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Harding CJ, Bischoff M, Bergkessel M, Czekster CM. An anti-biofilm cyclic peptide targets a secreted aminopeptidase from P. aeruginosa. Nat Chem Biol 2023; 19:1158-1166. [PMID: 37386135 PMCID: PMC10449631 DOI: 10.1038/s41589-023-01373-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/26/2023] [Indexed: 07/01/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes serious illness, especially in immunocompromised individuals. P. aeruginosa forms biofilms that contribute to growth and persistence in a wide range of environments. Here we investigated the aminopeptidase, P. aeruginosa aminopeptidase (PaAP) from P. aeruginosa, which is highly abundant in the biofilm matrix. PaAP is associated with biofilm development and contributes to nutrient recycling. We confirmed that post-translational processing was required for activation and PaAP is a promiscuous aminopeptidase acting on unstructured regions of peptides and proteins. Crystal structures of wild-type enzymes and variants revealed the mechanism of autoinhibition, whereby the C-terminal propeptide locks the protease-associated domain and the catalytic peptidase domain into a self-inhibited conformation. Inspired by this, we designed a highly potent small cyclic-peptide inhibitor that recapitulates the deleterious phenotype observed with a PaAP deletion variant in biofilm assays and present a path toward targeting secreted proteins in a biofilm context.
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Affiliation(s)
- Christopher John Harding
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, UK
| | - Marcus Bischoff
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, UK
- Centre of Biophotonics, University of St Andrews, St Andrews, UK
| | | | - Clarissa Melo Czekster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, UK.
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2
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Axelrad I, Safrin M, Cahan R, Suh SJ, Ohman DE, Kessler E. Extracellular proteolytic activation of Pseudomonas aeruginosa aminopeptidase (PaAP) and insight into the role of its non-catalytic N-terminal domain. PLoS One 2021; 16:e0252970. [PMID: 34133429 PMCID: PMC8208579 DOI: 10.1371/journal.pone.0252970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/25/2021] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa secretes several endopeptidases, including elastase, alkaline proteinase (Apr), a lysine-specific endopeptidase (LysC), and an aminopeptidase (PaAP), all of which are important virulence factors. Activation of the endopeptidases requires removal of an inhibitory N-terminal propeptide. Activation of pro-PaAP, in contrast, requires C-terminal processing. The activating proteases of pro-PaAP and their cleavage site(s) have not yet been defined. Studying pro-PaAP processing in a wild type P. aeruginosa strain and strains lacking either elastase or both elastase and Apr, we detected three processing variants, each ~56 kDa in size (AP56). Activity assays and N- and C-terminal sequence analyses of these variants pointed at LysC as the principal activating protease, cleaving a Lys512-Ala513 peptide bond at the C-terminal end of pro-PaAP. Elastase and/or Apr are required for activation of LysC, suggesting both are indirectly involved in activation of PaAP. To shed light on the function(s) of the N-terminal domain of AP56, we purified recombinant AP56 and generated from it the 28 kDa catalytic domain (AP28). The kinetic constants (Km and Kcat) for hydrolysis of Leu-, Lys-, Arg- and Met-p-nitroanilide (pNA) derivatives by AP56 and AP28 were then determined. The catalytic coefficients (Kcat/Km) for hydrolysis of all four substrates by AP28 and AP56 were comparable, indicating that the non-catalytic domain is not involved in hydrolysis of small substrates. It may, however, regulate hydrolysis of natural peptides/proteins. Lys-pNA was hydrolyzed 2 to 3-fold more rapidly than Leu-pNA and ~8-fold faster than Arg- or Met-pNA, indicating that Lys-pNA was the preferred substrate.
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Affiliation(s)
- Itschak Axelrad
- Maurice and Gabriela Goldschleger Eye Research Institute, Tel Aviv University Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Mary Safrin
- Maurice and Gabriela Goldschleger Eye Research Institute, Tel Aviv University Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Rivka Cahan
- Maurice and Gabriela Goldschleger Eye Research Institute, Tel Aviv University Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Sang-Jin Suh
- Department of Biomedical Sciences, Texas A&M College of Dentistry, Dallas, Texas, United States of America
| | - Dennis E. Ohman
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, Virginia, United States of America
- McGuire Veterans Affairs Medical Center, Richmond, Virginia, United States of America
| | - Efrat Kessler
- Maurice and Gabriela Goldschleger Eye Research Institute, Tel Aviv University Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
- * E-mail:
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3
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Development of an effective fluorescence probe for discovery of aminopeptidase inhibitors to suppress biofilm formation. J Antibiot (Tokyo) 2019; 72:461-468. [PMID: 30894675 DOI: 10.1038/s41429-019-0166-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/28/2019] [Accepted: 02/28/2019] [Indexed: 12/13/2022]
Abstract
The human pathogen Pseudomonas aeruginosa can easily form biofilms. The extracellular matrix produced by the bacterial cells acts as a physical barrier to hinder the antibiotics treatment. It is necessary to destroy the biofilm in order to improve the efficacy of antibiotics. However, it has been a significant challenge to develop effective small molecules targeting the components of biofilm matrix. In this study, we report the development of a new effective fluorescence probe that could be used in the high throughput screening to identify novel small molecule inhibitors targeting the most abundant component in the biofilm formation: P. aeruginosa aminopeptidase (PaAP). Through screening of an in-house chemical library, a commercially available drug, balsalazide, has been identified as a novel PaAP inhibitor, which exhibited remarkable anti-biofilm effect. Our study indicated that the newly developed fluorescence probe is applicable in exploring new aminopeptidase inhibitors, and it also warrants further investigation of balsalazide as a new anti-biofilm agent to treat P. aeruginosa infection in combination with known antibiotics.
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Flores-Fernández CN, Cárdenas-Fernández M, Dobrijevic D, Jurlewicz K, Zavaleta AI, Ward JM, Lye GJ. Novel extremophilic proteases from Pseudomonas aeruginosa M211 and their application in the hydrolysis of dried distiller's grain with solubles. Biotechnol Prog 2018; 35:e2728. [PMID: 30304581 DOI: 10.1002/btpr.2728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 11/09/2022]
Abstract
Proteases are the most important group of industrial enzymes and they can be used in several fields including biorefineries for the valorization of industrial byproducts. In this study, we purified and characterized novel extremophilic proteases produced by a Pseudomonas aeruginosa strain isolated from Mauritia flexuosa palm swamps soil samples in Peruvian Amazon. In addition, we tested their ability to hydrolyze distillers dried grains with solubles (DDGS) protein. Three alkaline and thermophilic serine proteases named EI, EII, and EIII with molecular weight of 35, 40, and 55 kDa, respectively, were purified. EI and EIII were strongly inhibited by EDTA and Pefabloc being classified as serine-metalloproteases, while EII was completely inhibited only by Pefabloc being classified as a serine protease. In addition, EI and EII exhibited highest enzymatic activity at pH 8, while EIII at pH 11 maintaining almost 100% of it at pH 12. All the enzymes demonstrated optimum activity at 60°C. Enzymatic activity of EI was strongly stimulated in presence of Mn2+ (6.9-fold), EII was stimulated by Mn2+ (3.7-fold), while EIII was slightly stimulated by Zn2+ , Ca2+ , and Mg2+ . DDGS protein hydrolysis using purified Pseudomonas aeruginosa M211 proteases demonstrated that, based on glycine released, EIII presented the highest proteolytic activity toward DDGS. This enzyme enabled the release 63% of the total glycine content in wheat DDGS protein, 2.2-fold higher that when using the commercial Pronase®. Overall, our results indicate that this novel extremopreoteases have a great potential to be applied in DDGS hydrolysis. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2728, 2019.
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Affiliation(s)
- Carol N Flores-Fernández
- Facultad de Farmacia y Bioquímica, Laboratorio de Biología Molecular, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Max Cárdenas-Fernández
- Dept. of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, London, WC1E 6BT, U.K
| | - Dragana Dobrijevic
- Dept. of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, London, WC1E 6BT, U.K
| | - Kosma Jurlewicz
- Dept. of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, London, WC1E 6BT, U.K
| | - Amparo I Zavaleta
- Facultad de Farmacia y Bioquímica, Laboratorio de Biología Molecular, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - John M Ward
- Dept. of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, London, WC1E 6BT, U.K
| | - Gary J Lye
- Dept. of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, London, WC1E 6BT, U.K
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Zhao T, Zhang Y, Wu H, Wang D, Chen Y, Zhu MJ, Ma LZ. Extracellular aminopeptidase modulates biofilm development of Pseudomonas aeruginosa by affecting matrix exopolysaccharide and bacterial cell death. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:583-593. [PMID: 30047246 DOI: 10.1111/1758-2229.12682] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
Biofilm bacteria are embedded within a self-secreted extracellular matrix that contains a considerable amount of proteins including many extracellular enzymes. However, little is known about the roles of such enzymes in biofilm development. Here, we studied Pseudomonas aeruginosa aminopeptidase (PaAP, encoded by PA2939 that we named the gene as paaP in this study), a quorum-sensing-regulated enzyme and one of the most abundant extracellular proteins in the biofilm matrix of this opportunistic pathogen and environmental bacterium. We found that deletion of paaP in P. aeruginosa increased initial attachment and biofilm formation at early stages of biofilm development. After 24 h growth, loss of PaAP resulted in substantial cell death and biofilm disruption. Bacterial cell death was independent of biofilm matrix polysaccharide Psl, while biofilm disruption was due to the degradation of Psl matrix by dead-bacteria-released glycosyl hydrolase PslG, thereby leading to biofilm dispersion. PaAP functioned extracellularly and aminopeptidase catalytic activity was essential for its effect on biofilm development. Our data reveal an important role of extracellular aminopeptidase in biofilm development, suggesting PaAP as a therapeutic target for preventing P. aeruginosa infection and combating biofilm-related complications.
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Affiliation(s)
- Tianhu Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Biological Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhuan Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Biological Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huijun Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Biological Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Biological Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei-Jun Zhu
- School of Food Science, Washington State University, Pullman, Washington 99164, USA
| | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Biological Science, University of Chinese Academy of Sciences, Beijing 100049, China
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Nandan A, Nampoothiri KM. Molecular advances in microbial aminopeptidases. BIORESOURCE TECHNOLOGY 2017; 245:1757-1765. [PMID: 28599921 DOI: 10.1016/j.biortech.2017.05.103] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 05/22/2023]
Abstract
Aminopeptidases are exopeptidases that catalyze the hydrolysis of amino acid residues from the N terminus of peptides and proteins. They are widely and diversely used for protein hydrolysis in industrial and research applications. They form a large enzyme family in microorganisms and most of the sequenced microbial genomes contain several aminopeptidase coding genes. Various approaches are being used to enhance the yield and desired properties of these enzymes to make it more suited for industrial applications. Novel aminopeptidases are being developed by site directed mutagenesis and recombinant DNA technology with improved substrate specificity and stability. This review focuses on its classification and recent advancements in the molecular studies pertaining to this enzyme.
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Affiliation(s)
- Arya Nandan
- CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India
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7
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Sierra EM, Pereira MR, Maester TC, Gomes-Pepe ES, Mendoza ER, Lemos EGDM. Halotolerant aminopeptidase M29 from Mesorhizobium SEMIA 3007 with biotechnological potential and its impact on biofilm synthesis. Sci Rep 2017; 7:10684. [PMID: 28878230 PMCID: PMC5587760 DOI: 10.1038/s41598-017-10932-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/16/2017] [Indexed: 12/04/2022] Open
Abstract
The aminopeptidase gene from Mesorhizobium SEMIA3007 was cloned and overexpressed in Escherichia coli. The enzyme called MesoAmp exhibited optimum activity at pH 8.5 and 45 °C and was strongly activated by Co2+ and Mn2+. Under these reaction conditions, the enzyme displayed Km and kcat values of 0.2364 ± 0.018 mM and 712.1 ± 88.12 s−1, respectively. Additionally, the enzyme showed remarkable stability in organic solvents and was active at high concentrations of NaCl, suggesting that the enzyme might be suitable for use in biotechnology. MesoAmp is responsible for 40% of the organism’s aminopeptidase activity. However, the enzyme’s absence does not affect bacterial growth in synthetic broth, although it interfered with biofilm synthesis and osmoregulation. To the best of our knowledge, this report describes the first detailed characterization of aminopeptidase from Mesorhizobium and suggests its importance in biofilm formation and osmotic stress tolerance. In summary, this work lays the foundation for potential biotechnological applications and/or the development of environmentally friendly technologies and describes the first solvent- and halo-tolerant aminopeptidases identified from the Mesorhizobium genus and its importance in bacterial metabolism.
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Affiliation(s)
- Elwi Machado Sierra
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil.,Universidad Simón Bolívar, Barranquilla, Colombia
| | | | | | - Elisangela Soares Gomes-Pepe
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil.,Institute for Research in Bioenergy (IPBEN), Jaboticabal, São Paulo State, Brazil
| | - Elkin Rodas Mendoza
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil
| | - Eliana G de Macedo Lemos
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil. .,Institute for Research in Bioenergy (IPBEN), Jaboticabal, São Paulo State, Brazil. .,Av. Prof. Paulo Donato Castellane, s/n. Jaboticabal, Post code 14884-900, São Paulo State, Brazil.
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Yang D, Yu X, Wu Y, Chen X, Wei H, Shah NP, Xu F. Enhancing flora balance in the gastrointestinal tract of mice by lactic acid bacteria from Chinese sourdough and enzyme activities indicative of metabolism of protein, fat, and carbohydrate by the flora. J Dairy Sci 2016; 99:7809-7820. [DOI: 10.3168/jds.2016-11467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/17/2016] [Indexed: 01/16/2023]
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9
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Wu YT, Zhou ND, Zhou ZM, Gao XX, Tian YP. A thermo-stable lysine aminopeptidase fromPseudomonas aeruginosa: Isolation, purification, characterization, and sequence analysis. J Basic Microbiol 2014; 54:1110-9. [DOI: 10.1002/jobm.201300752] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/13/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Yan Tao Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; Wuxi China
| | - Nan Di Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; Wuxi China
| | - Zhe Min Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; Wuxi China
| | - Xin Xing Gao
- Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; Wuxi China
| | - Ya Ping Tian
- Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; Wuxi China
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Hydrophobic Substitution of Surface Residues Affects Lipase Stability in Organic Solvents. Mol Biotechnol 2013; 56:360-8. [DOI: 10.1007/s12033-013-9716-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Chen SH, Cao MJ, Su WJ, Wu GP. Purification and characterization of a novel leucine aminopeptidase from the earthworm Eisenia foetida. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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