesh M, Morowvat MH. In Silico Investigation of Signal Peptide Sequences to Enhance Secretion of CD44 Nanobodies Expressed in Escherichia coli. Curr Pharm Biotechnol 2021; 22:1192-1205. [PMID: 33045964 DOI: 10.2174/1389201021666201012162904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/01/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The selection of a suitable signal peptide that can direct recombinant proteins from the cytoplasm to the extracellular space is an important criterion affecting the production of recombinant proteins in Escherichia coli, a widely used host. Nanobodies are currently attracting the attention of scientists as antibody alternatives due to their specific properties and feasibility of production in E. coli. OBJECTIVE CD44 nanobodies constitute a potent therapeutic agent that can block CD44/HA interaction in cancer and inflammatory diseases. This molecule may also function as a drug against cancer cells and has been produced previously in E. coli without a signal peptide sequence. The goal of this project was to find a suitable signal peptide to direct CD44 nanobody extracellular secretion in E. coli that will potentially lead to optimization of experimental methods and facilitate downstream steps such as purification. METHODS We analyzed 40 E. coli derived signal peptides retrieved from the Signal Peptide database and selected the best candidate signal peptides according to relevant criteria including signal peptide probability, stability, and physicochemical features, which were evaluated using signalP software version 4.1 and the ProtParam tool, respectively. RESULTS In this in silico study, suitable candidate signal peptide(s) for CD44 nanobody secretory expression were identified. CSGA, TRBC, YTFQ, NIKA, and DGAL were selected as appropriate signal peptides with acceptable D-scores, and appropriate physicochemical and structural properties. Following further analysis, TRBC was selected as the best signal peptide to direct CD44 nanobody expression to the extracellular space of E. coli. CONCLUSION The selected signal peptide, TRBC is the most suitable to promote high-level secretory production of CD44 nanobodies in E. coli and potentially will be useful for scaling up CD44 nanobody production in experimental research as well as in other CD44 nanobody applications. However, experimental work is needed to confirm the data.
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Affiliation(s)
- Soudabeh Kavousipour
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Shiva Mohammadi
- Department of Biotechnology, School of Advanced Medical Science and Technologies, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ebrahim Eftekhar
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mahdi Barazesh
- School of Paramedical, Gerash University of Medical Sciences, Gerash, Iran
| | - Mohammad H Morowvat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran P.O. Box 71468-64685, Shiraz, Iran
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The "beauty in the beast"-the multiple uses of Priestia megaterium in biotechnology. Appl Microbiol Biotechnol 2021; 105:5719-5737. [PMID: 34263356 PMCID: PMC8390425 DOI: 10.1007/s00253-021-11424-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 01/05/2023]
Abstract
Abstract Over 30 years, the Gram-positive bacterium Priestia megaterium (previously known as Bacillus megaterium) was systematically developed for biotechnological applications ranging from the production of small molecules like vitamin B12, over polymers like polyhydroxybutyrate (PHB) up to the in vivo and in vitro synthesis of multiple proteins and finally whole-cell applications. Here we describe the use of the natural vitamin B12 (cobalamin) producer P. megaterium for the elucidation of the biosynthetic pathway and the subsequent systematic knowledge-based development for production purposes. The formation of PHB, a natural product of P. megaterium and potential petro-plastic substitute, is covered and discussed. Further important biotechnological characteristics of P. megaterium for recombinant protein production including high protein secretion capacity and simple cultivation on value-added carbon sources are outlined. This includes the advanced system with almost 30 commercially available expression vectors for the intracellular and extracellular production of recombinant proteins at the g/L scale. We also revealed a novel P. megaterium transcription-translation system as a complementary and versatile biotechnological tool kit. As an impressive biotechnology application, the formation of various cytochrome P450 is also critically highlighted. Finally, whole cellular applications in plant protection are completing the overall picture of P. megaterium as a versatile giant cell factory. Key points • The use of Priestia megaterium for the biosynthesis of small molecules and recombinant proteins through to whole-cell applications is reviewed. • P. megaterium can act as a promising alternative host in biotechnological production processes.
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Marasinghe SD, Jo E, Hettiarachchi SA, Lee Y, Eom TY, Gang Y, Kang YH, Oh C. Characterization of glycoside hydrolase family 11 xylanase from Streptomyces sp. strain J103; its synergetic effect with acetyl xylan esterase and enhancement of enzymatic hydrolysis of lignocellulosic biomass. Microb Cell Fact 2021; 20:129. [PMID: 34238305 PMCID: PMC8265113 DOI: 10.1186/s12934-021-01619-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/25/2021] [Indexed: 11/18/2022] Open
Abstract
Background Xylanase-containing enzyme cocktails are used on an industrial scale to convert xylan into value-added products, as they hydrolyse the β-1,4-glycosidic linkages between xylopyranosyl residues. In the present study, we focused on xynS1, the glycoside hydrolase (GH) 11 xylanase gene derived from the Streptomyces sp. strain J103, which can mediate XynS1 protein synthesis and lignocellulosic material hydrolysis. Results xynS1 has an open reading frame with 693 base pairs that encodes a protein with 230 amino acids. The predicted molecular weight and isoelectric point of the protein were 24.47 kDa and 7.92, respectively. The gene was cloned into the pET-11a expression vector and expressed in Escherichia coli BL21(DE3). Recombinant XynS1 (rXynS1) was purified via His-tag affinity column chromatography. rXynS1 exhibited optimal activity at a pH of 5.0 and temperature of 55 °C. Thermal stability was in the temperature range of 50–55 °C. The estimated Km and Vmax values were 51.4 mg/mL and 898.2 U/mg, respectively. One millimolar of Mn2+ and Na+ ions stimulated the activity of rXynS1 by up to 209% and 122.4%, respectively, and 1 mM Co2+ and Ni2+ acted as inhibitors of the enzyme. The mixture of rXynS1, originates from Streptomyces sp. strain J103 and acetyl xylan esterase (AXE), originating from the marine bacterium Ochrovirga pacifica, enhanced the xylan degradation by 2.27-fold, compared to the activity of rXynS1 alone when Mn2+ was used in the reaction mixture; this reflected the ability of both enzymes to hydrolyse the xylan structure. The use of an enzyme cocktail of rXynS1, AXE, and commercial cellulase (Celluclast® 1.5 L) for the hydrolysis of lignocellulosic biomass was more effective than that of commercial cellulase alone, thereby increasing the relative activity 2.3 fold. Conclusion The supplementation of rXynS1 with AXE enhanced the xylan degradation process via the de-esterification of acetyl groups in the xylan structure. Synergetic action of rXynS1 with commercial cellulase improved the hydrolysis of pre-treated lignocellulosic biomass; thus, rXynS1 could potentially be used in several industrial applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01619-x.
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Affiliation(s)
- Svini Dileepa Marasinghe
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Eunyoung Jo
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Sachithra Amarin Hettiarachchi
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.,Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences and Technology, University of Ruhuna, Matara, Sri Lanka
| | - Youngdeuk Lee
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Tae-Yang Eom
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yehui Gang
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yoon-Hyeok Kang
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chulhong Oh
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea. .,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.
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83
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Bhandari BK, Lim CS, Gardner PP. TISIGNER.com: web services for improving recombinant protein production. Nucleic Acids Res 2021; 49:W654-W661. [PMID: 33744969 PMCID: PMC8265118 DOI: 10.1093/nar/gkab175] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/17/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022] Open
Abstract
Experiments that are planned using accurate prediction algorithms will mitigate failures in recombinant protein production. We have developed TISIGNER (https://tisigner.com) with the aim of addressing technical challenges to recombinant protein production. We offer three web services, TIsigner (Translation Initiation coding region designer), SoDoPE (Soluble Domain for Protein Expression) and Razor, which are specialised in synonymous optimisation of recombinant protein expression, solubility and signal peptide analysis, respectively. Importantly, TIsigner, SoDoPE and Razor are linked, which allows users to switch between the tools when optimising genes of interest.
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Affiliation(s)
- Bikash K Bhandari
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Paul P Gardner
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
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84
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Liu X, Meng L, Wang X, Yang Y, Zhonghu BAI. Effect of Clp protease from Corynebacterium glutamicum on heterologous protein expression. Protein Expr Purif 2021; 189:105928. [PMID: 34217803 DOI: 10.1016/j.pep.2021.105928] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/25/2022]
Abstract
The protease present in a host may reduce the yield and biological activity of heterologous proteins. In this study, we used protease overexpression and deletion strategies to examine the effect of the Clp protease system in Corynebacterium glutamicum on the recombinant protein and to produce a highly efficient heterologous protein expression host. In this study, we identified seven genes in the Clp protease family in Corynebacterium glutamicum ATCC 13032 through bioinformatics analysis, and studied their effects on the enhanced green fluorescent protein (EGFP) reporter protein. The fluorescence intensity of the knockout strain was significantly higher, and the effect of the clpS deletion strain was the most obvious. To verify the universal effect of the lack of clpS, the excellent industrial strain C. glutamicum 1.15647 was transformed to form recombinant 15647-ΔclpS. Based on the results, 15647-ΔclpS had a more significant effect on improving protein expression. Furthermore, recombinant human teriparatide (rhPTH) and variable domain of heavy chain of heavy-chain antibody (VHH) were selected to verify the universal applicability of the knockout strain for expressing heterologous proteins. Accordingly, we found that protease deficiency could increase the production of heterologous proteins. Finally, through a large-scale fermentation, the 15647-ΔclpS strain was used to produce VHH. Its yield was approximately 530 mg/L, which was 65% higher than that of WT-15647. In this study, a host that could effectively increase heterologous protein expression was successfully obtained.
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Affiliation(s)
- Xiuxia Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
| | - Lihong Meng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Xinyue Wang
- National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Yankun Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - B A I Zhonghu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
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85
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Slater SL, Mavridou DAI. Harnessing the potential of bacterial oxidative folding to aid protein production. Mol Microbiol 2021; 116:16-28. [PMID: 33576091 DOI: 10.1111/mmi.14700] [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: 12/18/2020] [Revised: 02/09/2021] [Indexed: 11/30/2022]
Abstract
Protein folding is central to both biological function and recombinant protein production. In bacterial expression systems, which are easy to use and offer high protein yields, production of the protein of interest in its native fold can be hampered by the limitations of endogenous posttranslational modification systems. Disulfide bond formation, entailing the covalent linkage of proximal cysteine amino acids, is a fundamental posttranslational modification reaction that often underpins protein stability, especially in extracytoplasmic environments. When these bonds are not formed correctly, the yield and activity of the resultant protein are dramatically decreased. Although the mechanism of oxidative protein folding is well understood, unwanted or incorrect disulfide bond formation often presents a stumbling block for the expression of cysteine-containing proteins in bacteria. It is therefore important to consider the biochemistry of prokaryotic disulfide bond formation systems in the context of protein production, in order to take advantage of the full potential of such pathways in biotechnology applications. Here, we provide a critical overview of the use of bacterial oxidative folding in protein production so far, and propose a practical decision-making workflow for exploiting disulfide bond formation for the expression of any given protein of interest.
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Affiliation(s)
- Sabrina L Slater
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX, USA
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86
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Kubiak AM, Bailey TS, Dubois LJ, Theys J, Lambin P. Efficient Secretion of Murine IL-2 From an Attenuated Strain of Clostridium sporogenes, a Novel Delivery Vehicle for Cancer Immunotherapy. Front Microbiol 2021; 12:669488. [PMID: 34168629 PMCID: PMC8217651 DOI: 10.3389/fmicb.2021.669488] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Despite a history dating back to the 1800s, using Clostridium bacteria to treat cancer has not advanced beyond the observation that they can colonise and partially destroy solid tumours. Progress has been hampered by their inability to eradicate the viable portion of tumours, and an instinctive anxiety around injecting patients with a bacterium whose close relatives cause tetanus and botulism. However, recent advances in techniques to genetically engineer Clostridium species gives cause to revisit this concept. This paper illustrates these developments through the attenuation of C. sporogenes to enhance its clinical safety, and through the expression and secretion of an immunotherapeutic. An 8.6 kb sequence, corresponding to a haemolysin operon, was deleted from the genome and replaced with a short non-coding sequence. The resultant phenotype of this strain, named C. sporogenes-NT, showed a reduction of haemolysis to levels similar to the probiotic strain, C. butyricum M588. Comparison to the parental strain showed no change in growth or sporulation. Following injection of tumour-bearing mice with purified spores of the attenuated strain, high levels of germination were detected in all tumours. Very low levels of spores and vegetative cells were detected in the spleen and lymph nodes. The new strain was transformed with four different murine IL-2-expressing plasmids, differentiated by promoter and signal peptide sequences. Biologically active mIL-2, recovered from the extracellular fraction of bacterial cultures, was shown to stimulate proliferation of T cells. With this investigation we propose a new, safer candidate for intratumoral delivery of cancer immunotherapeutics.
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Affiliation(s)
- Aleksandra M Kubiak
- The M-Lab, Department of Precision Medicine, GROW - School of Oncology, Maastricht University, Maastricht, Netherlands.,Exomnis Biotech BV, Oxfordlaan, Maastricht, Netherlands
| | - Tom S Bailey
- The M-Lab, Department of Precision Medicine, GROW - School of Oncology, Maastricht University, Maastricht, Netherlands
| | - Ludwig J Dubois
- The M-Lab, Department of Precision Medicine, GROW - School of Oncology, Maastricht University, Maastricht, Netherlands
| | - Jan Theys
- The M-Lab, Department of Precision Medicine, GROW - School of Oncology, Maastricht University, Maastricht, Netherlands
| | - Philippe Lambin
- The M-Lab, Department of Precision Medicine, GROW - School of Oncology, Maastricht University, Maastricht, Netherlands
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87
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So you want to express your protein in Escherichia coli? Essays Biochem 2021; 65:247-260. [PMID: 33955451 DOI: 10.1042/ebc20200170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/27/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Recombinant proteins have been extensively employed as therapeutics for the treatment of various critical and life-threatening diseases and as industrial enzymes in high-value industrial processes. Advances in genetic engineering and synthetic biology have broadened the horizon of heterologous protein production using multiple expression platforms. Selection of a suitable expression system depends on a variety of factors ranging from the physicochemical properties of the target protein to economic considerations. For more than 40 years, Escherichia coli has been an established organism of choice for protein production. This review aims to provide a stepwise approach for any researcher embarking on the journey of recombinant protein production in E. coli. We present an overview of the challenges associated with heterologous protein expression, fundamental considerations connected to the protein of interest (POI) and designing expression constructs, as well as insights into recently developed technologies that have contributed to this ever-growing field.
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88
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Yahaya RSR, Normi YM, Phang LY, Ahmad SA, Abdullah JO, Sabri S. Molecular strategies to increase keratinase production in heterologous expression systems for industrial applications. Appl Microbiol Biotechnol 2021; 105:3955-3969. [PMID: 33937928 DOI: 10.1007/s00253-021-11321-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/19/2022]
Abstract
Keratinase is an important enzyme that can degrade recalcitrant keratinous wastes to form beneficial recyclable keratin hydrolysates. Keratinase is not only important as an alternative to reduce environmental pollution caused by chemical treatments of keratinous wastes, but it also has industrial significance. Currently, the bioproduction of keratinase from native keratinolytic host is considered low, and this hampers large-scale usage of the enzyme. Straightforward approaches of cloning and expression of recombinant keratinases from native keratinolytic host are employed to elevate the amount of keratinase produced. However, this is still insufficient to compensate for the lack of its large-scale production to meet the industrial demands. Hence, this review aimed to highlight the various sources of keratinase and the strategies to increase its production in native keratinolytic hosts. Molecular strategies to increase the production of recombinant keratinase such as plasmid selection, promoter engineering, chromosomal integration, signal peptide and propeptide engineering, codon optimization, and glycoengineering were also described. These mentioned strategies have been utilized in heterologous expression hosts, namely, Escherichia coli, Bacillus sp., and Pichia pastoris, as they are most widely used for the heterologous propagations of keratinases to further intensify the production of recombinant keratinases adapted to better suit the large-scale demand for them. KEY POINTS: • Molecular strategies to enhance keratinase production in heterologous hosts. • Construction of a prominent keratinolytic host from a native strain. • Patent analysis of keratinase production shows rapid high interest in molecular field.
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Affiliation(s)
- Radin Shafierul Radin Yahaya
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Lai Yee Phang
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Janna Ong Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia.
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia.
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89
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Zhang K, Tan R, Yao D, Su L, Xia Y, Wu J. Enhanced Production of Soluble Pyrococcus furiosus α-Amylase in Bacillus subtilis through Chaperone Co-Expression, Heat Treatment and Fermentation Optimization. J Microbiol Biotechnol 2021; 31:570-583. [PMID: 33753701 PMCID: PMC9723276 DOI: 10.4014/jmb.2101.01039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022]
Abstract
Pyrococcus furiosus α-amylase can hydrolyze α-1,4 linkages in starch and related carbohydrates under hyperthermophilic condition (~ 100°C), showing great potential in a wide range of industrial applications, while its relatively low productivity from heterologous hosts has limited the industrial applications. Bacillus subtilis, a gram-positive bacterium, has been widely used in industrial production for its non-pathogenic and powerful secretory characteristics. This study was conducted to increase production of P. furiosus α-amylase in B. subtilis through three strategies. Initial experiments showed that co-expression of P. furiosus molecular chaperone peptidyl-prolyl cis-trans isomerase through genomic integration mode, using a CRISPR/Cas9 system, increased soluble amylase production. Therefore, considering that native P. furiosus α-amylase is produced within a hyperthermophilic environment and is highly thermostable, heat treatment of intact culture at 90°C for 15 min was performed, thereby greatly increasing soluble amylase production. After optimization of the culture conditions (nitrogen source, carbon source, metal ion, temperature and pH), experiments in a 3-L fermenter yielded a soluble activity of 3,806.7 U/ml, which was 3.3- and 28.2-fold those of a control without heat treatment (1,155.1 U/ml) and an empty expression vector control (135.1 U/ml), respectively. This represents the highest P. furiosus α-amylase production reported to date and should promote innovation in the starch liquefaction process and related industrial productions. Meanwhile, heat treatment, which may promote folding of aggregated P. furiosus α-amylase into a soluble, active form through the transfer of kinetic energy, may be of general benefit when producing proteins from thermophilic archaea.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Ruiting Tan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Dongbang Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Yongmei Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China,Corresponding author Phone: 86-510-85327802 Fax: 86-510-85326653 E-mail:
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90
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Hernández-Rollán C, Falkenberg KB, Rennig M, Bertelsen AB, Ipsen JØ, Brander S, Daley DO, Johansen KS, Nørholm MHH. LyGo: A Platform for Rapid Screening of Lytic Polysaccharide Monooxygenase Production. ACS Synth Biol 2021; 10:897-906. [PMID: 33797234 DOI: 10.1021/acssynbio.1c00034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Environmentally friendly sources of energy and chemicals are essential constituents of a sustainable society. An important step toward this goal is the utilization of biomass to supply building blocks for future biorefineries. Lytic polysaccharide monooxygenases (LPMOs) are enzymes that play a critical role in breaking the chemical bonds in the most abundant polymers found in recalcitrant biomass, such as cellulose and chitin. To use them in industrial processes they need to be produced in high titers in cell factories. Predicting optimal strategies for producing LPMOs is often nontrivial, and methods allowing for screening several strategies simultaneously are therefore needed. Here, we present a standardized platform for cloning LPMOs. The platform allows users to combine gene fragments with 14 different expression vectors in a simple 15 min reaction, thus enabling rapid exploration of several gene contexts, hosts, and expression strategies in parallel. The open-source LyGo platform is accompanied by easy-to-follow online protocols for both cloning and expression. As a demonstration of its utility, we explore different strategies for expressing several different LPMOs in Escherichia coli, Bacillus subtilis, and Komagataella phaffii.
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Affiliation(s)
- Cristina Hernández-Rollán
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Kristoffer B. Falkenberg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Maja Rennig
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
- Mycropt ApS, Kongens Lyngby, 2800, Denmark
| | - Andreas B. Bertelsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Johan Ø. Ipsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark
| | - Søren Brander
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, 1958, Denmark
| | - Daniel O. Daley
- Mycropt ApS, Kongens Lyngby, 2800, Denmark
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 10691, Sweden
| | - Katja S. Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, 1958, Denmark
| | - Morten H. H. Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
- Mycropt ApS, Kongens Lyngby, 2800, Denmark
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91
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Garcion C, Béven L, Foissac X. Comparison of Current Methods for Signal Peptide Prediction in Phytoplasmas. Front Microbiol 2021; 12:661524. [PMID: 33841387 PMCID: PMC8026896 DOI: 10.3389/fmicb.2021.661524] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
Although phytoplasma studies are still hampered by the lack of axenic cultivation methods, the availability of genome sequences allowed dramatic advances in the characterization of the virulence mechanisms deployed by phytoplasmas, and highlighted the detection of signal peptides as a crucial step to identify effectors secreted by phytoplasmas. However, various signal peptide prediction methods have been used to mine phytoplasma genomes, and no general evaluation of these methods is available so far for phytoplasma sequences. In this work, we compared the prediction performance of SignalP versions 3.0, 4.0, 4.1, 5.0 and Phobius on several sequence datasets originating from all deposited phytoplasma sequences. SignalP 4.1 with specific parameters showed the most exhaustive and consistent prediction ability. However, the configuration of SignalP 4.1 for increased sensitivity induced a much higher rate of false positives on transmembrane domains located at N-terminus. Moreover, sensitive signal peptide predictions could similarly be achieved by the transmembrane domain prediction ability of TMHMM and Phobius, due to the relatedness between signal peptides and transmembrane regions. Beyond the results presented herein, the datasets assembled in this study form a valuable benchmark to compare and evaluate signal peptide predictors in a field where experimental evidence of secretion is scarce. Additionally, this study illustrates the utility of comparative genomics to strengthen confidence in bioinformatic predictions.
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Affiliation(s)
- Christophe Garcion
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Villenave d'Ornon, France
| | - Laure Béven
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Villenave d'Ornon, France
| | - Xavier Foissac
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Villenave d'Ornon, France
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92
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Enhanced extracellular Bacillus stearothermophilus α-amylase production in Bacillus subtilis by balancing the entire secretion process in an optimal strain. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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93
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Hua R, Liu J, Li Y, Fan Y, Zeng B, Geng G, Li Q. Novel Functional Recombinant Human Follicle-Stimulating Hormone Acquired from Goat Milk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2793-2804. [PMID: 33645971 DOI: 10.1021/acs.jafc.0c07208] [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: 06/12/2023]
Abstract
An animal mammary bioreactor is regarded as an excellent biological system which is applied to produce large-scale recombinant proteins in milk. However, there are no effective methods to produce a large amount of some pharmaceutical proteins, such as human follicle-stimulating hormone (FSH), by large animal mammary gland bioreactors due to the fact that accumulation of excessive bioactive FSH might cause serious diseases in animals. Here, we report a novel strategy of preparing recombinant human FSH (rhFSH) from goat mammary glands, which could avoid the accumulation of bioactive FSH in goats. First, the single inactive FSHα and FSHβ subunits expressed in goat mammary epithelial cells and goat mammary glands were performed to reassemble in vitro and were found to self-assemble into a complete heterodimer rhFSH at 4 °C and pH 7.4. Further, a cyclic adenosine monophosphate (cAMP) induction assay showed that the cAMP levels in cell lysate of HEK 293/FSHR cells were increased by about 8-fold in reassembled rhFSH groups than that in the control group (P < 0.01). Pharmacokinetic analysis indicated that the reassembled rhFSH from goat mammary glands was comparable to that of the commercially available Gonal-F (P > 0.05). In addition, the increasing dose of reassembled rhFSH significantly promoted ovulation of mouse and ovary weight gain of Sprague Dawley rat compared with the control groups and maximum values were up to 3-fold (P < 0.01) and 2.8-fold (P < 0.01), respectively. The reassembled rhFSH showed a similar effect to Gonal-F in inducing expression of FSH target genes in vivo and activating the PI3K pathway in granulosa cells. Our study developed a novel method to produce rhFSH and provided the basis for preparing FSH by the goat mammary gland bioreactor with less health problems on the producing animals.
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Affiliation(s)
- Rongmao Hua
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
| | - Jianxi Liu
- Institute of Special Environmental Medicine, Nantong University, Nantong 226019, P. R. China
| | - Yuan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
| | - Yan Fan
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, P. R. China
| | - Bin Zeng
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, P. R. China
| | - Guoxia Geng
- College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling 712100, P. R. China
| | - Qingwang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
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94
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Gonzalez-Perez D, Ratcliffe J, Tan SK, Wong MCM, Yee YP, Nyabadza N, Xu JH, Wong TS, Tee KL. Random and combinatorial mutagenesis for improved total production of secretory target protein in Escherichia coli. Sci Rep 2021; 11:5290. [PMID: 33674702 PMCID: PMC7935960 DOI: 10.1038/s41598-021-84859-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/22/2021] [Indexed: 11/17/2022] Open
Abstract
Signal peptides and secretory carrier proteins are commonly used to secrete heterologous recombinant protein in Gram-negative bacteria. The Escherichia coli osmotically-inducible protein Y (OsmY) is a carrier protein that secretes a target protein extracellularly, and we have previously applied it in the Bacterial Extracellular Protein Secretion System (BENNY) to accelerate directed evolution. In this study, we reported the first application of random and combinatorial mutagenesis on a carrier protein to enhance total secretory target protein production. After one round of random mutagenesis followed by combining the mutations found, OsmY(M3) (L6P, V43A, S154R, V191E) was identified as the best carrier protein. OsmY(M3) produced 3.1 ± 0.3 fold and 2.9 ± 0.8 fold more secretory Tfu0937 β-glucosidase than its wildtype counterpart in E. coli strains BL21(DE3) and C41(DE3), respectively. OsmY(M3) also produced more secretory Tfu0937 at different cultivation temperatures (37 °C, 30 °C and 25 °C) compared to the wildtype. Subcellular fractionation of the expressed protein confirmed the essential role of OsmY in protein secretion. Up to 80.8 ± 12.2% of total soluble protein was secreted after 15 h of cultivation. When fused to a red fluorescent protein or a lipase from Bacillus subtillis, OsmY(M3) also produced more secretory protein compared to the wildtype. In this study, OsmY(M3) variant improved the extracellular production of three proteins originating from diverse organisms and with diverse properties, clearly demonstrating its wide-ranging applications. The use of random and combinatorial mutagenesis on the carrier protein demonstrated in this work can also be further extended to evolve other signal peptides or carrier proteins for secretory protein production in E. coli.
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Affiliation(s)
- David Gonzalez-Perez
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
- Department of Drug Discovery, Moffitt Cancer Center & Research Institute, Stabile Research Building, 12902 Magnolia Dr, Tampa, FL, 33612, USA
| | - James Ratcliffe
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Shu Khan Tan
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Mary Chen May Wong
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Yi Pei Yee
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Natsai Nyabadza
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Jian-He Xu
- Laboratory of Biocatalysis and Bioprocessing, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Tuck Seng Wong
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK.
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, 12120, Pathum Thani, Thailand.
| | - Kang Lan Tee
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK.
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95
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Shi L, Liu H, Gao S, Weng Y, Zhu L. Enhanced Extracellular Production of IsPETase in Escherichia coli via Engineering of the pelB Signal Peptide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2245-2252. [PMID: 33576230 DOI: 10.1021/acs.jafc.0c07469] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Poly(ethylene terephthalate) (PET) is one of the most commonly used plastics worldwide and its accumulation in the environment is a global problem. PETase from Ideonella sakaiensis 201-F6 was reported to exhibit higher hydrolytic activity and specificity for PET than other enzymes at ambient temperature. Enzymatic degradation of PET using PETase provides an attractive approach for plastic degradation and recycling. In this work, extracellular PETase was achieved by Escherichia coli BL21 using a Sec-dependent translocation signal peptide, pelB, for secretion. Furthermore, engineering of the pelB through random mutagenesis and screening was performed to improve the secretion efficiency of PETase. Evolved pelB enabled higher PETase secretion by up to 1.7-fold. The improved secretion of PETase led to more efficient hydrolysis of the PET model compound, bis (2-hydroxyethyl) terephthalic acid (BHET), PET powder, and PET film. Our study presents the first example of the increasing secretion of PETase by an engineered signal peptide, providing a promising approach to obtain extracellular PETase for efficient enzymatic degradation of PET.
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Affiliation(s)
- Lixia Shi
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Haifeng Liu
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, Graz 8010, Austria
| | - Songfeng Gao
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yunxuan Weng
- Beijing Key Laboratory of Quality Evaluation Technology for Hygiene and Safety of Plastics, Beijing Technology and Business University, Beijing 100048, China
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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96
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Rational design of signal peptides for improved MtC1LPMO production in Bacillus amyloliquefaciens. Int J Biol Macromol 2021; 175:262-269. [PMID: 33561461 DOI: 10.1016/j.ijbiomac.2021.02.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 11/21/2022]
Abstract
A high-throughput screening system was established by employing enhanced green fluorescent protein as a screenable fusion tag to evaluate the expression and secretion of a lytic polysaccharide monooxygenase (MtC1LPMO) using 20 Sec-type signal peptides (SPs) from Bacillus amyloliquefaciens 111018. Among these, 10 SPs were found to be better than the native SP of MtC1LPMO. The protein expression and secretion levels using SP12 (MNITNWAAILQLQSMALQSISNTGTASS) were the highest among all SPs, with 4.1- and 2.1-fold increases over the native SP, respectively. Then, the amino acids of the 10 best SPs were analyzed, and the results indicated that the most abundant amino acid of the N-region was K, those of the H-region were L, F, A and V, and the C-region contained an AXA motif. Additionally, we found that the protein expression level gradually improved along with the increasing folding free energies of the SP-encoding part of the mRNA. Finally, the SPs were rationally designed to improve the expression and secretion level of MtC1LPMO. An increased positive charge of the SP N-region was found to enhance the protein expression and secretion level, as long as the folding free energy of the mRNA did not change significantly.
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97
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Xu JM, Cao HT, Wang M, Ma BJ, Wang LY, Zhang K, Cheng F, Xue YP, Zheng YG. Development of a Combination Fermentation Strategy to Simultaneously Increase Biomass and Enzyme Activity of D-amino Acid Oxidase Expressed in Escherichia coli. Appl Biochem Biotechnol 2021; 193:2029-2042. [PMID: 33538962 DOI: 10.1007/s12010-021-03519-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/27/2021] [Indexed: 12/13/2022]
Abstract
D-amino acid oxidase (DAAO) is widely used in the industrial preparation of L-amino acids, and cultivating Escherichia coli (E. coli) expressing DAAO for the biosynthesis of L-phosphinothricin (L-PPT) is very attractive. At present, the biomass production of DAAO by fermentation is still limited in large-scale industrial applications because the expression of DAAO during the fermentation process inhibits the growth of host cells, which limits higher cell density. In this study, the factors that inhibit the growth of bacterial cells during a 5-L fed-batch fermentation process were explored, and the fermentation process was optimized by co-expressing catalase (CAT), by balancing the biomass and the enzyme activity, and by adding exogenous D-alanine (D-Ala) to relieve the limitation of DAAO on the cells and optimize fermentation. Under optimal conditions, the DO-STAT feeding mode with DO controlled at 30% ± 5% and the addition of 27.5 g/L lactose mixed with 2 g/L D-Ala during induction at 28 °C resulted in the production of 26.03 g dry cell weight (DCW)/L biomass and 390.0 U/g DCW specific activity of DAAO; an increase of 78% and 84%, respectively, compared with the initial fermentation conditions. The fermentation strategy was successfully scale-up to a 5000-L fermenter.
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Affiliation(s)
- Jian-Miao Xu
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Hui-Ting Cao
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ming Wang
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Bao-Jian Ma
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Liu-Yu Wang
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Kai Zhang
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Feng Cheng
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ya-Ping Xue
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China. .,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China. .,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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98
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Nicchi S, Giuliani M, Giusti F, Pancotto L, Maione D, Delany I, Galeotti CL, Brettoni C. Decorating the surface of Escherichia coli with bacterial lipoproteins: a comparative analysis of different display systems. Microb Cell Fact 2021; 20:33. [PMID: 33531008 PMCID: PMC7853708 DOI: 10.1186/s12934-021-01528-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/23/2021] [Indexed: 11/10/2022] Open
Abstract
Background The display of recombinant proteins on cell surfaces has a plethora of applications including vaccine development, screening of peptide libraries, whole-cell biocatalysts and biosensor development for diagnostic, industrial or environmental purposes. In the last decades, a wide variety of surface display systems have been developed for the exposure of recombinant proteins on the surface of Escherichia coli, such as autotransporters and outer membrane proteins. Results In this study, we assess three approaches for the surface display of a panel of heterologous and homologous mature lipoproteins in E. coli: four from Neisseria meningitidis and four from the host strain that are known to be localised in the inner leaflet of the outer membrane. Constructs were made carrying the sequences coding for eight mature lipoproteins, each fused to the delivery portion of three different systems: the autotransporter adhesin involved in diffuse adherence-I (AIDA-I) from enteropathogenic E. coli, the Lpp’OmpA chimaera and a truncated form of the ice nucleation protein (INP), InaK-NC (N-terminal domain fused with C-terminal one) from Pseudomonas syringae. In contrast to what was observed for the INP constructs, when fused to the AIDA-I or Lpp’OmpA, most of the mature lipoproteins were displayed on the bacterial surface both at 37 and 25 °C as demonstrated by FACS analysis, confocal and transmission electron microscopy. Conclusions To our knowledge this is the first study that compares surface display systems using a number of passenger proteins. We have shown that the experimental conditions, including the choice of the carrier protein and the growth temperature, play an important role in the translocation of mature lipoproteins onto the bacterial surface. Despite all the optimization steps performed with the InaK-NC anchor motif, surface exposure of the passenger proteins used in this study was not achieved. For our experimental conditions, Lpp’OmpA chimaera has proved to be an efficient surface display system for the homologous passenger proteins although cell lysis and phenotype heterogeneity were observed. Finally, AIDA-I was found to be the best surface display system for mature lipoproteins (especially heterologous ones) in the E. coli host strain with no inhibition of growth and only limited phenotype heterogeneity.
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Affiliation(s)
- Sonia Nicchi
- GSK, via Fiorentina 1, 53100, Siena, Italy.,Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
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99
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Li J, Solhi L, Goddard-Borger ED, Mathieu Y, Wakarchuk WW, Withers SG, Brumer H. Four cellulose-active lytic polysaccharide monooxygenases from Cellulomonas species. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:29. [PMID: 33485381 PMCID: PMC7828015 DOI: 10.1186/s13068-020-01860-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/13/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The discovery of lytic polysaccharide monooxygenases (LPMOs) has fundamentally changed our understanding of microbial lignocellulose degradation. Cellulomonas bacteria have a rich history of study due to their ability to degrade recalcitrant cellulose, yet little is known about the predicted LPMOs that they encode from Auxiliary Activity Family 10 (AA10). RESULTS Here, we present the comprehensive biochemical characterization of three AA10 LPMOs from Cellulomonas flavigena (CflaLPMO10A, CflaLPMO10B, and CflaLPMO10C) and one LPMO from Cellulomonas fimi (CfiLPMO10). We demonstrate that these four enzymes oxidize insoluble cellulose with C1 regioselectivity and show a preference for substrates with high surface area. In addition, CflaLPMO10B, CflaLPMO10C, and CfiLPMO10 exhibit limited capacity to perform mixed C1/C4 regioselective oxidative cleavage. Thermostability analysis indicates that these LPMOs can refold spontaneously following denaturation dependent on the presence of copper coordination. Scanning and transmission electron microscopy revealed substrate-specific surface and structural morphological changes following LPMO action on Avicel and phosphoric acid-swollen cellulose (PASC). Further, we demonstrate that the LPMOs encoded by Cellulomonas flavigena exhibit synergy in cellulose degradation, which is due in part to decreased autoinactivation. CONCLUSIONS Together, these results advance understanding of the cellulose utilization machinery of historically important Cellulomonas species beyond hydrolytic enzymes to include lytic cleavage. This work also contributes to the broader mapping of enzyme activity in Auxiliary Activity Family 10 and provides new biocatalysts for potential applications in biomass modification.
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Affiliation(s)
- James Li
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Laleh Solhi
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Ethan D Goddard-Borger
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Yann Mathieu
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Stephen G Withers
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Department of Botany, University of British Columbia, 3200 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada.
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100
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Wu F, Ma J, Cha Y, Lu D, Li Z, Zhuo M, Luo X, Li S, Zhu M. Using inexpensive substrate to achieve high-level lipase A secretion by Bacillus subtilis through signal peptide and promoter screening. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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