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Peng Z, Zhang J, Song Y, Guo R, Du G, Chen J. Engineered pro-peptide enhances the catalytic activity of keratinase to improve the conversion ability of feather waste. Biotechnol Bioeng 2021; 118:2559-2571. [PMID: 33788275 DOI: 10.1002/bit.27771] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/22/2021] [Accepted: 03/28/2021] [Indexed: 01/28/2023]
Abstract
Keratinase is an attractive industrial enzyme that can specifically catalyze keratin waste to obtain value-added products. A challenge to the application of keratinase is improving catalytic capacity to achieve efficient hydrolysis. In this study, we effectively expressed the keratinase gene from Bacillus licheniformis BBE11-1 in Bacillus subtilis WB600 based on pro-peptide engineering. Partial deletion of the pro-peptide sequence and the substitution of amino acid at the pro-peptide cleavage site (P1) suggested that the "chaperone effect" and "cleavage efficiency" of the pro-peptide determine the activity of the mature enzyme. Subsequently, seven target sites that can increase the activity of the mature enzyme by 16%-66% were obtained through the multiple sequence alignment of pro-peptides and site-directed mutation. We further performed combinatorial mutations at six sites based on the design principle of three-codon saturation mutations and obtained mutant 2-D12 (236.8 KU/mg) with a mature enzyme activity of 186% of the original (127.6 KU/mg). Finally, continuous fermentation was carried out in a 5-L bioreactor for 22 h, and the activity of the 2-D12 mature enzyme was increased to 391.6 KU/mg. Most importantly, 2-D12 could degrade more than 90% of feather waste into amino acids and peptides within 12 h with the aid of sulfite.
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Affiliation(s)
- Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yang Song
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Rong Guo
- Wuhan Institute of Industrial Control Technology Co., Ltd., Wuhan, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jian Chen
- School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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Han L, Cui W, Suo F, Miao S, Hao W, Chen Q, Guo J, Liu Z, Zhou L, Zhou Z. Development of a novel strategy for robust synthetic bacterial promoters based on a stepwise evolution targeting the spacer region of the core promoter in Bacillus subtilis. Microb Cell Fact 2019; 18:96. [PMID: 31142347 PMCID: PMC6540529 DOI: 10.1186/s12934-019-1148-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/22/2019] [Indexed: 01/06/2023] Open
Abstract
Background Promoter evolution by synthetic promoter library (SPL) is a powerful approach to development of functional synthetic promoters to synthetic biology. However, it requires much tedious and time-consuming screenings because of the plethora of different variants in SPL. Actually, a large proportion of mutants in the SPL are significantly lower in strength, which contributes only to fabrication of a promoter library with a continuum of strength. Thus, to effectively obtain the evolved synthetic promoter exhibiting higher strength, it is essential to develop novel strategies to construct mutant library targeting the pivotal region rather than the arbitrary region of the template promoter. In this study, a strategy termed stepwise evolution targeting the spacer of core promoter (SETarSCoP) was established in Bacillus subtilis to effectively evolve the strength of bacterial promoter. Results The native promoter, PsrfA, from B. subtilis, which exhibits higher strength than the strong promoter P43, was set as the parental template. According to the comparison of conservation of the spacer sequences between − 35 box and − 10 box among a set of strong and weak native promoter, it revealed that 7-bp sequence immediately upstream of the − 10 box featured in the regulation of promoter strength. Based on the conservative feature, two rounds of consecutive evolution were performed targeting the hot region of PsrfA. In the first round, a primary promoter mutation library (pPML) was constructed by mutagenesis targeting the 3-bp sequence immediately upstream of the − 10 box of the PsrfA. Subsequently, four evolved mutants from pPML were selected to construction of four secondary promoter mutation libraries (sPMLs) based on mutagenesis of the 4-bp sequence upstream of the first-round target. After the consecutive two-step evolution, the mutant PBH4 was identified and verified to be a highly evolved synthetic promoter. The strength of PBH4 was higher than PsrfA by approximately 3 times. Moreover, PBH4 also exhibited broad suitability for different cargo proteins, such as β-glucuronidase and nattokinase. The proof-of-principle test showed that SETarSCoP successfully evolved both constitutive and inducible promoters. Conclusion Comparing with the commonly used SPL strategy, SETarSCoP facilitates the evolution process to obtain strength-evolved synthetic bacterial promoter through fabrication and screening of small-scale mutation libraries. This strategy will be a promising method to evolve diverse bacterial promoters to expand the toolbox for synthetic biology. Electronic supplementary material The online version of this article (10.1186/s12934-019-1148-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laichuang Han
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Wenjing Cui
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Feiya Suo
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Shengnan Miao
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Wenliang Hao
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qiaoqing Chen
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Junling Guo
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zhongmei Liu
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Li Zhou
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zhemin Zhou
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, 214122, Jiangsu, China.
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Ilinskaya O, Ulyanova V, Lisevich I, Dudkina E, Zakharchenko N, Kusova A, Faizullin D, Zuev Y. The Native Monomer of Bacillus Pumilus Ribonuclease Does Not Exist Extracellularly. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4837623. [PMID: 30402481 PMCID: PMC6196983 DOI: 10.1155/2018/4837623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/18/2018] [Indexed: 01/06/2023]
Abstract
Supported by crystallography studies, secreted ribonuclease of Bacillus pumilus (binase) has long been considered to be monomeric in form. Recent evidence obtained using native polyacrylamide gel electrophoresis and size-exclusion chromatography suggests that binase is in fact dimeric. To eliminate ambiguity and contradictions in the data we have measured conformational changes, hypochromic effect, and hydrodynamic radius of binase. The immutability of binase secondary structure upon transition from low to high protein concentration was registered, suggesting the binase dimerization immediately after translocation through the cell membrane and leading to detection of binase dimers only in the culture fluid regardless of ribonuclease concentration. Our results made it necessary to take a fresh look at the binase stability and cytotoxicity towards virus-infected or tumor cells.
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Affiliation(s)
- Olga Ilinskaya
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia
| | - Vera Ulyanova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia
| | - Irina Lisevich
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia
| | - Elena Dudkina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia
| | - Nataliya Zakharchenko
- Kazan Institute of Biochemistry and Biophysics of FRC Kazan Scientific Center of RAS, Kazan 420008, Russia
| | - Alexandra Kusova
- Kazan Institute of Biochemistry and Biophysics of FRC Kazan Scientific Center of RAS, Kazan 420008, Russia
| | - Dzhigangir Faizullin
- Kazan Institute of Biochemistry and Biophysics of FRC Kazan Scientific Center of RAS, Kazan 420008, Russia
| | - Yuriy Zuev
- Kazan Institute of Biochemistry and Biophysics of FRC Kazan Scientific Center of RAS, Kazan 420008, Russia
- Kazan State Power Engineering University, Kazan 420066, Russia
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Exploitation of Bacillus subtilis as a robust workhorse for production of heterologous proteins and beyond. World J Microbiol Biotechnol 2018; 34:145. [DOI: 10.1007/s11274-018-2531-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/05/2018] [Indexed: 10/28/2022]
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Kumar N, Pandey R, Prabhu AA, Venkata Dasu V. Genetic and substrate-level modulation of Bacillus subtilis physiology for enhanced extracellular human interferon gamma production. Prep Biochem Biotechnol 2018; 48:391-401. [PMID: 29688129 DOI: 10.1080/10826068.2018.1446157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Human interferon-gamma (hIFNG) production is limited by various gene-level bottlenecks including translation, protein folding, and secretion which depends upon the physiological state of the organism. In this study gene-level and substrate-level modulations have been used to control Bacillus subtilis physiology for >15 fold extracellular soluble hIFNG production. Two variants of the native human interferon-gamma gene (hifng) were designed and synthesized, namely, cohifnghis and cohifng having codon adaptation index 25.33 and 26.89% higher than the native gene, respectively. BScoIFNG and BScoIFNGhis with ΔG of -100.0 and -113.7 kcal mol-1 resulted in 30 and 6.5% higher hIFNG compared to the native gene in complex medium. BScoIFNG produced 1.53 fold higher hIFNG using glucose-based defined medium as compared to the complex medium by modulating the physiological parameter growth rate from 0.35 to 0.26 hr-1. Further modulatory effect of various phosphotransferase transport system (PTS) and no-PTS sugars, sugar alcohols, and organic acids was quantified on the physiology of B. subtilis WB800N for extracellular hIFNG production. Sorbitol and glycerol emerged as the best hIFNG producers with lowest growth and substrate consumption rates. BScoIFNG produced maximum 3.15 mg L-1 hIFNG at 50 g L-1 glycerol with highest hIFNG yield (Yp/x = 0.136) and lowest substrate uptake rate (qs = 0.26).
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Affiliation(s)
- Nitin Kumar
- a Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam , India
| | - Rajat Pandey
- a Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam , India
| | - Ashish Anand Prabhu
- a Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam , India
| | - Veeranki Venkata Dasu
- a Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam , India
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Lakowitz A, Godard T, Biedendieck R, Krull R. Mini review: Recombinant production of tailored bio-pharmaceuticals in different Bacillus strains and future perspectives. Eur J Pharm Biopharm 2017; 126:27-39. [PMID: 28606596 DOI: 10.1016/j.ejpb.2017.06.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/30/2017] [Accepted: 06/07/2017] [Indexed: 01/06/2023]
Abstract
Bio-pharmaceuticals like antibodies, hormones and growth factors represent about one-fifth of commercial pharmaceuticals. Host candidates of growing interest for recombinant production of these proteins are strains of the genus Bacillus, long being established for biotechnological production of homologous and heterologous proteins. Bacillus strains benefit from development of efficient expression systems in the last decades and emerge as major industrial workhorses for recombinant proteins due to easy cultivation, non-pathogenicity and their ability to secrete recombinant proteins directly into extracellular medium allowing cost-effective downstream processing. Their broad product portfolio of pharmaceutically relevant recombinant proteins described in research include antibody fragments, growth factors, interferons and interleukins, insulin, penicillin G acylase, streptavidin and different kinases produced in various cultivation systems like microtiter plates, shake flasks and bioreactor systems in batch, fed-batch and continuous mode. To further improve production and secretion performance of Bacillus, bottlenecks and limiting factors concerning proteases, chaperones, secretion machinery or feedback mechanisms can be identified on different cell levels from genomics and transcriptomics via proteomics to metabolomics and fluxomics. For systematical identification of recurring patterns characteristic of given regulatory systems and key genetic targets, systems biology and omics-technology provide suitable and promising approaches, pushing Bacillus further towards industrial application for recombinant pharmaceutical protein production.
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Affiliation(s)
- Antonia Lakowitz
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-List-Straβe 35a, 38106 Braunschweig, Germany; Braunschweig Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Thibault Godard
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-List-Straβe 35a, 38106 Braunschweig, Germany; Braunschweig Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Rebekka Biedendieck
- Braunschweig Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; Institute of Microbiology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-List-Straβe 35a, 38106 Braunschweig, Germany; Braunschweig Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany.
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7
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Wang Z, Lv P, Luo W, Yuan Z, He D. Expression in Pichia pastoris and characterization of Rhizomucor miehei lipases containing a new propeptide region. J GEN APPL MICROBIOL 2017; 62:25-30. [PMID: 26923128 DOI: 10.2323/jgam.62.25] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A large number of propeptide regions from various proteins have been identified which function as intramolecular chaperones and assist the folding of the respective functional domains. The same polypeptide can fold into an altered conformation because of a mutated intramolecular chaperone and can maintain the "memory" of the folding process (new physicochemical properties). Two new kinds of Rhizomucor miehei lipase (RML) were constructed by replacing its propeptide region with that from either Rhizopus chinensis lipase (RCL) or Rhizopus oryzae lipase (ROL). The enzymatic properties were also analyzed and compared between wild-type RML and the mutants. The results indicated that the same polypeptide can fold into different conformations because of changes in the propeptide region.
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Affiliation(s)
- Zhiyuan Wang
- Key Laboratory of Renewable Energy and Gas Hydrate, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences
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Jakob RP, Koch JR, Burmann BM, Schmidpeter PAM, Hunkeler M, Hiller S, Schmid FX, Maier T. Dimeric Structure of the Bacterial Extracellular Foldase PrsA. J Biol Chem 2014; 290:3278-92. [PMID: 25525259 DOI: 10.1074/jbc.m114.622910] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Secretion of proteins into the membrane-cell wall space is essential for cell wall biosynthesis and pathogenicity in Gram-positive bacteria. Folding and maturation of many secreted proteins depend on a single extracellular foldase, the PrsA protein. PrsA is a 30-kDa protein, lipid anchored to the outer leaflet of the cell membrane. The crystal structure of Bacillus subtilis PrsA reveals a central catalytic parvulin-type prolyl isomerase domain, which is inserted into a larger composite NC domain formed by the N- and C-terminal regions. This domain architecture resembles, despite a lack of sequence conservation, both trigger factor, a ribosome-binding bacterial chaperone, and SurA, a periplasmic chaperone in Gram-negative bacteria. Two main structural differences are observed in that the N-terminal arm of PrsA is substantially shortened relative to the trigger factor and SurA and in that PrsA is found to dimerize in a unique fashion via its NC domain. Dimerization leads to a large, bowl-shaped crevice, which might be involved in vivo in protecting substrate proteins from aggregation. NMR experiments reveal a direct, dynamic interaction of both the parvulin and the NC domain with secretion propeptides, which have been implicated in substrate targeting to PrsA.
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Affiliation(s)
- Roman P Jakob
- From the Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland and
| | - Johanna R Koch
- the Laboratorium für Biochemie and Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Björn M Burmann
- From the Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland and
| | - Philipp A M Schmidpeter
- the Laboratorium für Biochemie and Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Moritz Hunkeler
- From the Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland and
| | - Sebastian Hiller
- From the Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland and
| | - Franz X Schmid
- the Laboratorium für Biochemie and Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Timm Maier
- From the Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland and
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Kakeshita H, Kageyama Y, Endo K, Tohata M, Ara K, Ozaki K, Nakamura K. Secretion of biologically-active human interferon-β by Bacillus subtilis. Biotechnol Lett 2011; 33:1847-52. [DOI: 10.1007/s10529-011-0636-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 04/20/2011] [Indexed: 12/20/2022]
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