1
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Wei CH, Wang ZW, Dai JH, Xiao K, Yu HR, Qu FS, Rong HW, He JG, Ngo HH. Enhanced anaerobic digestion performance and sludge filterability by membrane microaeration for anaerobic membrane bioreactor application. BIORESOURCE TECHNOLOGY 2024; 402:130787. [PMID: 38703955 DOI: 10.1016/j.biortech.2024.130787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Slow dissolution/hydrolysis of insoluble/macromolecular organics and poor sludge filterability restrict the application potential of anaerobic membrane bioreactor (AnMBR). Bubble-free membrane microaeration was firstly proposed to overcome these obstacles in this study. The batch anaerobic digestion tests feeding insoluble starch and soluble peptone with and without microaeration showed that microaeration led to a 65.7-144.8% increase in methane production and increased critical flux of microfiltration membrane via driving the formation of large sludge flocs and the resultant improvement of sludge settleability. The metagenomic and bioinformatic analyses showed that microaeration significantly enriched the functional genes and bacteria for polysaccharide and protein hydrolysis, microaeration showed little negative effects on the functional genes involved in anaerobic metabolisms, and substrate transfer from starch to peptone significantly affected the functional genes and microbial community. This study demonstrates the dual synergism of microaeration to enhance the dissolution/hydrolysis/acidification of insoluble/macromolecular organics and sludge filterability for AnMBR application.
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Affiliation(s)
- Chun-Hai Wei
- Department of Municipal Engineering, School of Civil Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou 510006, China.
| | - Zheng-Wei Wang
- Department of Municipal Engineering, School of Civil Engineering, Guangzhou University, Guangzhou 510006, China
| | - Jian-Hua Dai
- Department of Municipal Engineering, School of Civil Engineering, Guangzhou University, Guangzhou 510006, China
| | - Kang Xiao
- Beijing Yanshan Earth Critical Zone National Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Hua-Rong Yu
- Department of Municipal Engineering, School of Civil Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou 510006, China
| | - Fang-Shu Qu
- Department of Municipal Engineering, School of Civil Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou 510006, China
| | - Hong-Wei Rong
- Department of Municipal Engineering, School of Civil Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou 510006, China
| | - Jun-Guo He
- Department of Municipal Engineering, School of Civil Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou 510006, China
| | - Huu Hao Ngo
- Centre for Technology in Water and Wastewater, University of Technology, Sydney NSW 2007, Australia
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2
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Yunus J, Wan Dagang WRZ, Jamaluddin H, Jemon K, Mohamad SE, Jonet MA. Bacterial biofilm growth and perturbation by serine protease from Bacillus sp. Arch Microbiol 2024; 206:138. [PMID: 38436775 DOI: 10.1007/s00203-024-03857-0] [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: 12/19/2023] [Revised: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 03/05/2024]
Abstract
In nature, bacteria are ubiquitous and can be categorized as beneficial or harmless to humans, but most bacteria have one thing in common which is their ability to produce biofilm. Biofilm is encased within an extracellular polymeric substance (EPS) which provides resistance against antimicrobial agents. Protease enzymes have the potential to degrade or promote the growth of bacterial biofilms. In this study, the effects of a recombinant intracellular serine protease from Bacillus sp. (SPB) on biofilms from Staphylococcus aureus, Acinetobacter baumannii, and Pseudomonas aeruginosa were analyzed. SPB was purified using HisTrap HP column and concentrated using Amicon 30 ultra-centrifugal filter. SPB was added with varying enzyme activity and assay incubation period after biofilms were formed in 96-well plates. SPB was observed to have contrasting effects on different bacterial biofilms, where biofilm degradations were observed for both 7-day-old A. baumannii (37.26%) and S. aureus (71.51%) biofilms. Meanwhile, SPB promoted growth of P. aeruginosa biofilm up to 176.32%. Compatibility between protein components in S. aureus biofilm with SPB as well as a simpler membrane structure morphology led to higher biofilm degradation for S. aureus compared to A. baumannii. However, SPB promoted growth of P. aeruginosa biofilm due likely to its degrading protein factors that are responsible for biofilm detachment and dispersion, thus resulting in more multi-layered biofilm formation. Commercial protease Savinase which was used as a comparison showed degradation for all three bacterial biofilms. The results obtained are unique and will expand our understanding on the effects that bacterial proteases have toward biofilms.
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Affiliation(s)
- Julia Yunus
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Wan Rosmiza Zana Wan Dagang
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Haryati Jamaluddin
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Khairunadwa Jemon
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Shaza Eva Mohamad
- Department of Environmental Engineering and Green Technology (EGT), Malaysia Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Mohd Anuar Jonet
- Structural And Applied Genomics Centre, Malaysia Genome and Vaccine Institute (MGVI), National Institute of Biotechnology Malaysia (NIBM), Jalan Bangi, 43000, Kajang, Selangor, Malaysia
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3
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Falkenberg F, Kohn S, Bott M, Bongaerts J, Siegert P. Biochemical characterisation of a novel broad pH spectrum subtilisin from Fictibacillus arsenicus DSM 15822 T. FEBS Open Bio 2023; 13:2035-2046. [PMID: 37649135 PMCID: PMC10626276 DOI: 10.1002/2211-5463.13701] [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: 04/25/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023] Open
Abstract
Subtilisins from microbial sources, especially from the Bacillaceae family, are of particular interest for biotechnological applications and serve the currently growing enzyme market as efficient and novel biocatalysts. Biotechnological applications include use in detergents, cosmetics, leather processing, wastewater treatment and pharmaceuticals. To identify a possible candidate for the enzyme market, here we cloned the gene of the subtilisin SPFA from Fictibacillus arsenicus DSM 15822T (obtained through a data mining-based search) and expressed it in Bacillus subtilis DB104. After production and purification, the protease showed a molecular mass of 27.57 kDa and a pI of 5.8. SPFA displayed hydrolytic activity at a temperature optimum of 80 °C and a very broad pH optimum between 8.5 and 11.5, with high activity up to pH 12.5. SPFA displayed no NaCl dependence but a high NaCl tolerance, with decreasing activity up to concentrations of 5 m NaCl. The stability enhanced with increasing NaCl concentration. Based on its substrate preference for 10 synthetic peptide 4-nitroanilide substrates with three or four amino acids and its phylogenetic classification, SPFA can be assigned to the subgroup of true subtilisins. Moreover, SPFA exhibited high tolerance to 5% (w/v) SDS and 5% H2 O2 (v/v). The biochemical properties of SPFA, especially its tolerance of remarkably high pH, SDS and H2 O2 , suggest it has potential for biotechnological applications.
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Affiliation(s)
- Fabian Falkenberg
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Sophie Kohn
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Michael Bott
- Institute of Bio‐ and Geosciences, IBG‐1: BiotechnologyForschungszentrum JülichGermany
| | - Johannes Bongaerts
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Petra Siegert
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
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4
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Cheng JH, Zhao WX, Cao HY, Wang Z, Wang Y, Sheng Q, Chen Y, Wang P, Chen XL, Zhang YZ. Mechanistic Insight Into the Production of Collagen Oligopeptides by the S8 Family Protease A4095. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:603-614. [PMID: 36577515 DOI: 10.1021/acs.jafc.2c05402] [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: 06/17/2023]
Abstract
Collagen oligopeptides have wide applications in foods, pharmaceuticals, cosmetics, and others due to their high bioactivities and bioavailability. The S8 family is the second-largest family of serine proteases. Several collagenolytic proteases from this family have been reported to have good potential in the preparation of collagen oligopeptides, however, the underlying mechanism remains unknown. A4095 was the most abundant S8 protease secreted by the protease-producing bacterium Anoxybacillus caldiproteolyticus 1A02591. Here, we characterized A4095 as an S8 collagenolytic protease and illustrated its structural basis to produce collagen oligopeptides. Protease A4095 preferentially hydrolyzed the Y-Gly peptide bonds in denatured bovine bone collagen, leading to high production (62.48% <1000 Da) of collagen oligopeptides. Structural and mutational analyses indicated that A4095 has a unique S1' substrate-binding pocket to preferentially bind Gly, which is the structural determinant for the high production of collagen oligopeptides. This study provides mechanistic insight into the advantage of the S8 collagenolytic proteases in preparing collagen oligopeptides.
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Affiliation(s)
- Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Wen-Xiao Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Hai-Yan Cao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Zhen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Yan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Qi Sheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Yin Chen
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Peng Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao266237, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao266237, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao266237, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
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5
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Rasmussen CB, Scavenius C, Thøgersen IB, Harwood SL, Larsen Ø, Bjerga GEK, Stougaard P, Enghild JJ, Thøgersen MS. Characterization of a novel cold-adapted intracellular serine protease from the extremophile Planococcus halocryophilus Or1. Front Microbiol 2023; 14:1121857. [PMID: 36910232 PMCID: PMC9995970 DOI: 10.3389/fmicb.2023.1121857] [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: 12/12/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
The enzymes of microorganisms that live in cold environments must be able to function at ambient temperatures. Cold-adapted enzymes generally have less ordered structures that convey a higher catalytic rate, but at the cost of lower thermodynamic stability. In this study, we characterized P355, a novel intracellular subtilisin protease (ISP) derived from the genome of Planococcus halocryophilus Or1, which is a bacterium metabolically active down to -25°C. P355's stability and activity at varying pH values, temperatures, and salt concentrations, as well as its temperature-dependent kinetics, were determined and compared to an uncharacterized thermophilic ISP (T0099) from Parageobacillus thermoglucosidasius, a previously characterized ISP (T0034) from Planococcus sp. AW02J18, and Subtilisin Carlsberg (SC). The results showed that P355 was the most heat-labile of these enzymes, closely followed by T0034. P355 and T0034 exhibited catalytic constants (k cat ) that were much higher than those of T0099 and SC. Thus, both P355 and T0034 demonstrate the characteristics of the stability-activity trade-off that has been widely observed in cold-adapted proteases.
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Affiliation(s)
| | | | - Ida B Thøgersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Øivind Larsen
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bergen, Norway
| | | | - Peter Stougaard
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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6
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Liu W, Tang S, Peng J, Pan L, Wang J, Cheng H, Chen Z, Wang Y, Zhou H. Enhancing heterologous expression of a key enzyme for the biosynthesis of 2'-fucosyllactose. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:5162-5171. [PMID: 35289934 DOI: 10.1002/jsfa.11868] [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: 12/14/2021] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND 2'-Fucosyllactose (2'-FL) is the most abundant human milk oligosaccharide (HMO) in human milk and has important physiological functions. The market demand of 2'-FL is continuing to grow, but high production cost has limited its availability. To solve the dilemma, biosynthesis of 2'-FL has been proposed and is considered the most promising pathway for massive production. α-1,2-Fucosyltransferase is one of the key elements involved in its biosynthesis, but the limited intracellular accumulation and unstable properties of α-1,2-fucosyltransferases when expressed in host strains have become a major hurdle for the effective biosynthesis of 2'-FL. RESULTS A combinatorial engineering strategy of synergic modification of ribosome binding site, fusion peptide and enzyme gene was leveraged to enhance the soluble expression of α-1,2-fucosyltransferases and promote enzyme activity. The preferable combination was to employ an optimized ribosome binding site region to drive 3 × FLAG as a fusion partner along with the α-1,2-fucosyltransferase for expression in Escherichia coli (DE3) PlySs, and protein yield and enzyme activity were remarkably improved by 11.51-fold and 13.72-fold, respectively. CONCLUSION After finely tuning the synergy among different elements, the abundant protein yield and high enzyme activity confirmed that the drawbacks of heterologous expression in α-1,2-fucosyltransferase had been properly addressed. A suitable external environment further drives the efficient synthesis of α-1,2-fucosyltransferases. To our knowledge, this is the first report of a systematic and effective modification of α-1,2-fucosyltransferase expression, which could potentially serve as a guideline for industrial application. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Wenxian Liu
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Shizhe Tang
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jing Peng
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Lina Pan
- Ausnutria Dairy China Co. Ltd, Ausnutria Institute Food & Nutrition, Changsha, China
| | - Jiaqi Wang
- Ausnutria Dairy China Co. Ltd, Ausnutria Institute Food & Nutrition, Changsha, China
| | - Haina Cheng
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhu Chen
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yuguang Wang
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Hongbo Zhou
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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7
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Recombinant Production and Characterization of an Extracellular Subtilisin-Like Serine Protease from Acinetobacter baumannii of Fermented Food Origin. Protein J 2021; 40:419-435. [PMID: 33870461 PMCID: PMC8053418 DOI: 10.1007/s10930-021-09986-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2021] [Indexed: 12/20/2022]
Abstract
Acinetobacter baumannii is a ubiquitous bacteria that is increasingly becoming a formidable nosocomial pathogen. Due to its clinical relevance, studies on the bacteria's secretory molecules especially extracellular proteases are of interest primarily in relation to the enzyme's role in virulence. Besides, favorable properties that extracellular proteases possess may be exploited for commercial use thus there is a need to investigate extracellular proteases from Acinetobacter baumannii to gain insights into their catalytic properties. In this study, an extracellular subtilisin-like serine protease from Acinetobacter baumannii designated as SPSFQ that was isolated from fermented food was recombinantly expressed and characterized. The mature catalytically active form of SPSFQ shared a high percentage sequence identity of 99% to extracellular proteases from clinical isolates of Acinetobacter baumannii and Klebsiella pneumoniae as well as a moderately high percentage identity to other bacterial proteases with known keratinolytic and collagenolytic activity. The homology model of mature SPSFQ revealed its structure is composed of 10 β-strands, 8 α-helices, and connecting loops resembling a typical architecture of subtilisin-like α/β motif. SPSFQ is catalytically active at an optimum temperature of 40 °C and pH 9. Its activity is stimulated in the presence of Ca2+ and severely inhibited in the presence of PMSF. SPSFQ also displayed the ability to degrade several tissue-associated protein substrates such as keratin, collagen, and fibrin. Accordingly, our study shed light on the catalytic properties of a previously uncharacterized extracellular serine protease from Acinetobacter baumannii that warrants further investigations into its potential role as a virulence factor in pathogenicity and commercial applications.
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8
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Hou Y, Lu F, Tian J, Tian Y. Cloning, Heterologous Expression and Characterization of an Intracellular Serine Protease from Bacillus sp. LCB10. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819050168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Fang Z, Sha C, Peng Z, Zhang J, Du G. Protein engineering to enhance keratinolytic protease activity and excretion in Escherichia coli and its scale-up fermentation for high extracellular yield. Enzyme Microb Technol 2018; 121:37-44. [PMID: 30554643 DOI: 10.1016/j.enzmictec.2018.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/09/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
Escherichia coli is one kind of the simple and excellent biosystem to overexpress heterologous enzymes, such as keratinolytic protease, an excellent enzyme to hydrolyze keratin substrate for broad industrial application. However, protein expression in E. coli frequently faces some problems such as inactive and inclusion body formation. This work described a series of protein engineering strategies of N-terminal propeptide replacement and site-directed mutagenesis to modify this enzyme activity and production. Site-directed mutagenesis (S180G/Y215S) on N-terminal propeptide altered mutant contributed to the highest specific activity (4725 ± 65 U/mg, more than 1300 U/mg improvement than wild-type enzyme). This comprehensive mutation also achieved 2.5-fold improvement of extracellular enzyme yield in shake-flask level. The fermentation strategies about optimizing glycerol feeding and inducing point in scale-up bioreactor resulted in tremendous leakage of keratinolytic protease (954 mg/L extracellular yield within 48 h, about 9.26-fold higher than the original shake-flask level) as well as cell lysis. Although this proposed strategy faces a major challenge to maintain cell integrity or viability, it still exists the opportunity to realize other enzymes extracellular expression in E. coli system and simplify downstream processing to meet the industrial application.
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Affiliation(s)
- Zhen Fang
- School of the Environment, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Chong Sha
- School of the Environment, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, Wuxi 214122, China
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10
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Bjerga GEK, Larsen Ø, Arsın H, Williamson A, García-Moyano A, Leiros I, Puntervoll P. Mutational analysis of the pro-peptide of a marine intracellular subtilisin protease supports its role in inhibition. Proteins 2018; 86:965-977. [PMID: 29907987 PMCID: PMC6220982 DOI: 10.1002/prot.25528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 11/06/2022]
Abstract
Intracellular subtilisin proteases (ISPs) have important roles in protein processing during the stationary phase in bacteria. Their unregulated protein degrading activity may have adverse effects inside a cell, but little is known about their regulatory mechanism. Until now, ISPs have mostly been described from Bacillus species, with structural data from a single homolog. Here, we study a marine ISP originating from a phylogenetically distinct genus, Planococcus sp. The enzyme was successfully overexpressed in E. coli, and is active in presence of calcium, which is thought to have a role in minor, but essential, structural rearrangements needed for catalytic activity. The ISP operates at alkaline pH and at moderate temperatures, and has a corresponding melting temperature around 60 °C. The high-resolution 3-dimensional structure reported here, represents an ISP with an intact catalytic triad albeit in a configuration with an inhibitory pro-peptide bound. The pro-peptide is removed in other homologs, but the removal of the pro-peptide from the Planococcus sp. AW02J18 ISP appears to be different, and possibly involves several steps. A first processing step is described here as the removal of 2 immediate N-terminal residues. Furthermore, the pro-peptide contains a conserved LIPY/F-motif, which was found to be involved in inhibition of the catalytic activity.
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Affiliation(s)
- Gro E K Bjerga
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
| | - Øivind Larsen
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
| | - Hasan Arsın
- Department of Biological Sciences, University of Bergen, Thormøhlens gate 53, Bergen, 5006, Norway
| | - Adele Williamson
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, 9037, Norway
| | - Antonio García-Moyano
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
| | - Ingar Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, 9037, Norway
| | - Pål Puntervoll
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
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11
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High-level expression of prolyl endopeptidase in Pichia pastoris using PLA 2 as a fusion partner. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Fang Z, Zhang J, Liu B, Du G, Chen J. Enhancement of the catalytic efficiency and thermostability of Stenotrophomonas sp. keratinase KerSMD by domain exchange with KerSMF. Microb Biotechnol 2015; 9:35-46. [PMID: 26552936 PMCID: PMC4720410 DOI: 10.1111/1751-7915.12300] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 05/17/2015] [Accepted: 05/18/2015] [Indexed: 11/29/2022] Open
Abstract
In this study, we enhanced the catalytic efficiency and thermostability of keratinase KerSMD by replacing its N/C-terminal domains with those from a homologous protease, KerSMF, to degrade feather waste. Replacement of the N-terminal domain generated a mutant protein with more than twofold increased catalytic activity towards casein. Replacement of the C-terminal domain obviously improved keratinolytic activity and increased the k(cat)/K(m) value on a synthetic peptide, succinyl-Ala-Ala-Pro-Phe-p-nitroanilide, by 54.5%. Replacement of both the N- and C-terminal domains generated a more stable mutant protein, with a Tm value of 64.60 ± 0.65°C and a half-life of 244.6 ± 2 min at 60°C, while deletion of the C-terminal domain from KerSMD or KerSMF resulted in mutant proteins exhibiting high activity under mesophilic conditions. These findings indicate that the pre-peptidase C-terminal domain and N-propeptide are not only important for substrate specificity, correct folding and thermostability but also support the ability of the enzyme to convert feather waste into feed additives.
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Affiliation(s)
- Zhen Fang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, 214122, China.,School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Baihong Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, 214122, China.,School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
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Morshed N, Echols N, Adams PD. Using support vector machines to improve elemental ion identification in macromolecular crystal structures. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1147-58. [PMID: 25945580 PMCID: PMC4427199 DOI: 10.1107/s1399004715004241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/01/2015] [Indexed: 11/11/2022]
Abstract
In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.
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Affiliation(s)
- Nader Morshed
- College of Letters and Science, University of California, Berkeley, CA 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
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Kobayashi H, Yoshida T, Miyakawa T, Tashiro M, Okamoto K, Yamanaka H, Tanokura M, Tsuge H. Structural Basis for Action of the External Chaperone for a Propeptide-deficient Serine Protease from Aeromonas sobria. J Biol Chem 2015; 290:11130-43. [PMID: 25784551 DOI: 10.1074/jbc.m114.622852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Indexed: 11/06/2022] Open
Abstract
Subtilisin-like proteases are broadly expressed in organisms ranging from bacteria to mammals. During maturation of these enzymes, N-terminal propeptides function as intramolecular chaperones, assisting the folding of their catalytic domains. However, we have identified an exceptional case, the serine protease from Aeromonas sobria (ASP), that lacks a propeptide. Instead, ORF2, a protein encoded just downstream of asp, appears essential for proper ASP folding. The mechanism by which ORF2 functions remains an open question, because it shares no sequence homology with any known intramolecular propeptide or other protein. Here we report the crystal structure of the ORF2-ASP complex and the solution structure of free ORF2. ORF2 consists of three regions: an N-terminal extension, a central body, and a C-terminal tail. Together, the structure of the central body and the C-terminal tail is similar to that of the intramolecular propeptide. The N-terminal extension, which is not seen in other subtilisin-like enzymes, is intrinsically disordered but forms some degree of secondary structure upon binding ASP. We also show that C-terminal (ΔC1 and ΔC5) or N-terminal (ΔN43 and ΔN64) deletion eliminates the ability of ORF2 to function as a chaperone. Characterization of the maturation of ASP with ORF2 showed that folding occurs in the periplasmic space and is followed by translocation into extracellular space and dissociation from ORF2, generating active ASP. Finally, a PSI-BLAST search revealed that operons encoding subtilases and their external chaperones are widely distributed among Gram-negative bacteria, suggesting that ASP and its homologs form a novel family of subtilases having an external chaperone.
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Affiliation(s)
- Hidetomo Kobayashi
- From the Laboratory of Molecular Microbiological Science, Faculty of Pharmaceutical Sciences, Hiroshima International University, Kure, Hiroshima 737-0112, Japan
| | - Toru Yoshida
- the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan
| | - Takuya Miyakawa
- the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Mitsuru Tashiro
- the Department of Chemistry, College of Science and Technology, Meisei University, Hodokubo, Hino, Tokyo 191-0042, Japan, and
| | - Keinosuke Okamoto
- the Department of Pharmacogenetics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Hiroyasu Yamanaka
- From the Laboratory of Molecular Microbiological Science, Faculty of Pharmaceutical Sciences, Hiroshima International University, Kure, Hiroshima 737-0112, Japan
| | - Masaru Tanokura
- the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hideaki Tsuge
- the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan,
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15
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Rigden DJ, Xu Q, Chang Y, Eberhardt RY, Finn RD, Rawlings ND. The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold. F1000Res 2014; 2:154. [PMID: 24555072 PMCID: PMC3901451 DOI: 10.12688/f1000research.2-154.v2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/19/2013] [Indexed: 12/03/2022] Open
Abstract
We report the crystal structure solution of the Intracellular Protease Inhibitor (IPI) protein from
Bacillus subtilis, which has been reported to be an inhibitor of the intracellular subtilisin Isp1 from the same organism. The structure of IPI is a variant of the all-beta, immunoglobulin (Ig) fold. It is possible that IPI is important for protein-protein interactions, of which inhibition of Isp1 is one. The intracellular nature of ISP is questioned, because an alternative ATG codon in the
ipi gene would produce a protein with an N-terminal extension containing a signal peptide. It is possible that alternative initiation exists, producing either an intracellular inhibitor or a secreted form that may be associated with the cell surface. Homologues of the IPI protein from other species are multi-domain proteins, containing signal peptides and domains also associated with the bacterial cell-surface. The cysteine peptidase inhibitors chagasin and amoebiasin also have Ig-like folds, but their topology differs significantly from that of IPI, and they share no recent common ancestor. A model of IPI docked to Isp1 shows similarities to other subtilisin:inhibitor complexes, particularly where the inhibitor interacts with the peptidase active site.
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Affiliation(s)
- Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Qingping Xu
- Joint Center for Structural Genomics, La Jolla CA, 92037, USA ; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park CA, 94025, USA
| | | | - Ruth Y Eberhardt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK ; European Molecular Biology Laboratory, European Bioinformatics Institute,Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Robert D Finn
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn VA, 20147, USA
| | - Neil D Rawlings
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK ; European Molecular Biology Laboratory, European Bioinformatics Institute,Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
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16
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Li Q, Chen AS, Gayen S, Kang C. ¹H, ¹³C and ¹⁵N chemical shift assignments for an intracellular proteinase inhibitor of Bacillus subtilis. BIOMOLECULAR NMR ASSIGNMENTS 2013; 7:129-132. [PMID: 22585087 DOI: 10.1007/s12104-012-9392-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/03/2012] [Indexed: 05/31/2023]
Abstract
Intracellular proteinases (ISPs) are the main component of the bacilli degradome and a distinctive class in different bacilli. An intracellular proteinase inhibitor of the bacteria Bacillus subtillis was shown to regulate the activity of ISP-1. To study the structure of this inhibitor, we report the resonance assignment for this protein with 119 amino acid. The data will allow us to perform structural study on this inhibitor to understand its mechanism for ISP-1 inhibition.
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Affiliation(s)
- Qingxin Li
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore, Singapore
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Chen K, Liu S, Wang G, Zhang D, Du G, Chen J, Shi Z. Enhancement of Streptomyces transglutaminase activity and pro-peptide cleavage efficiency by introducing linker peptide in the C-terminus of the pro-peptide. ACTA ACUST UNITED AC 2013; 40:317-25. [DOI: 10.1007/s10295-012-1221-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/30/2012] [Indexed: 01/05/2023]
Abstract
Abstract
Streptomyces transglutaminase (TGase) has been widely used in food, pharmaceutical and textile industries. Streptomyces TGase is naturally synthesized as zymogen (pro-TGase), which is then processed to produce active enzyme by removing its N-terminal pro-peptide. Although the pro-peptide is essential for TGase folding and secretion, few studies have been reported on improving the properties of TGase by pro-peptide engineering. In this study, we developed a new approach to improve the properties of TGase based on pro-peptide engineering. When the α-helix37G−42S in pro-peptide was substituted with three glycines and three alanines respectively, the mutants exhibited higher specific activity and the efficiency of pro-peptide cleavage was enhanced. To further improve the properties of TGase, relevant mutations were constructed by introducing linker peptides in the C-terminus of the pro-peptide. Mutants with GS (GGGGS) and PT (PTPPTTPT) linker peptide exhibited 1.28 fold and 1.5 fold higher specific activity than the wild-type enzyme, respectively. This new method could be used to improve the properties of TGase by pro-peptide modification, which is a promising technology for creating unique TGase with various beneficial properties.
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Affiliation(s)
- Kangkang Chen
- grid.258151.a 0000000107081323 School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi China
- grid.258151.a 0000000107081323 Key Laboratory of Industrial Biotechnology, Ministry of Education Jiangnan University Wuxi China
| | - Song Liu
- grid.258151.a 0000000107081323 School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi China
- grid.258151.a 0000000107081323 Key Laboratory of Industrial Biotechnology, Ministry of Education Jiangnan University Wuxi China
| | - Guangsheng Wang
- grid.258151.a 0000000107081323 School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi China
| | - Dongxu Zhang
- grid.258151.a 0000000107081323 School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi China
- grid.258151.a 0000000107081323 State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
| | - Guocheng Du
- grid.258151.a 0000000107081323 School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi China
- grid.258151.a 0000000107081323 The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education Jiangnan University Wuxi China
| | - Jian Chen
- grid.258151.a 0000000107081323 School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi China
- grid.258151.a 0000000107081323 National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University Wuxi China
| | - Zhongping Shi
- grid.258151.a 0000000107081323 School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi China
- grid.258151.a 0000000107081323 Key Laboratory of Industrial Biotechnology, Ministry of Education Jiangnan University Wuxi China
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18
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Gamble M, Künze G, Brancale A, Wilson KS, Jones DD. The role of substrate specificity and metal binding in defining the activity and structure of an intracellular subtilisin. FEBS Open Bio 2012; 2:209-15. [PMID: 23650602 PMCID: PMC3642151 DOI: 10.1016/j.fob.2012.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 07/02/2012] [Indexed: 11/25/2022] Open
Abstract
The dimeric intracellular subtilisin proteases (ISPs) found throughout Gram-positive bacteria are a structurally distinct class of the subtilase family. Unlike the vast majority of subtilisin-like proteases, the ISPs function exclusively within the cell, contributing the majority of observed cellular proteolytic activity. Given that they are active within the cell, little is known about substrate specificity and the role of stress signals such as divalent metal ions in modulating ISP function. We demonstrate that both play roles in defining the proteolytic activity of Bacillus clausii ISP and propose the molecular basis of their effects. Enzyme kinetics reveal that one particular synthetic tetrapeptide substrate, Phe-Ala-Ala-Phe-pNA, is hydrolysed with a catalytic efficiency ∼100-fold higher than any other tested. Heat-denatured whole proteins were found to be better substrates for ISP than the native forms. Substrate binding simulations suggest that the S1, S2 and S4 sites form defined binding pockets. The deep S1 cavity and wide S4 site are fully occupied by the hydrophobic aromatic side-chains of Phe. Divalent metal ions, probably Ca2+, are proposed to be important for ISP activity through structural changes. The presence of >0.01 mM EDTA inactivates ISP, with CD and SEC suggesting that the protein becomes less structured and potentially monomeric. Removal of Ca2+ at sites close to the dimer interface and the S1 pocket are thought to be responsible for the effect. These studies provide a new insight into the potential physiological function of ISPs, by reconciling substrate specificity and divalent metal binding to associate ISP with the unfolded protein response under stress conditions.
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Affiliation(s)
- Michael Gamble
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
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